MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'RNA' source. Tue, 16 Mar 2010 17:23:50 +0100 http://www.medworm.com/index.php?rid=3335832&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20197376%26dopt%3DAbstract Authors: Ellis JC, Brown DD, Brown JW Small nucleolar ribonucleoproteins (snoRNPs) are widely studied and characterized as guide RNAs for sequence-specific 2'-O-ribose methylation and psuedouridylation of ribosomal RNAs. In addition, snoRNAs have also been shown to interact with some tRNAs and direct alternative splicing in mRNA biogenesis. Recent advances in bioinformatics have resulted in new algorithms able to rapidly identify noncoding RNAs generally and snoRNAs specifically in genomic and metagenomic sequences, resulting in a rapid increase in the number and diversity of identified snoRNA sequences. The snoRNP database is a web-based collection of snoRNA and snoRNA-associated protein sequences from a wide range of species. The database currently contains 8994 snoRNA sequences from... RNA journals http://www.medworm.com/rss/comments.php?id=3335832 Tue, 02 Mar 2010 00:00:00 +0100 3335832 http://www.medworm.com/index.php?rid=3335831&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20197377%26dopt%3DAbstract Authors: Hallegger M, Sobala A, Smith CW Splicing of vertebrate introns involves recognition of three consensus elements at the 3' end. The branch point (BP) and polypyrimidine tract (PPT) are usually located within 40 nucleotides (nt) of the 3' splice site (3' ss), AG, but can be much more distant. A characteristic of the region between distant BPs (dBPs) and the 3' ss is the absence of intervening AG dinucleotides, leading to its designation as the "AG exclusion zone" (AGEZ). The human HTR4 gene, which encodes serotonin receptor 4 and has been associated with schizophrenia, bipolar disease, and gastrointestinal disorders, has four exons with extensive AGEZs. We have mapped the BPs for HTR4 exons 3, 4, 5, and g generated by in vitro splicing, and validated them by mutagenesis in exon-... RNA journals http://www.medworm.com/rss/comments.php?id=3335831 Tue, 02 Mar 2010 00:00:00 +0100 3335831 http://www.medworm.com/index.php?rid=3335835&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20194518%26dopt%3DAbstract Authors: Fernández N, Martínez-Salas E Translation initiation driven by internal ribosome entry site (IRES) elements is dependent on the structural organization of the IRES region. We have previously shown that a structural motif within the foot-and-mouth-disease virus IRES is recognized in vitro as substrate for the Synechocystis sp. RNase P ribozyme. Here we show that this structure-dependent endonuclease recognizes the IRES element in cultured cells, leading to inhibition of translation. Inhibition of IRES activity was dependent on the expression of the active ribozyme RNA subunit. Moreover, expression of the antisense sequence of the ribozyme did not inhibit IRES activity, demonstrating that stable RNA structures located upstream of the IRES element do not interfere with ... RNA journals http://www.medworm.com/rss/comments.php?id=3335835 Mon, 01 Mar 2010 00:00:00 +0100 3335835 http://www.medworm.com/index.php?rid=3335834&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20194519%26dopt%3DAbstract Authors: Janas T, Widmann JJ, Knight R, Yarus M Seven new arginine binding motifs have been selected from a heterogeneous RNA pool containing 17, 25, and 50mer randomized tracts, yielding 131 independently derived binding sites that are multiply isolated. The shortest 17mer random region is sufficient to build varied arginine binding sites using five different conserved motifs (motifs 1a, 1b, 1c, 2, and 4). Dissociation constants are in the fractional millimolar to millimolar range. Binding sites are amino acid side-chain specific and discriminate moderately between L- and D-stereoisomers of arginine, suggesting a molecular focus on side-chain guanidinium. An arginine coding triplet (codon/anticodon) is highly conserved within the largest family of Arg sites (72% of all sequences), as ... RNA journals http://www.medworm.com/rss/comments.php?id=3335834 Mon, 01 Mar 2010 00:00:00 +0100 3335834 http://www.medworm.com/index.php?rid=3335833&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20194520%26dopt%3DAbstract Authors: Lipfert J, Sim AY, Herschlag D, Doniach S Riboswitches are gene-regulating RNAs that are usually found in the 5'-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann c... RNA journals http://www.medworm.com/rss/comments.php?id=3335833 Mon, 01 Mar 2010 00:00:00 +0100 3335833 http://www.medworm.com/index.php?rid=3315229&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20185542%26dopt%3DAbstract Authors: Chen C, Deutscher MP RNase R is an important exoribonuclease that participates in the degradation of structured RNAs in Escherichia coli. In earlier work, it was shown that RNase R levels increase dramatically under certain stress conditions, particularly during cold shock and stationary phase. However, the regulatory processes that lead to this elevation are not well understood. We show here that the increase in RNase R in stationary phase is unaffected by the global regulators, RpoS and (p)ppGpp, and that it occurs despite a major reduction in rnr message. Rather, we find that RNase R is a highly unstable protein in exponential phase, with a half-life of approximately 10 min, and that the protein is stabilized in stationary phase, leading to its relative increase. RNase R is... RNA journals http://www.medworm.com/rss/comments.php?id=3315229 Thu, 25 Feb 2010 00:00:00 +0100 3315229 http://www.medworm.com/index.php?rid=3315228&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20185543%26dopt%3DAbstract Authors: Betney R, de Silva E, Krishnan J, Stansfield I In both prokaryotes and eukaryotes, the expression of a large number of genes is controlled by negative feedback, in some cases operating at the level of translation of the mRNA transcript. Of particular interest are those cases where the proteins concerned have cell-wide function in recognizing a particular codon or RNA sequence. Examples include the bacterial translation termination release factor RF2, initiation factor IF3, and eukaryote poly(A) binding protein. The regulatory loops that control their synthesis establish a negative feedback control mechanism based upon that protein's RNA sequence recognition function in translation (for example, stop codon recognition) without compromising the accurate recognition of that codon... RNA journals http://www.medworm.com/rss/comments.php?id=3315228 Thu, 25 Feb 2010 00:00:00 +0100 3315228 http://www.medworm.com/index.php?rid=3315227&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20185544%26dopt%3DAbstract Authors: Kiss DL, Andrulis ED The RNA processing exosome complex was originally defined as an evolutionarily conserved multisubunit complex of ribonucleases responsible for the processing and/or turnover of stable RNAs. The exosome complex is also involved in the surveillance of mRNAs in both the nucleus and the cytoplasm, including nonsense-mediated decay (NMD) targets. The detailed mechanisms for how individual exosome subunits participate in each of these RNA metabolic pathways remains unclear. Here, we use RNAi to deplete exosome subunits, the exonucleases Rrp6 and Dis3, and an exosome cofactor in Drosophila melanogaster S2 tissue culture cells and assay the effects on global mRNA levels using gene expression microarrays. Consistent with the RNA degradative activities ascribed to t... RNA journals http://www.medworm.com/rss/comments.php?id=3315227 Thu, 25 Feb 2010 00:00:00 +0100 3315227 http://www.medworm.com/index.php?rid=3307759&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20181738%26dopt%3DAbstract Authors: Haussecker D, Huang Y, Lau A, Parameswaran P, Fire AZ, Kay MA Competition between mammalian RNAi-related gene silencing pathways is well documented. It is therefore important to identify all classes of small RNAs to determine their relationship with RNAi and how they affect each other functionally. Here, we identify two types of 5'-phosphate, 3'-hydroxylated human tRNA-derived small RNAs (tsRNAs). tsRNAs differ from microRNAs in being essentially restricted to the cytoplasm and in associating with Argonaute proteins, but not MOV10. The first type belongs to a previously predicted Dicer-dependent class of small RNAs that we find can modestly down-regulate target genes in trans. The 5' end of type II tsRNA was generated by RNaseZ cleavage downstream from a tRNA gene, while the 3... RNA journals http://www.medworm.com/rss/comments.php?id=3307759 Wed, 24 Feb 2010 00:00:00 +0100 3307759 http://www.medworm.com/index.php?rid=3307758&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20181739%26dopt%3DAbstract Authors: Galão RP, Chari A, Alves-Rodrigues I, Lobão D, Mas A, Kambach C, Fischer U, Díez J LSm1-7 complexes promote cellular mRNA degradation, in addition to translation and replication of positive-strand RNA viruses such as the Brome mosaic virus (BMV). Yet, how LSm1-7 complexes act on their targets remains elusive. Here, we report that reconstituted recombinant LSm1-7 complexes directly bind to two distinct RNA-target sequences in the BMV genome, a tRNA-like structure at the 3'-untranslated region and two internal A-rich single-stranded regions. Importantly, in vivo analysis shows that these sequences regulate the translation and replication of the BMV genome. Furthermore, both RNA-target sequences resemble those found for Hfq, the LSm counterpart in bacteria, suggest... RNA journals http://www.medworm.com/rss/comments.php?id=3307758 Wed, 24 Feb 2010 00:00:00 +0100 3307758 http://www.medworm.com/index.php?rid=3307757&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20181740%26dopt%3DAbstract We present the characterization and structure of a complex containing one of Prp24's four RNA recognition motif (RRM) domains, RRM2, and a fragment of U6 RNA. NMR methods were used to identify the preferred U6 binding sequence of RRM2 (5'-GAGA-3'), measure the affinity of the interaction, and solve the structure of RRM2 bound to the hexaribonucleotide AGAGAU. Interdomain contacts observed between RRM2 and RRM3 in a crystal structure of the free protein are not detectable in solution. A structural model of RRM1 and RRM2 bound to a longer segment of U6 RNA is presented, and a partial mechanism for Prp24's annealing activity is proposed. PMID: 20181740 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=3307757 Wed, 24 Feb 2010 00:00:00 +0100 3307757 http://www.medworm.com/index.php?rid=3307761&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20179149%26dopt%3DAbstract Authors: Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, Von Arnim AG Upstream open reading frames (uORFs) are protein coding elements in the 5' leader of messenger RNAs. uORFs generally inhibit translation of the main ORF because ribosomes that perform translation elongation suffer either permanent or conditional loss of reinitiation competence. After conditional loss, reinitiation competence may be regained by, at the minimum, reacquisition of a fresh methionyl-tRNA. The conserved h subunit of Arabidopsis eukaryotic initiation factor 3 (eIF3) mitigates the inhibitory effects of certain uORFs. Here, we define more precisely how this occurs, by combining gene expression data from mutated 5' leaders of Arabidopsis AtbZip11 (At4g34590) and yeast GCN4 with a computational model of transla... RNA journals http://www.medworm.com/rss/comments.php?id=3307761 Tue, 23 Feb 2010 00:00:00 +0100 3307761 http://www.medworm.com/index.php?rid=3307760&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20179150%26dopt%3DAbstract Authors: Gu SQ, Cui X, Mou S, Mohr S, Yao J, Lambowitz AM Mobile group II introns encode a reverse transcriptase that binds the intron RNA to promote RNA splicing and intron mobility, the latter via reverse splicing of the excised intron into DNA sites, followed by reverse transcription. Previous work showed that the Lactococcus lactis Ll.LtrB intron reverse transcriptase, denoted LtrA protein, binds with high affinity to DIVa, a stem-loop structure at the beginning of the LtrA open reading frame and makes additional contacts with intron core regions that stabilize the active RNA structure for forward and reverse splicing. LtrA's binding to DIVa down-regulates its translation and is critical for initiation of reverse transcription. Here, by using high-throughput unigenic evolution anal... RNA journals http://www.medworm.com/rss/comments.php?id=3307760 Tue, 23 Feb 2010 00:00:00 +0100 3307760 http://www.medworm.com/index.php?rid=3294874&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20167653%26dopt%3DAbstract Authors: Giambasu GM, Lee TS, Sosa CP, Robertson MP, Scott WG, York DM The L1 ligase is an in vitro selected ribozyme that uses a noncanonically base-paired ligation site to catalyze regioselectively and regiospecifically the 5' to 3' phosphodiester bond ligation, a reaction relevant to origin of life hypotheses that invoke an RNA world scenario. The L1 ligase crystal structure revealed two different conformational states that were proposed to represent the active and inactive forms. It remains an open question as to what degree these two conformers persist as stable conformational intermediates in solution, and along what pathway are they able to interconvert. To explore these questions, we have performed a series of molecular dynamics simulations in explicit solvent of the inactive-a... RNA journals http://www.medworm.com/rss/comments.php?id=3294874 Thu, 18 Feb 2010 00:00:00 +0100 3294874 http://www.medworm.com/index.php?rid=3284260&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20159952%26dopt%3DAbstract Authors: Traphagen SJ, Dimarco MJ, Silliker ME Regions of the Didymium iridis mitochondrial genome were identified with similarity to typical mitochondrial genes; however, these regions contained numerous stop codons. We used RT-PCR and DNA sequencing to determine whether, through RNA editing, these regions were transcribed into mRNAs that could encode functional proteins. Ten putative gene regions were examined: atp1, atp6, atp8, atp9, cox1, cox2, cytb, nad4L, nad6, and nad7. The cDNA sequences of each gene could encode a functional mitochondrial protein that was highly conserved compared with homologous genes. The type of editing events and editing sequence features were very similar to those observed in the homologous genes of Physarum polycephalum, though the actual editing locatio... RNA journals http://www.medworm.com/rss/comments.php?id=3284260 Tue, 16 Feb 2010 00:00:00 +0100 3284260 http://www.medworm.com/index.php?rid=3271396&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20150330%26dopt%3DAbstract Authors: Bouhallier F, Allioli N, Lavial F, Chalmel F, Perrard MH, Durand P, Samarut J, Pain B, Rouault JP Spermatogenesis is a cyclic process in which diploid spermatogonia differentiate into haploid spermatozoa. This process is highly regulated, notably at the post-transcriptional level. MicroRNAs (miRNAs), single-stranded noncoding RNA molecules of about 20-25 nucleotides, are implicated in the regulation of many important biological pathways such as proliferation, apoptosis, and differentiation. We wondered whether miRNAs could play a role during spermatogenesis. The miRNA expression repertoire was tested in germ cells, and we present data showing that miR-34c was highly expressed only in these cells. Furthermore, our findings indicate that in male gonads, miR-34c expression is lar... RNA journals http://www.medworm.com/rss/comments.php?id=3271396 Thu, 11 Feb 2010 00:00:00 +0100 3271396 http://www.medworm.com/index.php?rid=3260038&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20145044%26dopt%3DAbstract Authors: Antonioli AH, Cochrane JC, Lipchock SV, Strobel SA The kink turn (K-turn) is an RNA structural motif found in many biologically significant RNAs. While most examples of the K-turn have a similar fold, the crystal structure of the Azoarcus group I intron revealed a novel RNA conformation, a reverse kink turn bent in the direction opposite that of a consensus K-turn. The reverse K-turn is bent toward the major grooves rather than the minor grooves of the flanking helices, yet the sequence differs from the K-turn consensus by only a single nucleotide. Here we demonstrate that the reverse bend direction is not solely defined by internal sequence elements, but is instead affected by structural elements external to the K-turn. It bends toward the major groove under the direction of ... RNA journals http://www.medworm.com/rss/comments.php?id=3260038 Tue, 09 Feb 2010 00:00:00 +0100 3260038 http://www.medworm.com/index.php?rid=3260039&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20142326%26dopt%3DAbstract Authors: Derelle R, Momose T, Manuel M, Da Silva C, Wincker P, Houliston E Replacement of mRNA 5' UTR sequences by short sequences trans-spliced from specialized, noncoding, spliced leader (SL) RNAs is an enigmatic phenomenon, occurring in a set of distantly related animal groups including urochordates, nematodes, flatworms, and hydra, as well as in Euglenozoa and dinoflagellates. Whether SL trans-splicing has a common evolutionary origin and biological function among different organisms remains unclear. We have undertaken a systematic identification of SL exons in cDNA sequence data sets from non-bilaterian metazoan species and their closest unicellular relatives. SL exons were identified in ctenophores and in hydrozoan cnidarians, but not in other cnidarians, placozoans, or sponges, ... RNA journals http://www.medworm.com/rss/comments.php?id=3260039 Mon, 08 Feb 2010 00:00:00 +0100 3260039 http://www.medworm.com/index.php?rid=3223771&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106952%26dopt%3DAbstract Authors: Gott JM, Somerlot BH, Gray MW The mitochondrial genome of Physarum polycephalum encodes five tRNAs, four of which are edited by nucleotide insertion. Two of these tRNAs, tRNA(met1) and tRNA(met2), contain predicted mismatches at the beginning (proximal end) of the acceptor stem. In addition, the putative 5' end of tRNA(met2) overlaps the 3' end of a small, abundant, noncoding RNA, which we term ppoRNA. These anomalies led us to hypothesize that these two Physarum mitochondrial tRNAs undergo additional editing events. Here, we show that tRNA(met1) and tRNA(met2) each has a nonencoded G at its 5' end. In contrast to the other nucleotides that are added to Physarum mitochondrial RNAs, these extra G residues are likely added post-transcriptionally based on (1) the absence of added... RNA journals http://www.medworm.com/rss/comments.php?id=3223771 Wed, 27 Jan 2010 00:00:00 +0100 3223771 http://www.medworm.com/index.php?rid=3223770&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106953%26dopt%3DAbstract Authors: Qin H, Chen F, Huan X, Machida S, Song J, Yuan YA Dicer or Dicer-like (DCL) protein is a catalytic component involved in microRNA (miRNA) or small interference RNA (siRNA) processing pathway, whose fragment structures have been partially solved. However, the structure and function of the unique DUF283 domain within dicer is largely unknown. Here we report the first structure of the DUF283 domain from the Arabidopsis thaliana DCL4. The DUF283 domain adopts an alpha-beta-beta-beta-alpha topology and resembles the structural similarity to the double-stranded RNA-binding domain. Notably, the N-terminal alpha helix of DUF283 runs cross over the C-terminal alpha helix orthogonally, therefore, N- and C-termini of DUF283 are in close proximity. Biochemical analysis shows that the DUF2... RNA journals http://www.medworm.com/rss/comments.php?id=3223770 Wed, 27 Jan 2010 00:00:00 +0100 3223770 http://www.medworm.com/index.php?rid=3223769&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106954%26dopt%3DAbstract Authors: Hengesbach M, Voigts-Hoffmann F, Hofmann B, Helm M Pseudouridine is the most abundant of more than 100 chemically distinct natural ribonucleotide modifications. Its synthesis consists of an isomerization reaction of a uridine residue in the RNA chain and is catalyzed by pseudouridine synthases. The unusual reaction mechanism has become the object of renewed research effort, frequently involving replacement of the substrate uridines with 5-fluorouracil (f(5)U). f(5)U is known to be a potent inhibitor of pseudouridine synthase activity, but the effect varies among the target pseudouridine synthases. Derivatives of f(5)U have previously been detected, which are thought to be either hydrolysis products of covalent enzyme-RNA adducts, or isomerization intermediates. Here we describ... RNA journals http://www.medworm.com/rss/comments.php?id=3223769 Wed, 27 Jan 2010 00:00:00 +0100 3223769 http://www.medworm.com/index.php?rid=3223768&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106955%26dopt%3DAbstract Authors: Górna MW, Pietras Z, Tsai YC, Callaghan AJ, Hernández H, Robinson CV, Luisi BF The Escherichia coli endoribonuclease RNase E is an essential enzyme having key roles in mRNA turnover and the processing of several structured RNA precursors, and it provides the scaffold to assemble the multienzyme RNA degradosome. The activity of RNase E is inhibited by the protein RraA, which can interact with the ribonuclease's degradosome-scaffolding domain. Here, we report that RraA can bind to the RNA helicase component of the degradosome (RhlB) and the two RNA-binding sites in the degradosome-scaffolding domain of RNase E. In the presence of ATP, the helicase can facilitate the exchange of RraA for RNA stably bound to the degradosome. Our data suggest that RraA can affect multiple... RNA journals http://www.medworm.com/rss/comments.php?id=3223768 Wed, 27 Jan 2010 00:00:00 +0100 3223768 http://www.medworm.com/index.php?rid=3223767&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106956%26dopt%3DAbstract Authors: Robart AR, O'Connor CM, Collins K Telomerase adds simple-sequence repeats to chromosome 3' ends to compensate for the loss of repeats with each round of genome replication. To accomplish this de novo DNA synthesis, telomerase uses a template within its integral RNA component. In addition to providing the template, the telomerase RNA subunit (TER) also harbors nontemplate motifs that contribute to the specialized telomerase catalytic cycle of reiterative repeat synthesis. Most nontemplate TER motifs function through linkage with the template, but in ciliate and vertebrate telomerases, a stem-loop motif binds telomerase reverse transcriptase (TERT) and reconstitutes full activity of the minimal recombinant TERT+TER RNP, even when physically separated from the template. Here, we ... RNA journals http://www.medworm.com/rss/comments.php?id=3223767 Wed, 27 Jan 2010 00:00:00 +0100 3223767 http://www.medworm.com/index.php?rid=3223766&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106957%26dopt%3DAbstract Authors: Rambo RP, Tainer JA Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through inv... RNA journals http://www.medworm.com/rss/comments.php?id=3223766 Wed, 27 Jan 2010 00:00:00 +0100 3223766 http://www.medworm.com/index.php?rid=3223765&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106958%26dopt%3DAbstract Authors: Baird NJ, Ferré-D'Amaré AR Riboswitches are structured mRNA elements that regulate gene expression upon binding specific cellular metabolites. It is thought that the highly conserved metabolite-binding domains of riboswitches undergo conformational change upon binding their cognate ligands. To investigate the generality of such a mechanism, we employed small-angle X-ray scattering (SAXS). We probed the nature of the global metabolite-induced response of the metabolite-binding domains of four different riboswitches that bind, respectively, thiamine pyrophosphate (TPP), flavin mononucleotide (FMN), lysine, and S-adenosyl methionine (SAM). We find that each RNA is unique in its global structural response to metabolite. Whereas some RNAs exhibit distinct free and bound c... RNA journals http://www.medworm.com/rss/comments.php?id=3223765 Wed, 27 Jan 2010 00:00:00 +0100 3223765 http://www.medworm.com/index.php?rid=3209436&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20100812%26dopt%3DAbstract We present a simple and fast method for large-scale purification of RNA oligonucleotides suitable for biochemical and structural studies. RNAs are transcribed in vitro with T7 RNA polymerase using linearized plasmid DNA templates. After addition of EDTA, the crude transcription reaction is subjected directly to weak anion-exchange chromatography using DEAE-sepharose to separate the T7 RNA polymerase, unincorporated rNTPs, small abortive transcripts, and the plasmid DNA template from the desired RNA product. The novel method does neither require tedious phenol/chloroform extraction of the T7 RNA polymerase nor denaturation of the RNA, which is desirable especially for larger RNAs. In addition, isotopically labeled rNTPs can be easily recycled from the column flow-through and oligomeric RNA ... RNA journals http://www.medworm.com/rss/comments.php?id=3209436 Mon, 25 Jan 2010 00:00:00 +0100 3209436 http://www.medworm.com/index.php?rid=3209435&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20100813%26dopt%3DAbstract Authors: Cao S, Giedroc DP, Chen SJ Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the ... RNA journals http://www.medworm.com/rss/comments.php?id=3209435 Mon, 25 Jan 2010 00:00:00 +0100 3209435 http://www.medworm.com/index.php?rid=3200800&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20089682%26dopt%3DAbstract Authors: Dubé A, Baumstark T, Bisaillon M, Perreault JP It is believed that peach latent mosaic viroid (PLMVd) strands of both the plus and minus polarities fold into similar secondary and tertiary structures. In order to verify this hypothesis, the behavior of both strands in three biophysical assays was examined. PLMVd transcripts of plus and minus polarity were found to exhibit distinct electrophoretic mobility properties under native conditions, to precipitate differently in the presence of lithium chloride, and to possess variable thermal denaturation profiles. Subsequently, the structure of PLMVd transcripts of minus polarity was elucidated by biochemical methods, thereby permitting comparison to the known structure of the plus polarity. Specifically, enzymatic probing, elec... RNA journals http://www.medworm.com/rss/comments.php?id=3200800 Wed, 20 Jan 2010 00:00:00 +0100 3200800 http://www.medworm.com/index.php?rid=3200799&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20089683%26dopt%3DAbstract Authors: Lardelli RM, Thompson JX, Yates JR, Stevens SW Eukaryotic pre-mRNA splicing is a complex process requiring the precise timing and action of >100 trans-acting factors. It has been known for some time that the two steps of splicing chemistry require three DEAH-box RNA helicase-like proteins, however, their mechanism of action at these steps has remained elusive. Spliceosomes arrested in vivo at the three helicase checkpoints were purified and first step-arrested spliceosomes were functionally characterized. We show that the first step of splicing requires a novel ATP-independent conformational change. Prp2p then catalyzes an ATP-dependent rearrangement displacing the SF3a and SF3b complexes from the branchpoint within the spliceosome. We propose a model in which SF3 prevents ... RNA journals http://www.medworm.com/rss/comments.php?id=3200799 Wed, 20 Jan 2010 00:00:00 +0100 3200799 http://www.medworm.com/index.php?rid=3194284&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20086050%26dopt%3DAbstract Authors: Miyoshi K, Miyoshi T, Hartig JV, Siomi H, Siomi MC In Drosophila, three types of endogenous small RNAs-microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), and endogenous small-interfering RNAs (endo-siRNAs or esiRNAs)-function as triggers in RNA silencing. Although piRNAs are produced independently of Dicer, miRNA and esiRNA biogenesis pathways require Dicer1 and Dicer2, respectively. Recent studies have shown that among the four isoforms of Loquacious (Loqs), Loqs-PB and Loqs-PD are involved in miRNA and esiRNA processing pathways, respectively. However, how these Loqs isoforms function in their respective small RNA biogenesis pathways remains elusive. Here, we show that Loqs-PD associates specifically with Dicer2 through its C-terminal domain. The Dicer2-Loqs-PD complex cont... RNA journals http://www.medworm.com/rss/comments.php?id=3194284 Tue, 19 Jan 2010 00:00:00 +0100 3194284 http://www.medworm.com/index.php?rid=3194283&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20086051%26dopt%3DAbstract In conclusion, our study confirms that the NuMRP and MtMRP enzymes are distinct entities with differing activities and protein components but a common RNA subunit, suggesting that the RNA must be playing a crucial role in catalytic activity. PMID: 20086051 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=3194283 Tue, 19 Jan 2010 00:00:00 +0100 3194283 http://www.medworm.com/index.php?rid=3194282&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20086052%26dopt%3DAbstract Authors: Darnell DK, Stanislaw S, Kaur S, Antin PB In situ hybridization is widely used to visualize transcribed sequences in embryos, tissues, and cells. For whole mount detection of mRNAs in embryos, hybridization with an antisense RNA probe is followed by visual or fluorescence detection of target mRNAs. A limitation of this approach is that a cDNA template of the target RNA must be obtained in order to generate the antisense RNA probe. Here we investigate the use of short (12-24 nucleotides) locked nucleic acid (LNA) containing DNA probes for whole mount in situ hybridization detection of mRNAs. Following extensive protocol optimization, we show that LNA probes can be used to localize several mRNAs of varying abundances in chicken embryos. LNA probes also detected alternatively spl... RNA journals http://www.medworm.com/rss/comments.php?id=3194282 Tue, 19 Jan 2010 00:00:00 +0100 3194282 http://www.medworm.com/index.php?rid=3180586&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20075163%26dopt%3DAbstract Authors: Schutz K, Hesselberth JR, Fields S The combination of ligation-based RNA capture methods and high-throughput sequencing has facilitated the characterization of transcriptomes and the identification of novel noncoding RNAs. However, current ligation-based RNA capture methods require RNA substrates with terminal 3'-hydroxyl groups, limiting their utility for identifying RNAs with modified termini like 2',3'-cyclic phosphates. Cyclic phosphate-terminated RNAs are generated by endonucleolytic cleavages and self-cleaving ribozymes and are found as stable modifications on cellular RNAs such as the U6 spliceosomal RNA. We developed a method that uses the Arabidopsis thaliana tRNA ligase to add an adaptor oligonucleotide to RNAs that terminate in 2',3'-cyclic phosphates. The adaptor a... RNA journals http://www.medworm.com/rss/comments.php?id=3180586 Thu, 14 Jan 2010 00:00:00 +0100 3180586 http://www.medworm.com/index.php?rid=3180585&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20075164%26dopt%3DAbstract Authors: Kharytonchyk S, Pedersen FS Retroviruses package their genome as RNA dimers linked together primarily by base-pairing between palindromic stem-loop (psl) sequences at the 5' end of genomic RNA. Retroviral RNA dimers usually in the range of 55 degrees C-70 degrees C. However, RNA dimers from virions of the feline endogenous gammaretrovirus RD114 were reported to melt only at 87 degrees C. We here report that the high thermal stability of RD114 RNA dimers generated from in vitro synthesized RNA is an effect of multiple dimerization sites located in the 5' region from the R region to sequences downstream from the splice donor (SD) site. By antisense oligonucleotide probing we were able to map at least five dimerization sites. Computational prediction revealed a possibility to for... RNA journals http://www.medworm.com/rss/comments.php?id=3180585 Thu, 14 Jan 2010 00:00:00 +0100 3180585 http://www.medworm.com/index.php?rid=3180584&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20075165%26dopt%3DAbstract Authors: Martel C, Dugré-Brisson S, Boulay K, Breton B, Lapointe G, Armando S, Trépanier V, Duchaîne T, Bouvier M, Desgroseillers L Transport of mRNA is an efficient mechanism to target proteins to specific regions of a cell. Although it is well documented that mRNAs are transported in ribonucleoprotein (RNP) complexes, several of the mechanisms involved in complex formation and localization are poorly understood. Staufen (Stau) 1, a double-stranded RNA-binding protein, is a well accepted marker of mRNA transport complexes. In this manuscript, we provide evidence that Stau1 self-associates in live cells using immunoprecipitation and bioluminescence resonance energy transfer (BRET) assays. The double-stranded RNA-binding domains dsRBD3 and dsRBD4 contributed about half of... RNA journals http://www.medworm.com/rss/comments.php?id=3180584 Thu, 14 Jan 2010 00:00:00 +0100 3180584 http://www.medworm.com/index.php?rid=3180583&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20075166%26dopt%3DAbstract Authors: Monteys AM, Spengler RM, Wan J, Tecedor L, Lennox KA, Xing Y, Davidson BL MicroRNAs (miRNAs) are RNA sequences of approximately 22 nucleotides that mediate post-transcriptional regulation of specific mRNAs. miRNA sequences are dispersed throughout the genome and are classified as intergenic (between genes) or intronic (embedded into a gene). Intergenic miRNAs are expressed by their own promoter, and until recently, it was supposed that intronic miRNAs are transcribed from their host gene. Here, we performed a genomic analysis of currently known intronic miRNA regions and observed that approximately 35% of intronic miRNAs have upstream regulatory elements consistent with promoter function. Among all intronic miRNAs, 30% have associated Pol II regulatory elements, including tran... RNA journals http://www.medworm.com/rss/comments.php?id=3180583 Thu, 14 Jan 2010 00:00:00 +0100 3180583 http://www.medworm.com/index.php?rid=3176670&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20071455%26dopt%3DAbstract Authors: Pais H, Nicolas FE, Soond SM, Swingler TE, Clark IM, Chantry A, Moulton V, Dalmay T mRNA profiling is routinely used to identify microRNA targets, however, this high-throughput technology is not suitable for identifying targets regulated only at protein level. Here, we have developed and validated a novel methodology based on computational analysis of promoter sequences combined with mRNA microarray experiments to reveal transcription factors that are direct microRNA targets at the protein level. Using this approach we identified Smad3, a key transcription factor in the TGFbeta signaling pathway, as a direct miR-140 target. We showed that miR-140 suppressed the TGFbeta pathway through repression of Smad3 and that TGFbeta suppressed the accumulation of miR-140 forming a double ... RNA journals http://www.medworm.com/rss/comments.php?id=3176670 Wed, 13 Jan 2010 00:00:00 +0100 3176670 http://www.medworm.com/index.php?rid=3153856&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20051491%26dopt%3DAbstract In this study, catalytically inactive polymerases were shown to participate productively in functional oligomer formation and catalysis, as assayed by RNA template elongation. Direct protein transduction to introduce either active or inactive polymerases into cells infected with mutant virus confirmed the structural role for polymerase molecules during infection. Therefore, we suggest that targeting the active sites of polymerase molecules is not likely to be the best antiviral strategy, as inactivated polymerases do not inhibit replication of other viruses in the same cell and can, in fact, be useful in RNA replication complexes. On the other hand, polymerases that could not participate in functional RNA replication complexes were those that contained mutations in the amino terminus, lead... RNA journals http://www.medworm.com/rss/comments.php?id=3153856 Tue, 05 Jan 2010 00:00:00 +0100 3153856 http://www.medworm.com/index.php?rid=3146553&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20047989%26dopt%3DAbstract Authors: Sheehy JP, Davis AR, Znosko BM Although tetraloops are one of the most frequently occurring secondary structure motifs in RNA, less than one-third of the 30 most frequently occurring RNA tetraloops have been thermodynamically characterized. Therefore, 24 stem-loop sequences containing common tetraloops were optically melted, and the thermodynamic parameters DeltaH degrees , DeltaS degrees , DeltaG degrees (37,) and T(M) for each stem-loop were determined. These new experimental values, on average, are 0.7 kcal/mol different from the values predicted for these tetraloops using the model proposed by Vecenie CJ, Morrow CV, Zyra A, Serra MJ. 2006. Biochemistry 45: 1400-1407. The data for the 24 tetraloops reported here were then combined with the data for 28 tetraloops that were p... RNA journals http://www.medworm.com/rss/comments.php?id=3146553 Mon, 04 Jan 2010 00:00:00 +0100 3146553 http://www.medworm.com/index.php?rid=3146552&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20047990%26dopt%3DAbstract Authors: Buck AH, Perot J, Chisholm MA, Kumar DS, Tuddenham L, Cognat V, Marcinowski L, Dölken L, Pfeffer S In mammals, microRNAs (miRNAs) can play diverse roles in viral infection through their capacity to regulate both host and viral genes. Recent reports have demonstrated that specific miRNAs change in expression level upon infection and can impact viral production and infectivity. It is clear that miRNAs are an integral component of viral-host interactions, and it is likely that both host and virus contain mechanisms to regulate miRNA expression and/or activity. To date, little is known about the mechanisms by which miRNAs are regulated in viral infection. Here we report the rapid down-regulation of miR-27a in multiple mouse cell lines as well as primary macrophages upon infec... RNA journals http://www.medworm.com/rss/comments.php?id=3146552 Mon, 04 Jan 2010 00:00:00 +0100 3146552 http://www.medworm.com/index.php?rid=3134250&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20042473%26dopt%3DAbstract Authors: Damianov A, Black DL The Fox proteins are a family of regulators that control the alternative splicing of many exons in neurons, muscle, and other tissues. Each of the three mammalian paralogs, Fox-1 (A2BP1), Fox-2 (RBM9), and Fox-3 (HRNBP3), produces proteins with a single RNA-binding domain (RRM) flanked by N- and C-terminal domains that are highly diversified through the use of alternative promoters and alternative splicing patterns. These genes also express protein isoforms lacking the second half of the RRM (FoxDeltaRRM), due to the skipping of a highly conserved 93-nt exon. Fox binding elements overlap the splice sites of these exons in Fox-1 and Fox-2, and the Fox proteins themselves inhibit exon inclusion. Unlike other cases of splicing autoregulation by RNA-binding pr... RNA journals http://www.medworm.com/rss/comments.php?id=3134250 Wed, 30 Dec 2009 00:00:00 +0100 3134250 http://www.medworm.com/index.php?rid=3134249&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20042474%26dopt%3DAbstract Authors: Wang WX, Wilfred BR, Hu Y, Stromberg AJ, Nelson PT MicroRNAs (miRNAs) play key roles in gene expression regulation by guiding Argonaute (AGO)-containing microribonucleoprotein (miRNP) effector complexes to target polynucleotides. There are still uncertainties about how miRNAs interact with mRNAs. Here we employed a biochemical approach to isolate AGO-containing miRNPs from human H4 tumor cells by co-immunoprecipitation (co-IP) with a previously described anti-AGO antibody. Co-immunoprecipitated (co-IPed) RNAs were subjected to downstream Affymetrix Human Gene 1.0 ST microarray analysis. During rigorous validation, the "RIP-Chip" assay identified target mRNAs specifically associated with AGO complexes. RIP-Chip was performed after transfecting brain-enriched miRNAs (miR-107, mi... RNA journals http://www.medworm.com/rss/comments.php?id=3134249 Wed, 30 Dec 2009 00:00:00 +0100 3134249 http://www.medworm.com/index.php?rid=3134255&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20040589%26dopt%3DAbstract In this study, we present highly convincing evidence for bacterial origin of the HSR1. No HSR1 sequence was found by exhaustive sequence similarity searches of the publicly available eukaryotic nucleotide sequence databases at the NCBI, including the expressed sequence tags, genome survey sequences, and high-throughput genomic sequences divisions of GenBank, as well as the Trace Archive database of whole genome shotgun sequences, and genome assemblies. Instead, a putative open reading frame (ORF) of HSR1 revealed strong similarity to the amino-terminal region of bacterial chloride channel proteins. Furthermore, the 5' flanking region of the putative HSR1 ORF showed similarity to the 5' upstream regions of the bacterial protein genes. We propose that the HSR1 was derived from a bacterial ge... RNA journals http://www.medworm.com/rss/comments.php?id=3134255 Tue, 29 Dec 2009 00:00:00 +0100 3134255 http://www.medworm.com/index.php?rid=3134254&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20040590%26dopt%3DAbstract Authors: David M, Gabdank I, Ben-David M, Zilka A, Orr I, Barash D, Shapira M Heat shock proteins (HSPs) provide a useful system for studying developmental patterns in the digenetic Leishmania parasites, since their expression is induced in the mammalian life form. Translation regulation plays a key role in control of protein coding genes in trypanosomatids, and is directed exclusively by elements in the 3' untranslated region (UTR). Using sequential deletions of the Leishmania Hsp83 3' UTR (888 nucleotides [nt]), we mapped a region of 150 nt that was required, but not sufficient for preferential translation of a reporter gene at mammalian-like temperatures, suggesting that changes in RNA structure could be involved. An advanced bioinformatics package for prediction of RNA folding (UNA... RNA journals http://www.medworm.com/rss/comments.php?id=3134254 Tue, 29 Dec 2009 00:00:00 +0100 3134254 http://www.medworm.com/index.php?rid=3134253&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20040591%26dopt%3DAbstract Authors: Lin CL, Evans V, Shen S, Xing Y, Richter JD CPEB is a sequence-specific RNA binding protein that promotes polyadenylation-induced translation in early development, during cell cycle progression and cellular senescence, and following neuronal synapse stimulation. It controls polyadenylation and translation through other interacting molecules, most notably the poly(A) polymerase Gld2, the deadenylating enzyme PARN, and the eIF4E-binding protein Maskin. Here, we report that CPEB shuttles between the nucleus and cytoplasm and that its export occurs via the CRM1-dependent pathway. In the nucleus of Xenopus oocytes, CPEB associates with lampbrush chromosomes and several proteins involved in nuclear RNA processing. CPEB also interacts with Maskin in the nucleus as well as with CPE-co... RNA journals http://www.medworm.com/rss/comments.php?id=3134253 Tue, 29 Dec 2009 00:00:00 +0100 3134253 http://www.medworm.com/index.php?rid=3134252&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20040592%26dopt%3DAbstract Authors: Didiano D, Cochella L, Tursun B, Hobert O 3' Untranslated region (UTR)-dependent post-transcriptional regulation has emerged as a critical mechanism of controlling gene expression in various physiological contexts, including cellular differentiation events. Here, we examine the regulation of the 3'UTR of the die-1 transcription factor in a single neuron of the nematode C. elegans. This 3'UTR shows the intriguing feature of being differentially regulated across the animal's left/right axis. In the left gustatory neuron, ASEL, in which DIE-1 protein is normally expressed in adult animals, the 3'UTR confers no regulatory information, while in the right gustatory neuron, ASER, where DIE-1 is normally not expressed, this 3'UTR confers negative regulatory information. Here, we syste... RNA journals http://www.medworm.com/rss/comments.php?id=3134252 Tue, 29 Dec 2009 00:00:00 +0100 3134252 http://www.medworm.com/index.php?rid=3134251&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20040593%26dopt%3DAbstract Authors: Galiveti CR, Rozhdestvensky TS, Brosius J, Lehrach H, Konthur Z In recent years the improvements in high-throughput gene expression analysis have led to the discovery of numerous non-protein-coding RNA (npcRNA) molecules. They form an abundant class of untranslated RNAs that have shown to play a crucial role in different biochemical pathways in the cell. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an efficient tool to measure RNA abundance and gene expression levels in tiny amounts of material. Despite its sensitivity, the lack of appropriate internal controls necessary for accurate data analysis is a limiting factor for its application in npcRNA in npcRNA research. Common internal controls applied are protein-coding reference genes, als... RNA journals http://www.medworm.com/rss/comments.php?id=3134251 Tue, 29 Dec 2009 00:00:00 +0100 3134251 http://www.medworm.com/index.php?rid=3129013&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20038629%26dopt%3DAbstract We present an approach that combines rule-based filters and a Bayesian Classifier to identify a class of snoRNAs (H/ACA) without requiring target sequence information. It takes advantage of unique attributes of their genomic organization and improved species-specific motif characterization to predict snoRNAs that may otherwise be difficult to discover. Searches in the genomes of Caenorhabditis elegans and the closely related Caenorhabditis briggsae suggest that our method performs well compared to recent benchmark algorithms. Our results illustrate the benefits of training gene discovery engines on features restricted to particular phylogenetic groups and the utility of incorporating diverse data types in gene prediction. PMID: 20038629 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=3129013 Mon, 28 Dec 2009 00:00:00 +0100 3129013 http://www.medworm.com/index.php?rid=3129012&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20038630%26dopt%3DAbstract Authors: Brosseau JP, Lucier JF, Lapointe E, Durand M, Gendron D, Gervais-Bird J, Tremblay K, Perreault JP, Elela SA Most human messenger RNAs (mRNAs) are alternatively spliced and many exhibit disease-specific splicing patterns. However, the contribution of most splicing events to the development and maintenance of human diseases remains unclear. As the contribution of alternative splicing events to diagnosis and prognosis is becoming increasingly recognized, it becomes important to develop precise methods to quantify the abundance of these isoforms in clinical samples. Here we present a pipeline for real-time PCR annotation of splicing events (RASE) that allows accurate identification of a large number of splicing isoforms in human tissues. The RASE automatically designed specific pr... RNA journals http://www.medworm.com/rss/comments.php?id=3129012 Mon, 28 Dec 2009 00:00:00 +0100 3129012 http://www.medworm.com/index.php?rid=3129011&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20038631%26dopt%3DAbstract Authors: Weis F, Bron P, Rolland JP, Thomas D, Felden B, Gillet R In eubacteria, translation of defective messenger RNAs (mRNAs) produces truncated polypeptides that stall on the ribosome. A quality control mechanism referred to as trans-translation is performed by transfer-messenger RNA (tmRNA), a specialized RNA acting as both a tRNA and an mRNA, associated with small protein B (SmpB). So far, a clear view of the structural movements of both the protein and RNA necessary to perform accommodation is still lacking. By using a construct containing the tRNA-like domain as well as the extended helix H2 of tmRNA, we present a cryo-electron microscopy study of the process of accommodation. The structure suggests how tmRNA and SmpB move into the ribosome decoding site after the release of EF... RNA journals http://www.medworm.com/rss/comments.php?id=3129011 Mon, 28 Dec 2009 00:00:00 +0100 3129011 http://www.medworm.com/index.php?rid=3129010&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20038632%26dopt%3DAbstract Authors: Gagnon MG, Steinberg SV Here, we present a new recurrent RNA arrangement, the so-called adenosine wedge (A-wedge), which is found in three places of the ribosomal RNA in both ribosomal subunits. The arrangement has a hierarchical structure, consisting of elements previously described as recurrent motifs, namely, the along-groove packing motif, the A-minor and the hook-turn. Within the A-wedge, these elements are involved in different types of cause-effect relationships, providing together for the particular tertiary structure of the motif. PMID: 20038632 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=3129010 Mon, 28 Dec 2009 00:00:00 +0100 3129010 http://www.medworm.com/index.php?rid=3122420&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20032164%26dopt%3DAbstract Authors: Kennedy R, Lladser ME, Wu Z, Zhang C, Yarus M, De Sterck H, Knight R Different chemical and mutational processes within genomes give rise to sequences with different compositions and perhaps different capacities for evolution. The evolution of functional RNAs may occur on a "neutral network" in which sequences with any given function can easily mutate to sequences with any other. This neutral network hypothesis is more likely if there is a particular region of composition that contains sequences that are functional in general, and if many different functions are possible within this preferred region of composition. We show that sequence preferences in active sites recovered by in vitro selection combine with biophysical folding rules to support the neutral network hypothesis. ... RNA journals http://www.medworm.com/rss/comments.php?id=3122420 Wed, 23 Dec 2009 00:00:00 +0100 3122420 http://www.medworm.com/index.php?rid=3119243&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026621%26dopt%3DAbstract Authors: Moses J, Goodchild A, Rivory LP Transcriptional gene silencing has been reported with siRNA targeting the promoter region of genes. We tested several siRNAs directed against the human VEGF promoter. Of these, siVFp(-992) exhibited >/=50% suppression of VEGF production in two human cell lines. To determine the specificity of this siRNA-mediated suppression, plasmids were prepared to express a luciferase reporter under the control of VEGF promoters featuring wild-type, mutated, or deleted target sequences. siRNA transfection assays established sequence-specific inhibition of luciferase from the reporter plasmid featuring the wild-type VEGF promoter. However, siVFp(-992) also suppressed the luciferase expression from the plasmids with mutated or deleted target sites, suggestin... RNA journals http://www.medworm.com/rss/comments.php?id=3119243 Mon, 21 Dec 2009 00:00:00 +0100 3119243 http://www.medworm.com/index.php?rid=3119242&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026622%26dopt%3DAbstract Authors: Sheik Mohamed J, Gaughwin PM, Lim B, Robson P, Lipovich L The genetic networks controlling stem cell identity are the focus of intense interest, due to their obvious therapeutic potential as well as exceptional relevance to models of early development. Genome-wide mapping of transcriptional networks in mouse embryonic stem cells (mESCs) reveals that many endogenous noncoding RNA molecules, including long noncoding RNAs (lncRNAs), may play a role in controlling the pluripotent state. We performed a genome-wide screen that combined full-length mESC transcriptome genomic mapping data with chromatin immunoprecipitation genomic location maps of the key mESC transcription factors Oct4 and Nanog. We henceforth identified four mESC-expressed, conserved lncRNA-encoding genes residing p... RNA journals http://www.medworm.com/rss/comments.php?id=3119242 Mon, 21 Dec 2009 00:00:00 +0100 3119242 http://www.medworm.com/index.php?rid=3102556&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20008486%26dopt%3DAbstract Authors: Wurster SE, Maher LJ The yeast three-hybrid system (Y3H) is a powerful tool to select or confirm RNA-protein interactions. Target protein recognition of an RNA insert within a test transcript depends on at least three factors: intrinsic protein affinity for the properly folded insert, retention of RNA insert tertiary structure within a longer RNA transcript, and accessibility of the RNA insert to the target protein. Y3H reporter gene readout reflects the combination of these factors. Here, we discuss RNA insert tertiary structure and accessibility in the Y3H as "RNA display." We review evidence that RNA display can sometimes be optimized during Y3H selections that do not increase the intrinsic affinity of an RNA insert for a target protein. This situation is more likely when a... RNA journals http://www.medworm.com/rss/comments.php?id=3102556 Mon, 14 Dec 2009 00:00:00 +0100 3102556 http://www.medworm.com/index.php?rid=3102559&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20007328%26dopt%3DAbstract Authors: Jain R, Shuman S Hen1 is an RNA ribose 2'-O-methyltransferase that modifies the 3' terminal nucleoside of eukaryal small regulatory RNAs. Here, we report that Hen1 homologs are present in bacterial proteomes from eight different phyla. Bacterial Hen1 is encoded by the proximal ORF of a two-gene operon that also encodes polynucleotide kinase-phosphatase (Pnkp), an RNA repair enzyme. Purified recombinant Clostridium thermocellum Hen1 is a homodimer of a 465-amino acid polypeptide. CthHen1 catalyzes methyl transfer from AdoMet to the 3' terminal nucleoside of an RNA oligonucleotide, but is unreactive with a synonymous DNA oligonucleotide or an RNA with a single 3'-terminal deoxyribose sugar. CthHen1 is optimally active at alkaline pH and dependent on manganese. Activity is inhibi... RNA journals http://www.medworm.com/rss/comments.php?id=3102559 Wed, 09 Dec 2009 00:00:00 +0100 3102559 http://www.medworm.com/index.php?rid=3102558&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20007329%26dopt%3DAbstract Authors: Pavon-Eternod M, Wei M, Pan T, Kleiman L During its assembly, human HIV-1 selectively packages the tRNA(Lys) isoacceptors, including tRNA(Lys3), the primer for the reverse transcriptase. However, other low molecular weight RNA species are also seen in the virus. We profiled the tRNAs packaged into HIV-1 using microarray analysis and validated our results by two-dimensional gel electrophoresis and RT-PCR. In addition to tRNA(Lys) isoacceptors, tRNA(Asn) and the rare isoacceptor of tRNA(Ile) are also selectively packaged. In Gag viral-like particles missing the GagPol protein, overall tRNA incorporation is reduced by >80%. This reduction is significantly greater than can be accounted for by the reduction in tRNA(Lys) isoacceptors, tRNA(Asn) and tRNA(Ile), suggesting that inco... RNA journals http://www.medworm.com/rss/comments.php?id=3102558 Wed, 09 Dec 2009 00:00:00 +0100 3102558 http://www.medworm.com/index.php?rid=3102557&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20007330%26dopt%3DAbstract Authors: Wilusz JE, Spector DL Proper 3' end processing of a nascent transcript is critical for the functionality of the mature RNA. Although it has long been thought that virtually all long RNA polymerase II transcripts terminate in a poly(A) tail that is generated by endonucleolytic cleavage followed by polyadenylation, noncanonical 3' end processing mechanisms have recently been identified at several gene loci. Unexpectedly, enzymes with well-characterized roles in other RNA processing events, such as tRNA biogenesis and pre-mRNA splicing, cleave these nascent transcripts to generate their mature 3' ends despite the presence of nearby polyadenylation signals. In fact, the presence of multiple potential 3' end cleavage sites is the norm at many human genes, and recent work suggests t... RNA journals http://www.medworm.com/rss/comments.php?id=3102557 Wed, 09 Dec 2009 00:00:00 +0100 3102557 http://www.medworm.com/index.php?rid=3056959&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19952115%26dopt%3DAbstract Authors: Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM Group II introns are large ribozymes that act as self-splicing and retrotransposable RNA molecules. They are of great interest because of their potential evolutionary relationship to the eukaryotic spliceosome, their continued influence on the organization of many genomes in bacteria and eukaryotes, and their potential utility as tools for gene therapy and biotechnology. One of the most interesting features of group II introns is their relative lack of nucleobase conservation and covariation, which has long suggested that group II intron structures are stabilized by numerous unusual tertiary interactions and backbone-mediated contacts. Here, we provide a detailed description of the tertiary interaction networks wit... RNA journals http://www.medworm.com/rss/comments.php?id=3056959 Tue, 01 Dec 2009 00:00:00 +0100 3056959 http://www.medworm.com/index.php?rid=3056958&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19952116%26dopt%3DAbstract Authors: Ge Q, Ilves H, Dallas A, Kumar P, Shorenstein J, Kazakov SA, Johnston BH Small hairpin RNAs (shRNAs) are widely used in RNAi studies and typically consist of a stem of 19-29 base pairs (bp), a loop of at least 4 nucleotides (nt), and a dinucleotide overhang at the 3' end. Compared with shRNAs with 21-29 bp stems, we have found that shRNAs with 19-bp or shorter stems (sshRNAs) possess some unique structure-activity features that depend on whether the antisense strand is positioned 5' or 3' to the loop (L- or R-type sshRNAs, respectively). L sshRNAs can have IC(50)s in the very low picomolar range, and sshRNAs with nominal loop sizes of 1 or 4 nt were at least as active as those with longer loops. L sshRNAs remained highly potent even when the 3' end of the antisense strand was ... RNA journals http://www.medworm.com/rss/comments.php?id=3056958 Tue, 01 Dec 2009 00:00:00 +0100 3056958 http://www.medworm.com/index.php?rid=3056957&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19952117%26dopt%3DAbstract Authors: Shaul S, Berel D, Benjamini Y, Graur D It has been suggested that tRNA acceptor stems specify an operational RNA code for amino acids. In the last 20 years several attributes of the putative code have been elucidated for a small number of model organisms. To gain insight about the ensemble attributes of the code, we analyzed 4925 tRNA sequences from 102 bacterial and 21 archaeal species. Here, we used a classification and regression tree (CART) methodology, and we found that the degrees of degeneracy or specificity of the RNA codes in both Archaea and Bacteria differ from those of the genetic code. We found instances of taxon-specific alternative codes, i.e., identical acceptor stem determinants encrypting different amino acids in different species, as well as instances of amb... RNA journals http://www.medworm.com/rss/comments.php?id=3056957 Tue, 01 Dec 2009 00:00:00 +0100 3056957 http://www.medworm.com/index.php?rid=3048628&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19946040%26dopt%3DAbstract Authors: Bagby SC, Bergman NH, Shechner DM, Yen C, Bartel DP The class I ligase was among the first ribozymes to have been isolated from random sequences and represents the catalytic core of several RNA-directed RNA polymerase ribozymes. The ligase is also notable for its catalytic efficiency and structural complexity. Here, we report an improved version of this ribozyme, arising from selection that targeted the kinetics of the chemical step. Compared with the parent ribozyme, the improved ligase achieves a modest increase in rate enhancement under the selective conditions and shows a sharp reduction in [Mg(2+)] dependence. Analysis of the sequences and kinetics of successful clones suggests which mutations play the greatest part in these improvements. Moreover, backbone and nucleobase... RNA journals http://www.medworm.com/rss/comments.php?id=3048628 Tue, 01 Dec 2009 00:00:00 +0100 3048628 http://www.medworm.com/index.php?rid=3048627&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19946041%26dopt%3DAbstract Authors: Keren I, Bezawork-Geleta A, Kolton M, Maayan I, Belausov E, Levy M, Mett A, Gidoni D, Shaya F, Ostersetzer-Biran O Mitochondria (mt) in plants house about 20 group-II introns, which lie within protein-coding genes required in both organellar genome expression and respiration activities. While in nonplant systems the splicing of group-II introns is mediated by proteins encoded within the introns themselves (known as "maturases"), only a single maturase ORF (matR) has retained in the mitochondrial genomes in plants; however, its putative role(s) in the splicing of organellar introns is yet to be established. Clues to other proteins are scarce, but these are likely encoded within the nucleus as there are no obvious candidates among the remaining ORFs within the mtDNA. Intriguingl... RNA journals http://www.medworm.com/rss/comments.php?id=3048627 Tue, 01 Dec 2009 00:00:00 +0100 3048627 http://www.medworm.com/index.php?rid=3048626&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19948765%26dopt%3DAbstract Authors: Keating KS, Toor N, Perlman PS, Pyle AM Group II introns are self-splicing, mobile genetic elements that have fundamentally influenced the organization of terrestrial genomes. These large ribozymes remain important for gene expression in almost all forms of bacteria and eukaryotes and they are believed to share a common ancestry with the eukaryotic spliceosome that is required for processing all nuclear pre-mRNAs. The three-dimensional structure of a group IIC intron was recently determined by X-ray crystallography, making it possible to visualize the active site and the elaborate network of tertiary interactions that stabilize the molecule. Here we describe the molecular features of the active site in detail and evaluate their correspondence with prior biochemical, genetic, a... RNA journals http://www.medworm.com/rss/comments.php?id=3048626 Mon, 30 Nov 2009 00:00:00 +0100 3048626 http://www.medworm.com/index.php?rid=3048625&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19948766%26dopt%3DAbstract In this study, the effects of chemical modifications on the potency, serum stability, and innate immune response of sshRNAs were investigated. Deoxynucleotide substitution and 2'-O-methyl (2'-OMe) modification in the sense strand and loop did not affect silencing activity, but, unlike with siRNAs, when placed in the antisense strand these modifications were detrimental. Conjugation with bulky groups at the 5'-end of L sshRNAs or 3'-end of R sshRNAs had a negative impact on the potency. Unmodified sshRNAs in dimer form or with blunt ends were immunostimulatory. Some modifications such as 3'-end conjugation and phosphorothioate linkages on the backbone of the sshRNAs could also induce inflammatory cytokine production. However, 2'-OMe substitution of sshRNAs abrogated the innate immune respon... RNA journals http://www.medworm.com/rss/comments.php?id=3048625 Mon, 30 Nov 2009 00:00:00 +0100 3048625 http://www.medworm.com/index.php?rid=3048624&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19948767%26dopt%3DAbstract Authors: Bargaje R, Hariharan M, Scaria V, Pillai B Eukaryotic gene expression is controlled at the post-transcriptional level by small noncoding RNAs called microRNAs (miRNA). miRNAs play important roles during early development and participate in gene regulatory circuits in the cell. Different high-throughput expression analysis methods including microarrays, bead-based detection, and small RNA cloning have been applied to quantitatively detect miRNAs in various tissues, cell types, and biological conditions. High-throughput expression data was collected from public repositories and processed to create a database of miRNA expression profiles. Several commonly used normalization methods were compared to identify suitable methods for cross-platform comparison of high-throughput miRNA e... RNA journals http://www.medworm.com/rss/comments.php?id=3048624 Mon, 30 Nov 2009 00:00:00 +0100 3048624 http://www.medworm.com/index.php?rid=3048623&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19948768%26dopt%3DAbstract Authors: Diebel KW, Smith AL, van Dyk LF Murid herpesvirus 4 (MuHV-4) microRNAs were previously cloned from latently infected tumor cells and predicted to be processed from a series of RNA polymerase III primary transcripts. We detected maturely processed MuHV-4 miRNAs within total RNA from lytically infected cells in vitro and infected tissues ex vivo, using a highly sensitive reverse ligation meditated RT-PCR strategy. We determined that the MuHV-4 microRNAs are biologically active during infection by a luciferase reporter system. We experimentally demonstrated that transcription of the MuHV-4 microRNAs is by RNA polymerase III by alpha-amanitin insensitivity and by specific deletion of the RNA polymerase III type 2-like promoter elements of MuHV-4, resulting in the complete loss of ... RNA journals http://www.medworm.com/rss/comments.php?id=3048623 Mon, 30 Nov 2009 00:00:00 +0100 3048623 http://www.medworm.com/index.php?rid=3048622&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19948769%26dopt%3DAbstract Authors: Kulshina N, Edwards TE, Ferré-D'Amaré AR The thi-box riboswitch regulates gene expression in response to the intracellular concentration of thiamine pyrophosphate (TPP) in archaea, bacteria, and eukarya. To complement previous biochemical, genetic, and structural studies of this phylogenetically widespread RNA domain, we have characterized its interaction with TPP by isothermal titration calorimetry. This shows that TPP binding is highly dependent on Mg(2+) concentration. The dissociation constant decreases from approximately 200 nM at 0.5 mM Mg(2+) concentration to approximately 9 nM at 2.5 mM Mg(2+) concentration. Binding is enthalpically driven, but the unfavorable entropy of binding decreases as Mg(2+) concentration rises, suggesting that divalent cations serve t... RNA journals http://www.medworm.com/rss/comments.php?id=3048622 Mon, 30 Nov 2009 00:00:00 +0100 3048622 http://www.medworm.com/index.php?rid=3036257&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19939970%26dopt%3DAbstract Authors: Goforth JB, Anderson SA, Nizzi CP, Eisenstein RS Iron regulatory proteins (IRPs) are iron-regulated RNA binding proteins that, along with iron-responsive elements (IREs), control the translation of a diverse set of mRNA with 5' IRE. Dysregulation of IRP action causes disease with etiology that may reflect differential control of IRE-containing mRNA. IREs are defined by a conserved stem-loop structure including a midstem bulge at C8 and a terminal CAGUGH sequence that forms an AGU pseudo-triloop and N19 bulge. C8 and the pseudo-triloop nucleotides make the majority of the 22 identified bonds with IRP1. We show that IRP1 binds 5' IREs in a hierarchy extending over a ninefold range of affinities that encompasses changes in IRE binding affinity observed with human L-ferritin IRE m... RNA journals http://www.medworm.com/rss/comments.php?id=3036257 Wed, 25 Nov 2009 00:00:00 +0100 3036257 http://www.medworm.com/index.php?rid=3030884&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19934229%26dopt%3DAbstract Authors: Walters RW, Bradrick SS, Gromeier M MicroRNAs (miRNAs) regulate gene expression post-transcriptionally through binding specific sites within the 3' untranslated regions (UTRs) of their target mRNAs. Numerous investigations have documented repressive effects of miRNAs and identified factors required for their activity. However, the precise mechanisms by which miRNAs modulate gene expression are still obscure. Here, we have examined the effects of multiple miRNAs on diverse target transcripts containing artificial or naturally occurring 3' UTRs in human cell culture. In agreement with previous studies, we report that both the 5' m(7)G cap and 3' poly(A) tail are essential for maximum miRNA repression. These cis-acting elements also conferred miRNA susceptibility to target mRNAs ... RNA journals http://www.medworm.com/rss/comments.php?id=3030884 Tue, 24 Nov 2009 00:00:00 +0100 3030884 http://www.medworm.com/index.php?rid=3030883&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19934230%26dopt%3DAbstract Authors: Lee C, Kim N, Roy M, Graveley BR The arthropod Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of protein isoforms via combinatorial splicing of numerous alternative exons encoding immunoglobulin variable domains organized into three clusters referred to as the exon 4, 6, and 9 clusters. Dscam protein diversity is important for nervous system development and immune functions. We have performed extensive phylogenetic analyses of Dscam from 20 arthropods (each containing between 46 and 96 alternative exons) to reconstruct the detailed history of exon duplication and loss events that built this remarkable system over 450 million years of evolution. Whereas the structure of the exon 4 cluster is ancient, the exon 6 and 9 clusters have undergone mas... RNA journals http://www.medworm.com/rss/comments.php?id=3030883 Tue, 24 Nov 2009 00:00:00 +0100 3030883 http://www.medworm.com/index.php?rid=3030882&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19934231%26dopt%3DAbstract Authors: Belin S, Kindbeiter K, Hacot S, Albaret MA, Roca-Martinez JX, Thérizols G, Grosso O, Diaz JJ The ribosome is the central effector of protein synthesis, and its synthesis is intimately coordinated with that of proteins. At present, the most documented way to modulate ribosome biogenesis involves control of rDNA transcription by RNA polymerase I (RNA Pol I). Here we show that after infection of human cells with herpes simplex virus type 1 (HSV-1) the rate of ribosome biogenesis is modulated independently of RNA Pol I activity by a dramatic change in the rRNA maturation pathway. This process permits control of the ribosome biogenesis rate, giving the possibility of escaping ribosomal stress and eventually allowing assembly of specialized kinds of ribosomes. PMID: 1993423... RNA journals http://www.medworm.com/rss/comments.php?id=3030882 Tue, 24 Nov 2009 00:00:00 +0100 3030882 http://www.medworm.com/index.php?rid=3030885&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19933768%26dopt%3DAbstract Authors: Cibois M, Gautier-Courteille C, Vallée A, Paillard L Targeted inactivations of RNA-binding proteins (RNA-BPs) can lead to huge phenotypical defects. These defects are due to the deregulation of certain mRNAs. However, we generally do not know, among the hundreds of mRNAs that are normally controlled by one RNA-BP, which are responsible for the observed phenotypes. Here, we designed an antisense oligonucleotide ("target protector") that masks the binding site of the RNA-BP CUG-binding protein 1 (CUGBP1) on the mRNA Suppressor of Hairless [Su(H)] that encodes a key player of Notch signaling. We showed that injecting this oligonucleotide into Xenopus embryos specifically inhibited the binding of CUGBP1 to the mRNA. This caused the derepression of Su(H) mRNA, the overexpressi... RNA journals http://www.medworm.com/rss/comments.php?id=3030885 Mon, 23 Nov 2009 00:00:00 +0100 3030885 http://www.medworm.com/index.php?rid=3030887&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19933321%26dopt%3DAbstract Authors: Cao Q, Padmanabhan K, Richter JD Pumilio 2 (Pum2) interacts with the 3' UTR-containing pumilio binding element (PBE) of RINGO/SPY mRNA to repress translation in Xenopus oocytes. Here, we show that Pum2 also binds directly to the 5' 7mG cap structure; in so doing, it precludes eIF4E from binding the cap. Using deletion analysis, we have mapped the cap interaction domain of Pum2 to the amino terminus of the protein and identified a conserved tryptophan residue that mediates this specific interaction. Reporter mRNA-based assays demonstrate that Pum2 requires the conserved tryptophan to repress translation in injected Xenopus oocytes. Thus, in addition to its suggested role in regulating poly(A) tail length and mRNA stability, our results suggest that vertebrate Pumilio can repres... RNA journals http://www.medworm.com/rss/comments.php?id=3030887 Fri, 20 Nov 2009 00:00:00 +0100 3030887 http://www.medworm.com/index.php?rid=3030886&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19933322%26dopt%3DAbstract Authors: Andronescu MS, Pop C, Condon AE Accurate prediction of RNA pseudoknotted secondary structures from the base sequence is a challenging computational problem. Since prediction algorithms rely on thermodynamic energy models to identify low-energy structures, prediction accuracy relies in large part on the quality of free energy change parameters. In this work, we use our earlier constraint generation and Boltzmann likelihood parameter estimation methods to obtain new energy parameters for two energy models for secondary structures with pseudoknots, namely, the Dirks-Pierce (DP) and the Cao-Chen (CC) models. To train our parameters, and also to test their accuracy, we create a large data set of both pseudoknotted and pseudoknot-free secondary structures. In addition to structural ... RNA journals http://www.medworm.com/rss/comments.php?id=3030886 Fri, 20 Nov 2009 00:00:00 +0100 3030886 http://www.medworm.com/index.php?rid=3015520&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19926721%26dopt%3DAbstract Authors: Fisette JF, Toutant J, Dugré-Brisson S, Desgroseillers L, Chabot B The mammalian proteins hnRNP A1 and hnRNP H control many splicing decisions in viral and cellular primary transcripts. To explain some of these activities, we have proposed that self-interactions between bound proteins create an RNA loop that represses internal splice sites while simultaneously activating the external sites that are brought in closer proximity. Here we show that a variety of hnRNP H binding sites can affect 5' splice site selection. The addition of two sets of hnRNP H sites in a model pre-mRNA modulates 5' splice site selection cooperatively, consistent with the looping model. Notably, binding sites for hnRNP A1 and H on the same pre-mRNA can similarly collaborate to modulate 5' splice sit... RNA journals http://www.medworm.com/rss/comments.php?id=3015520 Thu, 19 Nov 2009 00:00:00 +0100 3015520 http://www.medworm.com/index.php?rid=3015519&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19926722%26dopt%3DAbstract Authors: Benarroch D, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Shuman S The Tgs proteins are structurally homologous AdoMet-dependent eukaryal enzymes that methylate the N2 atom of 7-methyl guanosine nucleotides. They have an imputed role in the synthesis of the 2,2,7-trimethylguanosine (TMG) RNA cap. Here we exploit a collection of cap-like substrates to probe the repertoire of three exemplary Tgs enzymes, from mammalian, protozoan, and viral sources, respectively. We find that human Tgs (hTgs1) is a bona fide TMG synthase adept at two separable transmethylation steps: (1) conversion of m(7)G to m(2,7)G, and (2) conversion of m(2,7)G to m(2,2,7)G. hTgs1 is unable to methylate G or m(2)G, signifying that both steps require an m(7)G cap. hTgs1 utilizes a broad range of m(7)G n... RNA journals http://www.medworm.com/rss/comments.php?id=3015519 Thu, 19 Nov 2009 00:00:00 +0100 3015519 http://www.medworm.com/index.php?rid=3015518&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19926723%26dopt%3DAbstract We report that in Drosophila tud(1) mutants, the piRNA pathway is intact and most transposons are not de-repressed. However, the localization of Aub in the germ plasm is severely reduced. These findings indicate that germ plasm assembly requires sDMA modification of Aub by dPRMT5, which, in turn, is required for binding to Tudor. Our study also suggests that the function of the piRNA pathway in PGC specification may be independent of its role in transposon control. PMID: 19926723 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=3015518 Thu, 19 Nov 2009 00:00:00 +0100 3015518 http://www.medworm.com/index.php?rid=3015517&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19926724%26dopt%3DAbstract Authors: Gagnon KT, Zhang X, Qu G, Biswas S, Suryadi J, Brown BA, Maxwell ES The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two doma... RNA journals http://www.medworm.com/rss/comments.php?id=3015517 Thu, 19 Nov 2009 00:00:00 +0100 3015517 http://www.medworm.com/index.php?rid=3015516&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19926725%26dopt%3DAbstract Authors: Kazerouninia A, Ngo B, Martinson HG The poly(A) signal has long been known for its role in directing the cleavage and polyadenylation of eukaryotic mRNA. In recent years its additional coordinating role in multiple related aspects of gene expression has also become increasingly clear. Here we use HeLa nuclear extracts to study two of these activities, poly(A) signal-dependent transcriptional pausing, which was originally proposed as a surveillance checkpoint, and poly(A) signal-dependent degradation (PDD) of unprocessed transcripts from weak poly(A) signals. We confirm directly, by measuring the length of RNA within isolated transcription elongation complexes, that a newly transcribed poly(A) signal reduces the rate of elongation by RNA polymerase II and causes the accumulatio... RNA journals http://www.medworm.com/rss/comments.php?id=3015516 Thu, 19 Nov 2009 00:00:00 +0100 3015516 http://www.medworm.com/index.php?rid=3008684&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19917635%26dopt%3DAbstract Authors: Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character-as is found in small interfering RNAs (siRNAs)-directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient loading of miRNA* strands in Ago2 favors duplexes with a paired cen... RNA journals http://www.medworm.com/rss/comments.php?id=3008684 Mon, 16 Nov 2009 00:00:00 +0100 3008684 http://www.medworm.com/index.php?rid=2940479&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19864433%26dopt%3DAbstract Authors: Zhang J, Dundas J, Lin M, Chen R, Wang W, Liang J Accurate free energy estimation is essential for RNA structure prediction. The widely used Turner's energy model works well for nested structures. For pseudoknotted RNAs, however, there is no effective rule for estimation of loop entropy and free energy. In this work we present a new free energy estimation method, termed the pseudoknot predictor in three-dimensional space (pk3D), which goes beyond Turner's model. Our approach treats nested and pseudoknotted structures alike in one unifying physical framework, regardless of how complex the RNA structures are. We first test the ability of pk3D in selecting native structures from a large number of decoys for a set of 43 pseudoknotted RNA molecules, with lengths ranging from 23 to ... RNA journals http://www.medworm.com/rss/comments.php?id=2940479 Wed, 28 Oct 2009 00:00:00 +0100 2940479 http://www.medworm.com/index.php?rid=2940488&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861420%26dopt%3DAbstract Authors: Bugaeva EY, Surkov S, Golovin AV, Ofverstedt LG, Skoglund U, Isaksson LA, Bogdanov AA, Shpanchenko OV, Dontsova OA Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA-ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy to... RNA journals http://www.medworm.com/rss/comments.php?id=2940488 Tue, 27 Oct 2009 00:00:00 +0100 2940488 http://www.medworm.com/index.php?rid=2940487&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861421%26dopt%3DAbstract Authors: Eamens AL, Smith NA, Curtin SJ, Wang MB, Waterhouse PM In Arabidopsis thaliana(Arabidopsis), DICER-LIKE1 (DCL1) functions together with the double-stranded RNA binding protein (dsRBP), DRB1, to process microRNAs (miRNAs) from their precursor transcripts prior to their transfer to the RNA-induced silencing complex (RISC). miRNA-loaded RISC directs RNA silencing of cognate mRNAs via ARGONAUTE1 (AGO1)-catalyzed cleavage. Short interefering RNAs (siRNAs) are processed from viral-derived or transgene-encoded molecules of double-stranded RNA (dsRNA) by the DCL/dsRBP partnership, DCL4/DRB4, and are also loaded to AGO1-catalyzed RISC for cleavage of complementary mRNAs. Here, we use an artificial miRNA (amiRNA) technology, transiently expressed in Nicotiana benthamiana, to produce a s... RNA journals http://www.medworm.com/rss/comments.php?id=2940487 Tue, 27 Oct 2009 00:00:00 +0100 2940487 http://www.medworm.com/index.php?rid=2940486&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861422%26dopt%3DAbstract Authors: Menzel P, Gorodkin J, Stadler PF User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practi... RNA journals http://www.medworm.com/rss/comments.php?id=2940486 Tue, 27 Oct 2009 00:00:00 +0100 2940486 http://www.medworm.com/index.php?rid=2940485&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861423%26dopt%3DAbstract Authors: Vendeix FA, Munoz AM, Agris PF The maturation of RNAs includes site-specific post-transcriptional modifications that contribute significantly to hydrogen bond formation within RNA and between different RNAs, especially in formation of mismatch base pairs. Thus, an understanding of the geometry and strength of the base-pairing of modified ribonucleoside 5'-monophosphates, previously not defined, is applicable to investigations of RNA structure and function and of the design of novel RNAs. The geometry and free energies of base-pairings were calculated in aqueous solution under neutral conditions with AMBER force fields and molecular dynamics simulations (MDSs). For example, unmodified uridines were observed to bind to uridine and cytidine with significant stability, but the rib... RNA journals http://www.medworm.com/rss/comments.php?id=2940485 Tue, 27 Oct 2009 00:00:00 +0100 2940485 http://www.medworm.com/index.php?rid=2940484&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861424%26dopt%3DAbstract Authors: Le P, Fisher PR, Barth C Transcription of the mitochondrial genome in Dictyostelium discoideum gives rise to eight major polycistronic RNA species that can be detected by Northern hybridization. In order to determine whether these transcripts could possibly derive from processing of even larger transcripts, reverse transcriptase polymerase chain reactions (RT-PCRs) were performed in an attempt to amplify the intervening regions between the eight major transcripts. All but one intervening region were successfully reverse transcribed and amplified, indicating that even larger transcripts existed and that the eight major transcripts detected previously may be the products of transcript processing. Southern hybridization analyses of DNA fragments representing the sequences between... RNA journals http://www.medworm.com/rss/comments.php?id=2940484 Tue, 27 Oct 2009 00:00:00 +0100 2940484 http://www.medworm.com/index.php?rid=2940483&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861425%26dopt%3DAbstract Authors: Hasenöhrl D, Fabbretti A, Londei P, Gualerzi CO, Bläsi U The function of initiation factors in and the sequence of events during translation initiation have been intensively studied in Bacteria and Eukaryotes, whereas in Archaea knowledge on these functions/processes is limited. By employing chemical probing, we show that translation initiation factor aIF1 of the model crenarchaeon Sulfolobus solfataricus binds to the same area on the ribosome as the bacterial and eukaryal orthologs. Fluorescence energy transfer assays (FRET) showed that aIF1, like its eukaryotic and bacterial orthologs, has a fidelity function in translation initiation complex formation, and that both aIF1 and aIF1A exert a synergistic effect in stimulating ribosomal association of the Met-tRNAi(Met... RNA journals http://www.medworm.com/rss/comments.php?id=2940483 Tue, 27 Oct 2009 00:00:00 +0100 2940483 http://www.medworm.com/index.php?rid=2940482&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861426%26dopt%3DAbstract Authors: Reid DC, Chang BL, Gunderson SI, Alpert L, Thompson WA, Fairbrother WG Many splicing factors interact with both mRNA and pre-mRNA. The identification of these interactions has been greatly improved by the development of in vivo cross-linking immunoprecipitation. However, the output carries a strong sampling bias in favor of RNPs that form on more abundant RNA species like mRNA. We have developed a novel in vitro approach for surveying binding on pre-mRNA, without cross-linking or sampling bias. Briefly, this approach entails specifically designed oligonucleotide pools that tile through a pre-mRNA sequence. The pool is then partitioned into bound and unbound fractions, which are quantified by a two-color microarray. We applied this approach to locating splicing factor binding s... RNA journals http://www.medworm.com/rss/comments.php?id=2940482 Tue, 27 Oct 2009 00:00:00 +0100 2940482 http://www.medworm.com/index.php?rid=2940481&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861427%26dopt%3DAbstract In this study, we sought to investigate the mechanism of internal initiation in yeast by assessing the functional role of nucleotides within the minimal URE2 IRES element, and delineating the cis-sequences that modulate levels of internal initiation using a monocistronic reporter vector. Furthermore, we compared the eIF2A sensitivity of the URE2 IRES element with some of the invasive growth IRES elements using DeltaeIF2A yeast. We found that the stability of the stem-loop structure within the minimal URE2 IRES element is not a critical determinant of optimal IRES activity, and the downstream sequences that modulate URE2 IRES-mediated translation can be defined to discrete regions within the URE2 coding region. Repression of internal initiation on the URE2 minimal IRES element by eIF2A is n... RNA journals http://www.medworm.com/rss/comments.php?id=2940481 Tue, 27 Oct 2009 00:00:00 +0100 2940481 http://www.medworm.com/index.php?rid=2940480&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861428%26dopt%3DAbstract Authors: Bissels U, Wild S, Tomiuk S, Holste A, Hafner M, Tuschl T, Bosio A MicroRNAs (miRNAs) are a species of small RNAs approximately 21-23-nucleotides long that have been shown to play an important role in many different cellular, developmental, and physiological processes. Accordingly, numerous PCR-, sequencing-, or hybridization-based methods have been established to identify and quantify miRNAs. Their short length results in a high dynamic range of melting temperatures and therefore impedes a proper selection of detection probes or optimized PCR primers. While miRNA microarrays allow for massive parallel and accurate relative measurement of all known miRNAs, they have so far been less useful as an assay for absolute quantification. Here, we present a microarray-based approach fo... RNA journals http://www.medworm.com/rss/comments.php?id=2940480 Tue, 27 Oct 2009 00:00:00 +0100 2940480 http://www.medworm.com/index.php?rid=2934733&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854870%26dopt%3DAbstract Authors: Vollmeister E, Haag C, Zarnack K, Baumann S, König J, Mannhaupt G, Feldbrügge M RNA-binding proteins constitute key factors of the post-transcriptional machinery. These regulatory proteins recognize specific elements within target transcripts to promote, for example, maturation, translation, or stability of mRNAs. In Ustilago maydis, evidence is accumulating that post-transcriptional processes are important to determine pathogenicity. Deletion of khd4, encoding a predicted RNA-binding protein with five K homology (KH) domains, causes aberrant cell morphology and reduced virulence. Here, we demonstrate that Khd4 recognizes the sequence AUACCC in vivo via its tandem KH domains 3 and 4. This sequence most likely functions as a regulatory RNA element in U. maydis, since ... RNA journals http://www.medworm.com/rss/comments.php?id=2934733 Fri, 23 Oct 2009 00:00:00 +0100 2934733 http://www.medworm.com/index.php?rid=2934732&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854871%26dopt%3DAbstract Authors: Grainger RJ, Barrass JD, Jacquier A, Rain JC, Beggs JD In Saccharomyces cerevisiae, Cwc21p is a protein of unknown function that is associated with the NineTeen Complex (NTC), a group of proteins involved in activating the spliceosome to promote the pre-mRNA splicing reaction. Here, we show that Cwc21p binds directly to two key splicing factors-namely, Prp8p and Snu114p-and becomes the first NTC-related protein known to dock directly to U5 snRNP proteins. Using a combination of proteomic techniques we show that the N-terminus of Prp8p contains an intramolecular fold that is a Snu114p and Cwc21p interacting domain (SCwid). Cwc21p also binds directly to the C-terminus of Snu114p. Complementary chemical cross-linking experiments reveal reciprocal protein footprints between the in... RNA journals http://www.medworm.com/rss/comments.php?id=2934732 Fri, 23 Oct 2009 00:00:00 +0100 2934732 http://www.medworm.com/index.php?rid=2934731&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19854872%26dopt%3DAbstract Authors: Lund E, Liu M, Hartley RS, Sheets MD, Dahlberg JE We show that microRNA-427 (miR-427) mediates the rapid deadenylation of maternal mRNAs after the midblastula transition (MBT) of Xenopus laevis embryogenesis. By MBT, the stage when the embryonic cell cycle is remodeled and zygotic transcription of mRNAs is initiated, each embryo has accumulated approximately 10(9) molecules of miR-427 processed from multimeric pri-miR-427 transcripts synthesized after fertilization. We demonstrate that the maternal mRNAs for cyclins A1 and B2 each contain a single miR-427 target sequence, spanning less than 30 nucleotides, that is both necessary and sufficient for deadenylation, and that inactivation of miR-427 leads to stabilization of the mRNAs. Although this deadenylation normally takes pla... RNA journals http://www.medworm.com/rss/comments.php?id=2934731 Fri, 23 Oct 2009 00:00:00 +0100 2934731 http://www.medworm.com/index.php?rid=2923801&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850906%26dopt%3DAbstract Authors: Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JW, Green PJ, Barton GJ, Hutvagner G Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA(Gln) is d... RNA journals http://www.medworm.com/rss/comments.php?id=2923801 Wed, 21 Oct 2009 23:00:00 +0100 2923801 http://www.medworm.com/index.php?rid=2923800&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850907%26dopt%3DAbstract Authors: Brown AL, Smith DW Microdissection techniques have the potential to allow for transcriptome analyses in specific populations of cells that are isolated from heterogeneous tissues such as the nervous system and certain cancers. Problematically, RNA is not stable under the labeling conditions usually needed to identify the cells of interest for microdissection. We have developed an immunolabeling method that utilizes a high salt buffer to stabilize RNA during prolonged antibody incubations. We first assessed RNA integrity by three methods and found that tissue incubated in high salt buffer for at least 20 h yielded RNA of similar quality to that for RNA extracted from fresh-frozen tissue, which is considered highest quality. Notably, the integrity was superior to that for RNA ex... RNA journals http://www.medworm.com/rss/comments.php?id=2923800 Wed, 21 Oct 2009 23:00:00 +0100 2923800 http://www.medworm.com/index.php?rid=2923799&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850908%26dopt%3DAbstract Authors: Nergadze SG, Farnung BO, Wischnewski H, Khoriauli L, Vitelli V, Chawla R, Giulotto E, Azzalin CM The longstanding dogma that telomeres, the heterochromatic extremities of linear eukaryotic chromosomes, are transcriptionally silent was overturned by the discovery that DNA-dependent RNA polymerase II (RNAPII) transcribes telomeric DNA into telomeric repeat-containing RNA (TERRA). Here, we show that CpG dinucleotide-rich DNA islands, shared among multiple human chromosome ends, promote transcription of TERRA molecules. TERRA promoters sustain cellular expression of reporter genes, are located immediately upstream of TERRA transcription start sites, and are bound by active RNAPII in vivo. Finally, the identified promoter CpG dinucleotides are methylated in vivo, and cytosine methy... RNA journals http://www.medworm.com/rss/comments.php?id=2923799 Wed, 21 Oct 2009 23:00:00 +0100 2923799 http://www.medworm.com/index.php?rid=2923798&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850909%26dopt%3DAbstract Authors: Zamboni M, Scarabino D, Tocchini-Valentini GP tRNA splicing is essential for the formation of tRNAs and therefore for gene expression. A circularly permuted sequence of an amber-suppressor pre-tRNA gene was inserted into the sequence encoding the mouse NEMO protein. We demonstrated that, in mouse cells, the hybrid pre-tRNA/pre-mRNAs can be spliced precisely at the sites of the pre-tRNA intron. This splicing reaction produces functional tRNAs that suppress amber codons as well as translatable mRNAs that sustain the NF-kappaB activation pathway. The RNA molecules extracted from mouse cells were amplified by RT-PCR, and their sequences were determined, confirming the identity of the splice junctions. We then applied the Archaea-express technology, in which an archaeal RNA endonuc... RNA journals http://www.medworm.com/rss/comments.php?id=2923798 Wed, 21 Oct 2009 23:00:00 +0100 2923798 http://www.medworm.com/index.php?rid=2923797&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850910%26dopt%3DAbstract Authors: Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ Expression profiling of the 5' ends of uncapped mRNAs ("degradome" sequencing) can be used to empirically catalog microRNA (miRNA) targets, to probe patterns of miRNA hairpin processing, to examine mRNA decay, and to analyze accumulation of endogenous short interfering RNA (siRNA) precursors. We sequenced and analyzed the degradome of the moss Physcomitrella patens, an important model system for functional genomic analyses in plant evolution. A total of 52 target mRNAs of 27 different Physcomitrella miRNA families were identified. Many targets of both more conserved and less conserved miRNA families encoded putative regulatory proteins. Remnants of MIRNA hairpin processing also populated the degradome data and indica... RNA journals http://www.medworm.com/rss/comments.php?id=2923797 Wed, 21 Oct 2009 23:00:00 +0100 2923797 http://www.medworm.com/index.php?rid=2923796&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850911%26dopt%3DAbstract Authors: Issur M, Geiss BJ, Bougie I, Picard-Jean F, Despins S, Mayette J, Hobdey SE, Bisaillon M The 5'-end of the flavivirus genome harbors a methylated (m7)GpppA(2'OMe) cap structure, which is generated by the virus-encoded RNA triphosphatase, RNA (guanine-N7) methyltransferase, nucleoside 2'-O-methyltransferase, and RNA guanylyltransferase. The presence of the flavivirus guanylyltransferase activity in NS5 has been suggested by several groups but has not been empirically proven. Here we provide evidence that the N-terminus of the flavivirus NS5 protein is a true RNA guanylyltransferase. We demonstrate that GTP can be used as a substrate by the enzyme to form a covalent GMP-enzyme intermediate via a phosphoamide bond. Mutational studies also confirm the importance of a specific lysi... RNA journals http://www.medworm.com/rss/comments.php?id=2923796 Wed, 21 Oct 2009 23:00:00 +0100 2923796 http://www.medworm.com/index.php?rid=2923795&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850912%26dopt%3DAbstract Authors: Kawashima T, Pellegrini M, Chanfreau GF The role of many splicing factors in pre-mRNA splicing and the involvement of these factors in the processing of specific transcripts have often been defined through the analysis of loss-of-function mutants in vivo. Here we show that inactivating the nonsense-mediated mRNA decay (NMD) results in an enhancement of splicing phenotypes associated with several S. cerevisiae splicing factor mutations. Tiling microarrays showed that inactivation of the NMD factor Upf1p in the prp17Delta and prp18Delta mutant strains results in a larger spectrum of splicing defects than what is observed in the single mutants, including new transcripts previously shown unaffected by Prp17p or Prp18p inactivation. Inactivation of Upf1p in the second step/recyclin... RNA journals http://www.medworm.com/rss/comments.php?id=2923795 Wed, 21 Oct 2009 23:00:00 +0100 2923795 http://www.medworm.com/index.php?rid=2923794&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850913%26dopt%3DAbstract Authors: Strunk BS, Karbstein K Ribosome assembly is required for cell growth in all organisms. Classic in vitro work in bacteria has led to a detailed understanding of the biophysical, thermodynamic, and structural basis for the ordered and correct assembly of ribosomal proteins on ribosomal RNA. Furthermore, it has enabled reconstitution of active subunits from ribosomal RNA and proteins in vitro. Nevertheless, recent work has shown that eukaryotic ribosome assembly requires a large macromolecular machinery in vivo. Many of these assembly factors such as ATPases, GTPases, and kinases hydrolyze nucleotide triphosphates. Because these enzymes are likely regulatory proteins, much work to date has focused on understanding their role in the assembly process. Here, we review these factors,... RNA journals http://www.medworm.com/rss/comments.php?id=2923794 Wed, 21 Oct 2009 23:00:00 +0100 2923794 http://www.medworm.com/index.php?rid=2923793&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850914%26dopt%3DAbstract Authors: Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D Structured RNAs must fold into their native structures and discriminate against a large number of alternative ones, an especially difficult task given the limited information content of RNA's nucleotide alphabet. The simplest motifs within structured RNAs are two helices joined by nonhelical junctions. To uncover the fundamental behavior of these motifs and to elucidate the underlying physical forces and challenges faced by structured RNAs, we computationally and experimentally studied a tethered duplex model system composed of two helices joined by flexible single- or double-stranded polyethylene glycol tethers, whose lengths correspond to those typically observed in junctions from structured RNAs. To dissect the ther... RNA journals http://www.medworm.com/rss/comments.php?id=2923793 Wed, 21 Oct 2009 23:00:00 +0100 2923793 http://www.medworm.com/index.php?rid=2923792&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850915%26dopt%3DAbstract Authors: Yao S, Sharp JS, Bechhofer DH RNase J1, a ribonuclease with 5' exonuclease and endonuclease activities, is an important factor in Bacillus subtilis mRNA decay. A model for RNase J1 endonuclease activity in mRNA turnover has RNase J1 binding to the 5' end and tracking to a target site downstream, where it makes a decay-initiating cleavage. The upstream fragment from this cleavage is degraded by 3' exonucleases; the downstream fragment is degraded by RNase J1 5' exonuclease activity. Previously, DeltaermC mRNA was used to show 5'-end dependence of mRNA turnover. Here we used DeltaermC mRNA to probe RNase J1-dependent degradation, and the results were consistent with aspects of the model. DeltaermC mRNA showed increased stability in a mutant strain that contained a reduced level ... RNA journals http://www.medworm.com/rss/comments.php?id=2923792 Wed, 21 Oct 2009 23:00:00 +0100 2923792 http://www.medworm.com/index.php?rid=2923802&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19846574%26dopt%3DAbstract Authors: Nimjee SM, Oney S, Volovyk Z, Bompiani KM, Long SB, Hoffman M, Sullenger BA Thrombin is a multifunctional protease that plays a key role in hemostasis, thrombosis, and inflammation. Most thrombin inhibitors currently used as antithrombotic agents target thrombin's active site and inhibit all of its myriad of activities. Exosites 1 and 2 are distinct regions on the surface of thrombin that provide specificity to its proteolytic activity by mediating binding to substrates, receptors, and cofactors. Exosite 1 mediates binding and cleavage of fibrinogen, proteolytically activated receptors, and some coagulation factors, while exosite 2 mediates binding to heparin and to platelet receptor GPIb-IX-V. The crystal structures of two nucleic acid ligands bound to thrombin have been solv... RNA journals http://www.medworm.com/rss/comments.php?id=2923802 Tue, 20 Oct 2009 23:00:00 +0100 2923802 http://www.medworm.com/index.php?rid=2852975&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19789211%26dopt%3DAbstract In this report, we employ quantitative genetic interaction mapping, mass spectrometry of tandem affinity-purified complexes, and microarray profiling to investigate genetic, physical, and functional interactions involving Cwc21. Combined data from these assays support multiple roles for Cwc21 in the formation and function of splicing complexes. Consistent with a role for Cwc21 at the core of the spliceosome, we observe strong genetic, physical, and functional interactions with Isy1, a protein previously implicated in the first catalytic step of splicing and splicing fidelity. Together, the results suggest multiple functions for Cwc21/SRm300 in the splicing process, including an important role in the activation of splicing in association with Isy1. PMID: 19789211 [PubMed - as supplied b... RNA journals http://www.medworm.com/rss/comments.php?id=2852975 Mon, 28 Sep 2009 23:00:00 +0100 2852975 http://www.medworm.com/index.php?rid=2834734&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19776155%26dopt%3DAbstract Authors: Poiata E, Meyer MM, Ames TD, Breaker RR Riboswitches that sense S-adenosylmethionine (SAM) are widely distributed throughout a variety of bacterial lineages. Four classes of SAM-binding riboswitches have been reported to date, constituting the most diverse collection of riboswitch classes that sense the same compound. Three of these classes, termed SAM-I, SAM-II, and SAM-III represent unique structures that form distinct binding pockets for the ligand. SAM-IV riboswitches carry different conserved sequence and structural features compared to other SAM riboswitches, but nucleotides and substructures corresponding to the ligand binding pocket are identical to SAM-I aptamers. In this article, we describe a fifth class of SAM binding aptamer, which we have termed SAM-V. SAM-V was ... RNA journals http://www.medworm.com/rss/comments.php?id=2834734 Tue, 22 Sep 2009 23:00:00 +0100 2834734 http://www.medworm.com/index.php?rid=2834733&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19776156%26dopt%3DAbstract Authors: Zhang Q, Al-Hashimi HM By simplifying the interpretation of nuclear magnetic resonance spin relaxation and residual dipolar couplings data, recent developments involving the elongation of RNA helices are providing new atomic insights into the dynamical properties that allow RNA structures to change functionally and adaptively. Domain elongation, in concert with spin relaxation measurements, has allowed the detailed characterization of a hierarchical network of local and collective motional modes occurring at nanosecond timescale that mirror the structural rearrangements that take place following adaptive recognition. The combination of domain elongation with residual dipolar coupling measurements has allowed the experimental three-dimensional visualization of very large amplit... RNA journals http://www.medworm.com/rss/comments.php?id=2834733 Tue, 22 Sep 2009 23:00:00 +0100 2834733 http://www.medworm.com/index.php?rid=2834732&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19776157%26dopt%3DAbstract Authors: De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA, Green PJ Cosuppression is a classical form of eukaryotic post-transcriptional gene silencing. It was first reported in transgenic petunia, where a sense transgene meant to overexpress the host Chalcone Synthase-A (CHS-A) gene caused the degradation of the homologous transcripts and the loss of flower pigmentation. In this work, we used deep sequencing technology to characterize in detail the small RNA population generated from the CHS-A sequence in cosuppressed transgenic petunia. Unexpectedly, two distinct small interfering RNAs (siRNAs) were found to vastly predominate. Our demonstration that they guide prominent cleavage events in CHS-A mRNA provides compelling and previously lackin... RNA journals http://www.medworm.com/rss/comments.php?id=2834732 Tue, 22 Sep 2009 23:00:00 +0100 2834732 http://www.medworm.com/index.php?rid=2834731&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19776158%26dopt%3DAbstract Authors: Cao D, Haussecker D, Huang Y, Kay MA Human hepatitis delta virus (HDV) is the only animal virus known to replicate its RNA genome using a host polymerase because its only virally encoded proteins, the small and large hepatitis delta antigens (HDAg-S and HDAg-L), lack polymerase activity. Although this makes HDV an ideal model system to study RNA-directed transcription in mammalian cells, little is known about the host factors involved in its replication. To comprehensively identify such host factors, we created a stable cell line carrying a functional FLAG-HDAg-S. Anti-Flag immunopurification and mass spectrometry identified >100 proteins associated with FLAG-HDAg-S, many of which had predicted roles in RNA metabolism. The biological relevance of this screen was strongly su... RNA journals http://www.medworm.com/rss/comments.php?id=2834731 Tue, 22 Sep 2009 23:00:00 +0100 2834731 http://www.medworm.com/index.php?rid=2834730&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19776159%26dopt%3DAbstract Authors: Chen X, Denison L, Levy M, Ellington AD Selection may prove to be a powerful tool for the generation of functional RNAs for in vivo genetic regulation. However, traditional in vitro selection schemes do not mimic physiological conditions, and in vivo selection schemes frequently use small pool sizes. Here we describe a hybrid in vitro/in vivo selection scheme that overcomes both of these disadvantages. In this new method, PCR-amplified expression templates are transfected into mammalian cells, transcribed hammerhead RNAs self-cleave, and the extracted, functional hammerhead ribozyme species are specifically amplified for the next round of selection. Using this method we have selected a number of cis-cleaving hammerhead ribozyme variants that are functional in vivo and lead to ... RNA journals http://www.medworm.com/rss/comments.php?id=2834730 Tue, 22 Sep 2009 23:00:00 +0100 2834730 http://www.medworm.com/index.php?rid=2821106&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767419%26dopt%3DAbstract Authors: Huranová M, Jablonski JA, Benda A, Hof M, Stanek D, Caputi M Expression of the nascent RNA transcript is regulated by its interaction with a number of proteins. The misregulation of such interactions can often result in impaired cellular functions that can lead to cancer and a number of diseases. Thus, our understanding of RNA-protein interactions within the cellular context is essential for the development of novel diagnostic and therapeutic tools. While there are many in vitro methods that analyze RNA-protein interactions in vivo approaches are scarce. Here we established a method based on fluorescence resonance energy transfer (FRET), which we term RNA-binding mediated FRET (RB-FRET), which determines RNA-protein interaction inside cells and tested it on hnRNP H protei... RNA journals http://www.medworm.com/rss/comments.php?id=2821106 Thu, 17 Sep 2009 23:00:00 +0100 2821106 http://www.medworm.com/index.php?rid=2821105&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767420%26dopt%3DAbstract Authors: Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript (Sox2ot), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2. We show that Sox2ot is a stable transcript expressed in mouse embryoni... RNA journals http://www.medworm.com/rss/comments.php?id=2821105 Thu, 17 Sep 2009 23:00:00 +0100 2821105 http://www.medworm.com/index.php?rid=2821104&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19767421%26dopt%3DAbstract Authors: Sinturel F, Pellegrini O, Xiang S, Tong L, Condon C, Bénard L The identification of RNases or RNase effectors is a continuous challenge, particularly given the current importance of RNAs in the control of genome expression. Here, we show that a fluorogenic RNA-DNA hybrid is a powerful tool for a real-time fluorescence detection and assay of exoribonucleases (RT-FeDEx). This RT-FeDEx assay provides a new strategy for the isolation, purification, and assay of known and unknown exoribonucleases. PMID: 19767421 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=2821104 Thu, 17 Sep 2009 23:00:00 +0100 2821104 http://www.medworm.com/index.php?rid=2786712&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19745027%26dopt%3DAbstract Authors: Willenbrock H, Salomon J, Søkilde R, Barken KB, Hansen TN, Nielsen FC, Møller S, Litman T Recently, next-generation sequencing has been introduced as a promising, new platform for assessing the copy number of transcripts, while the existing microarray technology is considered less reliable for absolute, quantitative expression measurements. Nonetheless, so far, results from the two technologies have only been compared based on biological data, leading to the conclusion that, although they are somewhat correlated, expression values differ significantly. Here, we use synthetic RNA samples, resembling human microRNA samples, to find that microarray expression measures actually correlate better with sample RNA content than expression measures obtained from sequencing dat... RNA journals http://www.medworm.com/rss/comments.php?id=2786712 Wed, 09 Sep 2009 23:00:00 +0100 2786712 http://www.medworm.com/index.php?rid=2786713&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19741022%26dopt%3DAbstract Authors: de la Peña M, Dufour D, Gallego J Three-way junction RNAs adopt a recurrent Y shape when two of the helices form a coaxial stack and the third helix establishes one or more tertiary contacts several base pairs away from the junction. In this review, the structure, distribution, and functional relevance of these motifs are examined. Structurally, the folds exhibit conserved junction topologies, and the distal tertiary interactions play a crucial role in determining the final shape of the structures. The junctions and remote tertiary contacts behave as flexible hinge motifs that respond to changes in the other region, providing these folds with switching mechanisms that have been shown to be functionally useful in a variety of contexts. In addition, the juxtaposition of RNA... RNA journals http://www.medworm.com/rss/comments.php?id=2786713 Tue, 08 Sep 2009 23:00:00 +0100 2786713 http://www.medworm.com/index.php?rid=2748496&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19717546%26dopt%3DAbstract Authors: Zhang J, Olsen GJ Messenger RNA (mRNA) processing plays important roles in gene expression in all domains of life. A number of cases of mRNA cleavage have been documented in Archaea, but available data are fragmentary. We have examined RNAs present in Methanocaldococcus (Methanococcus) jannaschii for evidence of RNA processing upstream of protein-coding genes. Of 123 regions covered by the data, 31 were found to be processed, with 30 including a cleavage site 12-16 nucleotides upstream of the corresponding translation start site. Analyses with 3'-RACE (rapid amplification of cDNA ends) and 5'-RACE indicate that the processing is endonucleolytic. Analyses of the sequences surrounding the processing sites for functional sites, sequence motifs, or potential RNA secondary structur... RNA journals http://www.medworm.com/rss/comments.php?id=2748496 Thu, 27 Aug 2009 23:00:00 +0100 2748496 http://www.medworm.com/index.php?rid=2745612&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19713328%26dopt%3DAbstract Authors: Saffran HA, Smiley JR X-chromosome linked inhibitor of apoptosis (XIAP) mRNA has been proposed to bear a stress-activated internal ribosome entry site (IRES) that stimulates translation under conditions that inhibit cap-dependent initiation. However, several reports have indicated that the strong activity of the XIAP IRES in certain bicistronic reporter assay systems stems from production of unintended monocistronic transcripts through splicing or cryptic promoter activity. Here we extend these findings by providing evidence that the XIAP IRES similarly provokes the production of monocistronic mRNA encompassing the 3' cistron in the betagal/CAT bicistronic reporter plasmid that was originally used to identify and characterize this putative IRES, through cryptic promoter activi... RNA journals http://www.medworm.com/rss/comments.php?id=2745612 Wed, 26 Aug 2009 23:00:00 +0100 2745612 http://www.medworm.com/index.php?rid=2741797&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19710183%26dopt%3DAbstract Authors: Rudolph MG, Klostermeier D DEAD box family helicases consist of a helicase core that is formed by two flexibly linked RecA-like domains. The helicase activity can be regulated by N- or C-terminal extensions flanking the core. Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) is the first DEAD box helicase that forms a dimer using a unique dimerization domain. In addition to the dimerization domain, Hera contains a C-terminal RNA binding domain (RBD) that shares sequence homology only to uncharacterized proteins of the Deinococcus/Thermus group. The crystal structure of Hera_RBD reveals the fold of an altered RNA recognition motif (RRM) with limited structural homology to the RBD of the DEAD box helicase YxiN from Bacillus subtilis. Comparison with RRM/RNA complex... RNA journals http://www.medworm.com/rss/comments.php?id=2741797 Tue, 25 Aug 2009 23:00:00 +0100 2741797 http://www.medworm.com/index.php?rid=2741796&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19710184%26dopt%3DAbstract Authors: Zhang L, Bao P, Leibowitz MJ, Zhang Y Pseudoknots play critical roles in packing the active structure of various functional RNAs. The importance of the P3-P7 pseudoknot in refolding of group I intron ribozymes has been recently appreciated, while little is known about the pseudoknot function in co-transcriptional folding. Here we used the Candida group I intron as a model to address the question. We show that co-transcriptional folding of the active self-splicing intron is twice as fast as refolding. The P3-P7 pseudoknot folds slowly during co-transcriptional folding at a rate constant similar to the folding of the active ribozyme, and folding of both P3-P7 and P1-P10 pseudoknots are inhibited by antisense oligonucleotides. We conclude that when RNA folding is coupled with tra... RNA journals http://www.medworm.com/rss/comments.php?id=2741796 Tue, 25 Aug 2009 23:00:00 +0100 2741796 http://www.medworm.com/index.php?rid=2741795&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19710185%26dopt%3DAbstract Authors: Parisien M, Cruz JA, Westhof E, Major F To benchmark progress made in RNA three-dimensional modeling and assess newly developed techniques, reliable and meaningful comparison metrics and associated tools are necessary. Generally, the average root-mean-square deviations (RMSDs) are quoted. However, RMSD can be misleading since errors are spread over the whole molecule and do not account for the specificity of RNA base interactions. Here, we introduce two new metrics that are particularly suitable to RNAs: the deformation index and deformation profile. The deformation index is calibrated by the interaction network fidelity, which considers base-base-stacking and base-base-pairing interactions within the target structure. The deformation profile highlights dissimilarities between... RNA journals http://www.medworm.com/rss/comments.php?id=2741795 Tue, 25 Aug 2009 23:00:00 +0100 2741795 http://www.medworm.com/index.php?rid=2741794&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19710186%26dopt%3DAbstract Authors: Müller M, Richter K, Heuck A, Kremmer E, Buchner J, Jansen RP, Niessing D In eukaryotic cells, dozens to hundreds of different mRNAs are localized by specialized motor-dependent transport complexes. One of the best-studied examples for directional mRNA transport is the localization of ASH1 mRNA in Saccharomyces cerevisiae. For transport, ASH1 mRNA is bound by the unusual RNA-binding protein She2p. Although previous results indicated that She2p forms dimers required for RNA binding and transcript localization, it remained unclear if the dimer constitutes the minimal RNA-binding unit assembling in vivo. By using analytical ultracentrifugation we found that She2p forms larger oligomeric complexes in solution. We also identified a point mutant that shows impaired oligomer for... RNA journals http://www.medworm.com/rss/comments.php?id=2741794 Tue, 25 Aug 2009 23:00:00 +0100 2741794 http://www.medworm.com/index.php?rid=2734786&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703939%26dopt%3DAbstract In this study, a program, MaxExpect, that predicts RNA secondary structure by maximizing the expected base-pair accuracy, is reported. This approach was first pioneered in the program CONTRAfold, using pair probabilities predicted with a statistical learning method. Here, a partition function calculation that utilizes the free energy change nearest-neighbor parameters is used to predict base-pair probabilities as well as probabilities of nucleotides being single-stranded. MaxExpect predicts both the optimal structure (having highest expected pair accuracy) and suboptimal structures to serve as alternative hypotheses for the structure. Tested on a large database of different types of RNA, the maximum expected accuracy structures are, on average, of higher accuracy than minimum free energy s... RNA journals http://www.medworm.com/rss/comments.php?id=2734786 Sun, 23 Aug 2009 23:00:00 +0100 2734786 http://www.medworm.com/index.php?rid=2734785&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703940%26dopt%3DAbstract We report that unadulterated cytoplasmic RNA uncovers differentially expressed mRNAs that otherwise would not have been detected when using whole cell RNA and that the inclusion of nuclear RNA has a large impact on whole cell gene expression microarray results by distorting the mRNA profile to the extent that a substantial number of false positives are generated. We conclude that to produce a valid profile of the steady-state mRNA population, the nuclear component must be excluded, and to arrive at a more realistic view of a cell's gene expression profile, the nuclear and cytoplasmic RNA fractions should be analyzed separately. PMID: 19703940 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=2734785 Sun, 23 Aug 2009 23:00:00 +0100 2734785 http://www.medworm.com/index.php?rid=2734784&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703941%26dopt%3DAbstract Authors: Ouellet J, Byrne M, Lilley DM The complete VS ribozyme comprises seven helical segments, connected by three three-way RNA junctions. In the presence of Mg(2+) ions, cleavage occurs within the internal loop of helix I. This requires the participation of a guanine (G638) within the helix I loop, and a remote adenine (A756) within an internal loop of helix VI. Previous structural studies have suggested that helix I docks into the fold of the remaining part of the ribozyme, bringing A756 and G638 close to the scissile phosphate to allow the cleavage reaction to proceed. We show here that while either A756C or G638A individually exhibit very low cleavage activity, a mixture of the two variants leads to cleavage of the A756C RNA, but not the G638A RNA. The rate of cleavage depends o... RNA journals http://www.medworm.com/rss/comments.php?id=2734784 Sun, 23 Aug 2009 23:00:00 +0100 2734784 http://www.medworm.com/index.php?rid=2723407&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19696158%26dopt%3DAbstract Authors: Kim S, Liu C, Halkidis K, Gamper HB, Hou YM The universally conserved CCA sequence is present at the 3' terminal 74-76 positions of all active tRNA molecules as a functional tag to participate in ribosome protein synthesis. The CCA enzyme catalyzes CCA synthesis in three sequential steps of nucleotide addition at rapid and identical rates. However, the kinetic determinant of each addition is unknown, thus limiting the insights into the kinetic basis of CCA addition. Using our recently developed single turnover kinetics of Escherichia coli CCA enzyme as a model, we show here that the identical rate of the stepwise CCA addition is determined by distinct kinetic parameters. Specifically, the kinetics of C74 and C75 addition is controlled by the chemistry of nucleotidyl transfer, ... RNA journals http://www.medworm.com/rss/comments.php?id=2723407 Wed, 19 Aug 2009 23:00:00 +0100 2723407 http://www.medworm.com/index.php?rid=2723406&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19696159%26dopt%3DAbstract Authors: Liang S, Connell GJ An RNA editing reaction that is both essential and specific to the trypanosomatid parasites is an attractive target for new drug development. Although high-throughput screening of chemical libraries is a powerful strategy often used to identify new drugs, the available in vitro editing assays do not have the necessary sensitivity and format for this approach to be feasible. A ruthenium labeled reporter RNA is described here that overcomes these limitations as it can both detect edited product in the low femtomole range and is ideal for high-throughput format. The reporter RNA consists of an RNA editing substrate linked to a streptavidin-binding aptamer that is initially held within an inactive conformation. An in vitro selection strategy optimized the linka... RNA journals http://www.medworm.com/rss/comments.php?id=2723406 Wed, 19 Aug 2009 23:00:00 +0100 2723406 http://www.medworm.com/index.php?rid=2717235&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19690099%26dopt%3DAbstract Authors: Tanaka N, Shuman S RNA 3'-phosphate cyclase (Rtc) enzymes are a widely distributed family that catalyze the synthesis of RNA 2',3' cyclic phosphate ends via an ATP-dependent pathway comprising three nucleotidyl transfer steps: reaction of Rtc with ATP to form a covalent Rtc-(histidinyl-N)-AMP intermediate and release PP(i); transfer of AMP from Rtc1 to an RNA 3'-phosphate to form an RNA(3')pp(5')A intermediate; and attack by the terminal nucleoside O2' on the 3'-phosphate to form an RNA 2',3' cyclic phosphate product and release AMP. Here we used the crystal structure of Escherichia coli RtcA to guide a mutational analysis of the human RNA cyclase Rtc1. An alanine scan defined seven conserved residues as essential for the Rtc1 RNA cyclization and autoadenylylation reactions. S... RNA journals http://www.medworm.com/rss/comments.php?id=2717235 Mon, 17 Aug 2009 23:00:00 +0100 2717235 http://www.medworm.com/index.php?rid=2717234&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19690100%26dopt%3DAbstract Authors: Ploner A, Ploner C, Lukasser M, Niederegger H, Hüttenhofer A In the recent past, several thousand noncoding RNA (ncRNA) genes have been predicted within eukaryal genomes. However, for their functional analysis only a few high-throughput methods are currently available to knock down selected ncRNA species, such as microRNAs, which are targeted by antisense probes, termed antagomirs. We thus compared the efficiencies of four knockdown strategies, previously mainly employed for the analysis of protein-coding genes, to study the function of ncRNAs, in particular, small nucleolar RNAs (snoRNAs). Thereby, the class of snoRNAs represents one of the most abundant ncRNA species. The majority of snoRNAs has been shown to mediate nucleotide modifications by targeting ribosomal RNAs ... RNA journals http://www.medworm.com/rss/comments.php?id=2717234 Mon, 17 Aug 2009 23:00:00 +0100 2717234 http://www.medworm.com/index.php?rid=2684319&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19661161%26dopt%3DAbstract We report that Drosophila cells form SGs in response to arsenite and heat shock. Drosophila SGs, like mammalian SGs, are distinct from but adjacent to processing bodies (PBs, sites of mRNA silencing and decay), require polysome disassembly, and are in dynamic equilibrium with polysomes. We further examine the role of the two Drosophila eIF2alpha kinases, PEK and GCN2, in regulating SG formation in response to heat and arsenite stress. While arsenite-induced SGs are dependent upon eIF2alpha phosphorylation, primarily via PEK, heat-induced SGs are phospho-eIF2alpha-independent. In contrast, heat-induced SGs require eIF2alpha phosphorylation in mammalian cells, as non-phosphorylatable eIF2alpha Ser51Ala mutant murine embryonic fibroblasts do not form SGs even after severe heat shock. These re... RNA journals http://www.medworm.com/rss/comments.php?id=2684319 Wed, 05 Aug 2009 23:00:00 +0100 2684319 http://www.medworm.com/index.php?rid=2680882&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19656866%26dopt%3DAbstract Authors: Yuan X, Shi K, Meskauskas A, Simon AE Precise temporal control is needed for RNA viral genomes to translate sufficient replication-required products before clearing ribosomes and initiating replication. A 3' translational enhancer in Turnip crinkle virus (TCV) overlaps an internal T-shaped structure (TSS) that binds to 60S ribosomal subunits. The higher-order structure in the region was examined through alteration of critical sequences revealing novel interactions between an H-type pseudoknot and upstream residues, and between the TSS and internal and terminal loops of an upstream hairpin. Our results suggest that the TSS forms a stable scaffold that allows for simultaneous interactions with external sequences through base pairings on both sides of its large internal symmetric... RNA journals http://www.medworm.com/rss/comments.php?id=2680882 Tue, 04 Aug 2009 23:00:00 +0100 2680882 http://www.medworm.com/index.php?rid=2680879&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19656867%26dopt%3DAbstract Authors: Pandya-Jones A, Black DL In metazoan organisms, pre-mRNA splicing is thought to occur during transcription, and it is postulated that these two processes are functionally coupled via still-unknown mechanisms. Current evidence supports co-transcriptional spliceosomal assembly, but there is little quantitative information on how much splicing is completed during RNA synthesis. Here we isolate nascent chromatin-associated RNA from free, nucleoplasmic RNA already released from the DNA template. Using a quantitative RT-PCR assay, we show that the majority of introns separating constitutive exons are already excised from the human c-Src and fibronectin pre-mRNAs that are still in the process of synthesis, and that these introns are removed in a general 5'-to-3' order. Introns flanki... RNA journals http://www.medworm.com/rss/comments.php?id=2680879 Tue, 04 Aug 2009 23:00:00 +0100 2680879 http://www.medworm.com/index.php?rid=2662810&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19643916%26dopt%3DAbstract Authors: Chowdhury A, Tharun S Decapping is a critical step in the conserved 5'-to-3' mRNA decay pathway of eukaryotes. The hetero-octameric Lsm1-7-Pat1 complex is required for normal rates of decapping in this pathway. This complex also protects the mRNA 3'-ends from trimming in vivo. To elucidate the mechanism of decapping, we analyzed multiple lsm1 mutants, lsm1-6, lsm1-8, lsm1-9, and lsm1-14, all of which are defective in decapping and 3'-end protection but unaffected in Lsm1-7-Pat1 complex integrity. The RNA binding ability of the mutant complex was found to be almost completely lost in the lsm1-8 mutant but only partially impaired in the other mutants. Importantly, overproduction of the Lsm1-9p- or Lsm1-14p-containing (but not Lsm1-8p-containing) mutant complexes in wild-type cel... RNA journals http://www.medworm.com/rss/comments.php?id=2662810 Wed, 29 Jul 2009 23:00:00 +0100 2662810 http://www.medworm.com/index.php?rid=2650374&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19635780%26dopt%3DAbstract Authors: Zhou R, Czech B, Brennecke J, Sachidanandam R, Wohlschlegel JA, Perrimon N, Hannon GJ Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are approximately 22-23 nucleotides (nt), ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of approximately 24-28 nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. ... RNA journals http://www.medworm.com/rss/comments.php?id=2650374 Sun, 26 Jul 2009 23:00:00 +0100 2650374 http://www.medworm.com/index.php?rid=2639792&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19628621%26dopt%3DAbstract Authors: Politz JC, Hogan EM, Pederson T There is increasing evidence that noncoding RNAs play a functional role in the nucleus. We previously reported that the microRNA (miRNA), miR-206, is concentrated in the nucleolus of rat myoblasts, as well as in the cytoplasm as expected. Here we have extended this finding. We show by cell/nuclear fractionation followed by microarray analysis that a number of miRNAs can be detected within the nucleolus of rat myoblasts, some of which are significantly concentrated there. Pronounced nucleolar localization is a specific phenomenon since other miRNAs are present at only very low levels in the nucleolus and occur at much higher levels in the nucleoplasm and/or the cytoplasm. We have further characterized a subset of these miRNAs using RT-qPCR and in... RNA journals http://www.medworm.com/rss/comments.php?id=2639792 Wed, 22 Jul 2009 23:00:00 +0100 2639792 http://www.medworm.com/index.php?rid=2639791&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19628622%26dopt%3DAbstract Authors: Liang XH, Liu Q, Fournier MJ The ribosome decoding center is rich in modified rRNA nucleotides and little is known about their effects. Here, we examine the consequences of systematically deleting eight pseudouridine and 2'-O-methylation modifications in the yeast decoding center. Loss of most modifications individually has no apparent effect on cell growth. However, deletions of 2-3 modifications in the A- and P-site regions can cause (1) reduced growth rates ( approximately 15%-50% slower); (2) reduced amino acid incorporation rates (14%-24% slower); and (3) a significant deficiency in free small subunits. Negative and positive interference effects were observed, as well as strong positional influences. Notably, blocking formation of a hypermodified pseudouridine in the P re... RNA journals http://www.medworm.com/rss/comments.php?id=2639791 Wed, 22 Jul 2009 23:00:00 +0100 2639791 http://www.medworm.com/index.php?rid=2639794&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19625386%26dopt%3DAbstract Authors: Mazauric MH, Leroy JL, Visscher K, Yoshizawa S, Fourmy D Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. When the ribosome encounters the pseudoknot barrier that resists unraveling, transient mRNA-tRNA dissociation at the decoding site, results in a shift of the reading frame. The eukaryotic frameshifting pseudoknot from the beet western yellow virus (BWYV) has been well characterized, both structurally and functionally. Here, we show that in order to obtain eukaryotic levels of frameshifting efficiencies using prokaryotic Escherichia coli ribosomes, which depend upon the structural integrity of the BWYV pseudoknot, it is necessary to shorten the mRNA spacer between the slippery sequence and the pseudoknot b... RNA journals http://www.medworm.com/rss/comments.php?id=2639794 Tue, 21 Jul 2009 23:00:00 +0100 2639794 http://www.medworm.com/index.php?rid=2639793&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19625387%26dopt%3DAbstract Authors: Sharma M, Bulusu G, Mitra A Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-fr... RNA journals http://www.medworm.com/rss/comments.php?id=2639793 Tue, 21 Jul 2009 23:00:00 +0100 2639793 http://www.medworm.com/index.php?rid=2634904&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19622678%26dopt%3DAbstract Authors: Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, Westhof E Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologs in sequence databases. We address several ontological issues related to RNA sequence alignments that are informed by structure. Multiple sequence alignments are usually shown as two-dimensional (2D) matrices, with rows representing individual sequences, and columns identifying nucleotides from different sequences that correspond structurally, functionally, and/or evolutionarily. However, the requirement that sequences and structures correspond ... RNA journals http://www.medworm.com/rss/comments.php?id=2634904 Mon, 20 Jul 2009 23:00:00 +0100 2634904 http://www.medworm.com/index.php?rid=2634903&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19622679%26dopt%3DAbstract Authors: Osenberg S, Dominissini D, Rechavi G, Eisenberg E A-to-I RNA editing is the conversion of adenosine to inosine in double-stranded cellular and viral RNAs. Recently, abundant hyperediting of human transcripts, affecting thousands of genes, has been reported. Most of these editing sites are confined to intramolecular hairpin double-stranded RNA (dsRNA) structures formed by pairing of neighboring, reversely oriented, primate-specific Alu repeats. The biological implication of this extensive modification is still a mystery. A number of studies have shown that heavily edited transcripts are often retained in the nucleus. A recent study found that the edited region in transcripts of the mouse Slc7a2 gene is post-transcriptionally cleaved upon stress, enabling the release of the mRNA... RNA journals http://www.medworm.com/rss/comments.php?id=2634903 Mon, 20 Jul 2009 23:00:00 +0100 2634903 http://www.medworm.com/index.php?rid=2634902&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19622680%26dopt%3DAbstract Authors: Gregory ST, Demirci H, Belardinelli R, Monshupanee T, Gualerzi C, Dahlberg AE, Jogl G The RsmG methyltransferase is responsible for N(7) methylation of G527 of 16S rRNA in bacteria. Here, we report the identification of the Thermus thermophilus rsmG gene, the isolation of rsmG mutants, and the solution of RsmG X-ray crystal structures at up to 1.5 A resolution. Like their counterparts in other species, T. thermophilus rsmG mutants are weakly resistant to the aminoglycoside antibiotic streptomycin. Growth competition experiments indicate a physiological cost to loss of RsmG activity, consistent with the conservation of the modification site in the decoding region of the ribosome. In contrast to Escherichia coli RsmG, which has been reported to recognize only intact 30S subunits... RNA journals http://www.medworm.com/rss/comments.php?id=2634902 Mon, 20 Jul 2009 23:00:00 +0100 2634902 http://www.medworm.com/index.php?rid=2626820&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19620234%26dopt%3DAbstract In this study, we found that removal of RsgA or inactivation of its ribosome small subunit-dependent GTPase activity provides Escherichia coli cells with resistance to high salt stress. Salt stress suppressed the defects in subunit assembly of the ribosome and processing of 16S rRNA as well as truncation of the 3' end of 16S rRNA in RsgA-deletion cells. In contrast, salt stress transiently impaired subunit assembly of the ribosome and processing of 16S rRNA and induced 3' truncation of 16S rRNA in wild-type cells. These results suggest that the action of RsgA on the ribosome, which usually facilitates maturation of the small subunit, disturbs it under a salt stress condition. Consistently, there was a drastic but transient decrease in the intracellular amount of RsgA after salt shock. Salt... RNA journals http://www.medworm.com/rss/comments.php?id=2626820 Sun, 19 Jul 2009 23:00:00 +0100 2626820 http://www.medworm.com/index.php?rid=2626819&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19620235%26dopt%3DAbstract Authors: Godfrey AC, White AE, Tatomer DC, Marzluff WF, Duronio RJ Metazoan replication-dependent histone mRNAs are not polyadenylated, and instead terminate in a conserved stem-loop structure generated by an endonucleolytic cleavage of the pre-mRNA involving U7 snRNP. U7 snRNP contains two like-Sm proteins, Lsm10 and Lsm11, which replace SmD1 and SmD2 in the canonical heptameric Sm protein ring that binds spliceosomal snRNAs. Here we show that mutations in either the Drosophila Lsm10 or the Lsm11 gene disrupt normal histone pre-mRNA processing, resulting in production of poly(A)+ histone mRNA as a result of transcriptional read-through to cryptic polyadenylation sites present downstream from each histone gene. This molecular phenotype is indistinguishable from that which we previously... RNA journals http://www.medworm.com/rss/comments.php?id=2626819 Sun, 19 Jul 2009 23:00:00 +0100 2626819 http://www.medworm.com/index.php?rid=2626818&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19620236%26dopt%3DAbstract Authors: Yao B, Li J, Huang H, Sun C, Wang Z, Fan Y, Chang Q, Li S, Xi J To date, approximately 700 microRNA (miRNA) molecules have been identified in humans. Accurate and sensitive quantification of miRNA levels will help unveil their biological functions. Here, we extend the isothermal ramification amplification (RAM) approach to a sensitive and specific real-time assay for quantitative analysis of miRNA. This RAM miRNA assay is based on the threshold cycle (C(T)) principle similar to that of real-time PCR. It has a dynamic range of at least seven orders of magnitude, allowing for the quantification of miRNA input from 10(3) to 10(10) copies per reaction (10 nM to 1 fM). The capabilities of discriminating single-base mismatch and distinguishing mature miRNAs from their precursors are... RNA journals http://www.medworm.com/rss/comments.php?id=2626818 Sun, 19 Jul 2009 23:00:00 +0100 2626818 http://www.medworm.com/index.php?rid=2626823&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19617314%26dopt%3DAbstract In this study, we used both biochemical and genetic methods to analyze the structure of Ntc90, and its function in maintaining the integrity of the NTC and in NTC-mediated spliceosome activation. Our results show that Ntc90 interacts with Ntc31, Ntc30, and other NTC components through different regions of the protein, and that its function may be regulated by Ntc31 and Ntc30. Ntc90 is not required for the association of Prp19, Ntc85, Ntc77, Ntc25, and Ntc20, or for their binding to the spliceosome. It is also not required for NTC-mediated spliceosome activation, but is required for the recruitment of Yju2, which is involved in the first catalytic reaction after the function of Prp2. Our results demonstrate a novel role of the NTC in recruiting splicing factors to the spliceosome after its ... RNA journals http://www.medworm.com/rss/comments.php?id=2626823 Thu, 16 Jul 2009 23:00:00 +0100 2626823 http://www.medworm.com/index.php?rid=2626822&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19617315%26dopt%3DAbstract In this study we investigate the affects of single nucleotide polymorphisms (SNPs) on the generation of mature miRNAs and their function, and report that naturally occurring SNPs can impair or enhance miRNA processing as well as alter the sites of processing. Since miRNAs are small functional units, single base changes in both the precursor elements as well as the mature miRNA sequence may drive the evolution of new microRNAs by altering their biological function. Finally, the miRNAs examined in this study are X-linked, suggesting that the mutant alleles could be determinants in the etiology of diseases. PMID: 19617315 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=2626822 Thu, 16 Jul 2009 23:00:00 +0100 2626822 http://www.medworm.com/index.php?rid=2626821&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19617316%26dopt%3DAbstract Authors: Barberan-Soler S, Lambert NJ, Zahler AM Alternative splicing coupled to nonsense-mediated decay (AS-NMD) is a mechanism for post-transcriptional regulation of gene expression. We analyzed the global effects of mutations in seven genes of the C. elegans NMD pathway on AS isoform ratios. We find that mutations in two NMD factors, smg-6 and smg-7, have weaker global effects relative to mutations in other smg genes. We did an in-depth analysis of 12 pre-mRNA splicing factor genes that are subject to AS-NMD. For four of these, changes in the ratio of alternatively spliced isoforms during development are caused by developmentally regulated inhibition of NMD, and not by changes in alternative splicing. Using sucrose gradient analysis of mRNAs undergoing translation, we find several e... RNA journals http://www.medworm.com/rss/comments.php?id=2626821 Thu, 16 Jul 2009 23:00:00 +0100 2626821 http://www.medworm.com/index.php?rid=2614492&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19605532%26dopt%3DAbstract Authors: Rhee AC, Somerlot BH, Parimi N, Gott JM RNAs in the mitochondria of Physarum polycephalum contain nonencoded nucleotides that are added during RNA synthesis. Essentially all steady-state RNAs are accurately and fully edited, yet the signals guiding these precise nucleotide insertions are presently unknown. To localize the regions of the template that are required for editing, we constructed a series of chimeric templates that substitute varying amounts of DNA either upstream of or downstream from C insertion sites. Remarkably, all sequences necessary for C addition are contained within approximately 9 base pairs on either side of the insertion site. In addition, our data strongly suggest that sequences within this critical region affect different steps in the editing reaction.... RNA journals http://www.medworm.com/rss/comments.php?id=2614492 Tue, 14 Jul 2009 23:00:00 +0100 2614492 http://www.medworm.com/index.php?rid=2614491&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19605533%26dopt%3DAbstract Authors: Romero-López C, Berzal-Herranz A The RNA genome of the hepatitis C virus (HCV) contains multiple conserved structural cis domains that direct protein synthesis, replication, and infectivity. The untranslatable regions (UTRs) play essential roles in the HCV cycle. Uncapped viral RNAs are translated via an internal ribosome entry site (IRES) located at the 5' UTR, which acts as a scaffold for recruiting multiple protein factors. Replication of the viral genome is initiated at the 3' UTR. Bioinformatics methods have identified other structural RNA elements thought to be involved in the HCV cycle. The 5BSL3.2 motif, which is embedded in a cruciform structure at the 3' end of the NS5B coding sequence, contributes to the three-dimensional folding of the entire 3' end of the gen... RNA journals http://www.medworm.com/rss/comments.php?id=2614491 Tue, 14 Jul 2009 23:00:00 +0100 2614491 http://www.medworm.com/index.php?rid=2543602&cid=s_33036_50_f&fid=33036&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19447915%26dopt%3DAbstract Authors: Netter C, Weber G, Benecke H, Wahl MC RNA recognition motifs (RRMs) constitute versatile macromolecular interaction platforms. They are found in many components of spliceosomes, in which they mediate RNA and protein interactions by diverse molecular strategies. The human U11/U12-65K protein of the minor spliceosome employs a C-terminal RRM to bind hairpin III of the U12 small nuclear RNA (snRNA). This interaction comprises one side of a molecular bridge between the U11 and U12 small nuclear ribonucleoprotein particles (snRNPs) and is reminiscent of the binding of the N-terminal RRMs in the major spliceosomal U1A and U2B'' proteins to hairpins in their cognate snRNAs. Here we show by mutagenesis and electrophoretic mobility shift assays that the beta-sheet surface and a neighbo... RNA journals http://www.medworm.com/rss/comments.php?id=2543602 Sun, 28 Jun 2009 01:43:24 +0100 2543602