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. Mon, 06 Feb 2012 09:32:21 +0100 http://www.medworm.com/index.php?rid=5636127&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%3D22279149%26dopt%3DAbstract Authors: Qin D, Liu Q, Devaraj A, Fredrick K Abstract The molecular mechanisms that govern translation initiation to ensure accuracy remain unclear. Here, we provide evidence that the subunit-joining step of initiation is controlled in part by a conformational change in the 1408 region of helix h44. First, chemical probing of 30S initiation complexes formed with either a cognate (AUG) or near-cognate (AUC) start codon shows that an IF1-dependent enhancement at A1408 is reduced in the presence of AUG. This change in reactivity is due to a conformational change rather than loss of IF1, because other portions of the IF1 footprint are unchanged and high concentrations of IF1 fail to diminish the reactivity difference seen at A1408. Second, mutations in h44 such as A1413C stimulate 50S ... RNA journals http://www.medworm.com/rss/comments.php?id=5636127 Wed, 25 Jan 2012 05:00:00 +0100 5636127 http://www.medworm.com/index.php?rid=5636126&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%3D22279150%26dopt%3DAbstract Authors: Bida JP, Maher LJ Abstract The importance of RNA tertiary structure is evident from the growing number of published high resolution NMR and X-ray crystallographic structures of RNA molecules. These structures provide insights into function and create a knowledge base that is leveraged by programs such as Assemble, ModeRNA, RNABuilder, NAST, FARNA, Mc-Sym, RNA2D3D, and iFoldRNA for tertiary structure prediction and design. While these methods sample native-like RNA structures during simulations, all struggle to capture the native RNA conformation after scoring. We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides i... RNA journals http://www.medworm.com/rss/comments.php?id=5636126 Wed, 25 Jan 2012 05:00:00 +0100 5636126 http://www.medworm.com/index.php?rid=5636125&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%3D22279151%26dopt%3DAbstract Authors: Sherman EM, Esquiaqui J, Elsayed G, Ye JD Abstract Comprised of two aptamers connected by a short nucleotide linker, the glycine riboswitch was the first example of naturally occurring RNA elements reported to bind small organic molecules cooperatively. Earlier works have shown binding of glycine to the second aptamer allows tertiary interactions to be made between the two aptamers, which facilitates binding of a separate glycine molecule to the first aptamer, leading to glycine-binding cooperativity. Prompted by a distinctive protection pattern in the linker region of a minimal glycine riboswitch construct, we have identified a highly conserved (>90%) leader-linker duplex involving leader nucleotides upstream of the previously reported consensus glycine riboswitch sequ... RNA journals http://www.medworm.com/rss/comments.php?id=5636125 Wed, 25 Jan 2012 05:00:00 +0100 5636125 http://www.medworm.com/index.php?rid=5636133&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%3D22274953%26dopt%3DAbstract Authors: Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crécy-Lagard V Abstract The methylation of pseudouridine (Ψ) at position 54 of tRNA, producing m(1)Ψ, is a hallmark of many archaeal species, but the specific methylase involved in the formation of this modification had yet to be characterized. A comparative genomics analysis had previously identified COG1901 (DUF358), part of the SPOUT superfamily, as a candidate for this missing methylase family. To test this prediction, the COG1901 encoding gene, HVO_1989, was deleted from the Haloferax volcanii genome. Analyses of modified base contents indicated that while m(1)Ψ was present in tRNA extracted from the wild-type strain, it was absent from tRNA extracted from the mutant strain. Express... RNA journals http://www.medworm.com/rss/comments.php?id=5636133 Tue, 24 Jan 2012 05:00:00 +0100 5636133 http://www.medworm.com/index.php?rid=5636132&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%3D22274954%26dopt%3DAbstract Authors: Wurm JP, Griese M, Bahr U, Held M, Heckel A, Karas M, Soppa J, Wöhnert J Abstract tRNAs from all three kingdoms of life contain a variety of modified nucleotides required for their stability, proper folding, and accurate decoding. One prominent example is the eponymous ribothymidine (rT) modification at position 54 in the T-arm of eukaryotic and bacterial tRNAs. In contrast, in most archaea this position is occupied by another hypermodified nucleotide: the isosteric N1-methylated pseudouridine. While the enzyme catalyzing pseudouridine formation at this position is known, the pseudouridine N1-specific methyltransferase responsible for this modification has not yet been experimentally identified. Here, we present biochemical and genetic evidence that the two homologous pro... RNA journals http://www.medworm.com/rss/comments.php?id=5636132 Tue, 24 Jan 2012 05:00:00 +0100 5636132 http://www.medworm.com/index.php?rid=5636131&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%3D22274955%26dopt%3DAbstract Authors: Buskiewicz IA, Burke JM Abstract The catalytic activity of the hammerhead ribozyme is limited by its ability to fold into the native tertiary structure. Analysis of folding has been hampered by a lack of assays that can independently monitor the environment of nucleobases throughout the ribozyme-substrate complex in real time. Here, we report the development and application of a new folding assay in which we use pyrrolo-cytosine (pyC) fluorescence to (1) probe active-site formation, (2) examine the ability of peripheral ribozyme domains to support native folding, (3) identify a pH-dependent conformational change within the ribozyme, and (4) explore its influence on the equilibrium between the folded and unfolded core of the hammerhead ribozyme. We conclude that the natural... RNA journals http://www.medworm.com/rss/comments.php?id=5636131 Tue, 24 Jan 2012 05:00:00 +0100 5636131 http://www.medworm.com/index.php?rid=5636130&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%3D22274956%26dopt%3DAbstract Authors: Meluzzi D, Olson KE, Dolan GF, Arya G, Müller UF Abstract Group I introns have been engineered into trans-splicing ribozymes capable of replacing the 3'-terminal portion of an external mRNA with their own 3'-exon. Although this design makes trans-splicing ribozymes potentially useful for therapeutic application, their trans-splicing efficiency is usually too low for medical use. One factor that strongly influences trans-splicing efficiency is the position of the target splice site on the mRNA substrate. Viable splice sites are currently determined using a biochemical trans-tagging assay. Here, we propose a rapid and inexpensive alternative approach to identify efficient splice sites. This approach involves the computation of the binding free energies between ribozyme and ... RNA journals http://www.medworm.com/rss/comments.php?id=5636130 Tue, 24 Jan 2012 05:00:00 +0100 5636130 http://www.medworm.com/index.php?rid=5636129&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%3D22274957%26dopt%3DAbstract This study is the biggest catalog of small noncoding RNAs reported to date in S. pneumoniae and provides a highly complete view of the small RNA network in this pathogen. PMID: 22274957 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5636129 Tue, 24 Jan 2012 05:00:00 +0100 5636129 http://www.medworm.com/index.php?rid=5636128&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%3D22274958%26dopt%3DAbstract Authors: Olson KE, Müller UF Abstract Group I intron ribozymes can repair mutated mRNAs by replacing the 3'-terminal portion of the mRNA with their own 3'-exon. This trans-splicing reaction has the potential to treat genetic disorders and to selectively kill cancer cells or virus-infected cells. However, these ribozymes have not yet been used in therapy, partially due to a low in vivo trans-splicing efficiency. Previous strategies to improve the trans-splicing efficiencies focused on designing and testing individual ribozyme constructs. Here we describe a method that selects the most efficient ribozymes from millions of ribozyme variants. This method uses an in vivo rescue assay where the mRNA of an inactivated antibiotic resistance gene is repaired by trans-splicing group I intro... RNA journals http://www.medworm.com/rss/comments.php?id=5636128 Tue, 24 Jan 2012 05:00:00 +0100 5636128 http://www.medworm.com/index.php?rid=5636135&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%3D22271759%26dopt%3DAbstract Authors: Daba A, Koromilas AE, Pantopoulos K Abstract Ferritin stores and detoxifies an excess of intracellular iron, and thereby plays an important role in the metabolism of this metal. As unshielded iron promotes oxidative stress, ferritin is crucial in maintaining cellular redox balance and may also modulate cell growth, survival, and apoptosis. The expression of ferritin is controlled by transcriptional and post-transcriptional mechanisms. In light of the well-established transcriptional induction of ferritin by inflammatory signals, we examined how ferritin mRNA translation responds to stress conditions. We first used HT1080 fibrosarcoma cells engineered for coumermycin-inducible expression of PKR, a stress kinase that inhibits protein synthesis in virus-infected cells by phos... RNA journals http://www.medworm.com/rss/comments.php?id=5636135 Mon, 23 Jan 2012 05:00:00 +0100 5636135 http://www.medworm.com/index.php?rid=5636134&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%3D22271760%26dopt%3DAbstract Authors: Schenk L, Meinel DM, Strässer K, Gerber AP Abstract The La-motif (LAM) is an ancient and ubiquitous RNA-binding domain defining a superfamily of proteins, which comprises the genuine La proteins and La-related proteins (LARPs). In contrast to La, which binds and stabilizes pre-tRNAs and other RNA polymerase III transcripts, data on function and RNA targets of the LARPs have remained scarce. We have undertaken a global approach to elucidate the previously suggested role of the yeast LARP Slf1p in copper homeostasis. By applying RNA-binding protein immunopurification-microarray (RIP-Chip) analysis, we show that Slf1p and its paralog Sro9p copurify with overlapping sets of hundreds of functionally related mRNAs, including many transcripts coding for ribosomal proteins and hi... RNA journals http://www.medworm.com/rss/comments.php?id=5636134 Mon, 23 Jan 2012 05:00:00 +0100 5636134 http://www.medworm.com/index.php?rid=5594422&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%3D22240577%26dopt%3DAbstract Authors: Weissbach R, Scadden AD Abstract Hyperediting by adenosine deaminases that acts on RNA (ADARs) may result in numerous Adenosine-to-Inosine (A-to-I) substitutions within long dsRNA. However, while countless RNAs may undergo hyperediting, the role for inosine-containing hyperedited dsRNA (IU-dsRNA) in cells is poorly understood. We have previously shown that IU-dsRNA binds specifically to various components of cytoplasmic stress granules, as well as to other proteins such as Tudor Staphylococcal Nuclease (Tudor-SN). Tudor-SN has been implicated in diverse roles in mammalian cells, including transcription, splicing, RNAi, and degradation. Moreover, we have shown that Tudor-SN interacts directly with stress granule proteins. Here we show that Tudor-SN localizes to cytoplasmic ... RNA journals http://www.medworm.com/rss/comments.php?id=5594422 Thu, 12 Jan 2012 05:00:00 +0100 5594422 http://www.medworm.com/index.php?rid=5594423&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%3D22237150%26dopt%3DAbstract Authors: Vaughn JN, Ellingson SR, Mignone F, von Arnim A Abstract The sequence elements that mediate post-transcriptional gene regulation often reside in the 5' and 3' untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 5' and 3' UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 3' UTR, motifs resembling PUMILIO-binding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 5' UTR, one maj... RNA journals http://www.medworm.com/rss/comments.php?id=5594423 Wed, 11 Jan 2012 05:00:00 +0100 5594423 http://www.medworm.com/index.php?rid=5504482&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%3D22124015%26dopt%3DAbstract Authors: Ward WL, Derose VJ Abstract Although the Hammerhead ribozyme (HHRz) has long been used as a model system in the field of ribozyme enzymology, several details of its mechanism are still not well understood. In particular, significant questions remain concerning the disposition and role of catalytic metals in the HHRz. Previous metal-rescue experiments using a "minimal" HHRz resulted in prediction of a catalytic metal that is bound in the A9/G10.1 site in the ground state of the reaction and that bridges to the scissile phosphate further along the reaction pathway. "Native" or extended HHRz constructs contain tertiary contacts that stabilize a more compact structure at moderate ionic strength. We performed Cd(2+) rescue experiments on an extended HHRz from Schistosoma manson... RNA journals http://www.medworm.com/rss/comments.php?id=5504482 Fri, 16 Dec 2011 02:01:00 +0100 5504482 http://www.medworm.com/index.php?rid=5504481&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%3D22124016%26dopt%3DAbstract Authors: Deryusheva S, Choleza M, Barbarossa A, Gall JG, Bordonné R Abstract The survival of motor neuron (SMN) protein plays an important role in the biogenesis of spliceosomal snRNPs and is one factor required for the integrity of nuclear Cajal bodies (CBs). CBs are enriched in small CB-specific (sca) RNAs, which guide the formation of pseudouridylated and 2'-O-methylated residues in the snRNAs. Because SMN-deficient cells lack typical CBs, we asked whether the modification of internal residues of major and minor snRNAs is defective in these cells. We mapped modified nucleotides in the major U2 and the minor U4atac and U12 snRNAs. Using both radioactive and fluorescent primer extension approaches, we found that modification of major and minor spliceosomal snRNAs is normal in SMN... RNA journals http://www.medworm.com/rss/comments.php?id=5504481 Fri, 16 Dec 2011 02:00:50 +0100 5504481 http://www.medworm.com/index.php?rid=5504480&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%3D22124017%26dopt%3DAbstract Authors: Liang W, Deutscher MP Abstract RNase R is a processive exoribonuclease that plays an important role in degradation of structured RNAs in Escherichia coli. RNase R is unstable in exponential phase cells; however, under certain stress conditions, RNase R levels increase dramatically due to its stabilization. Binding of tmRNA and SmpB to the C-terminal region of RNase R is required for its instability, and this binding is regulated by acetylation of a single residue, Lys544, in exponential phase cells. RNase R is not acetylated in stationary phase. We show here that only exponential phase RNase R is acetylated because the modifying enzyme, protein lysine acetyltransferase, Pka (YfiQ), is absent from late exponential and stationary phase cells. As a consequence, newly synthesi... RNA journals http://www.medworm.com/rss/comments.php?id=5504480 Fri, 16 Dec 2011 02:00:40 +0100 5504480 http://www.medworm.com/index.php?rid=5504479&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%3D22128341%26dopt%3DAbstract Authors: Meola N, Pizzo M, Alfano G, Surace EM, Banfi S Abstract Long noncoding RNAs (lncRNAs) are emerging as regulators of many basic cellular pathways. Several lncRNAs are selectively expressed in the developing retina, although little is known about their functional role in this tissue. Vax2os1 is a retina-specific lncRNA whose expression is restricted to the mouse ventral retina. Here we demonstrate that spatiotemporal misexpression of Vax2os1 determines cell cycle alterations in photoreceptor progenitor cells. In particular, the overexpression of Vax2os1 in the developing early postnatal mouse retina causes an impaired cell cycle progression of photoreceptor progenitors toward their final committed fate and a consequent delay of their differentiation processes. At later devel... RNA journals http://www.medworm.com/rss/comments.php?id=5504479 Fri, 16 Dec 2011 02:00:30 +0100 5504479 http://www.medworm.com/index.php?rid=5504478&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%3D22128342%26dopt%3DAbstract Authors: Pervouchine DD, Khrameeva EE, Pichugina MY, Nikolaienko OV, Gelfand MS, Rubtsov PM, Mironov AA Abstract Pre-mRNA structure impacts many cellular processes, including splicing in genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each gene, we now ... RNA journals http://www.medworm.com/rss/comments.php?id=5504478 Fri, 16 Dec 2011 02:00:21 +0100 5504478 http://www.medworm.com/index.php?rid=5504477&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%3D22128343%26dopt%3DAbstract Authors: Sachs R, Max KE, Heinemann U, Balbach J Abstract Bacterial cold shock proteins (CSPs) regulate the cellular response to temperature downshift. Their general principle of function involves RNA chaperoning and transcriptional antitermination. Here we present two crystal structures of cold shock protein B from Bacillus subtilis (Bs-CspB) in complex with either a hexanucleotide (5'-UUUUUU-3') or heptanucleotide (5'-GUCUUUA-3') single-stranded RNA (ssRNA). Hydrogen bonds and stacking interactions between RNA bases and aromatic sidechains characterize individual binding subsites. Additional binding subsites which are not occupied by the ligand in the crystal structure were revealed by NMR spectroscopy in solution on Bs-CspB·RNA complexes. Binding studies demonstrate that Bs-Csp... RNA journals http://www.medworm.com/rss/comments.php?id=5504477 Fri, 16 Dec 2011 02:00:11 +0100 5504477 http://www.medworm.com/index.php?rid=5450700&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%3D22090085%26dopt%3DAbstract Authors: PMID: 22090085 [PubMed - in process] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5450700 Mon, 28 Nov 2011 16:38:17 +0100 5450700 http://www.medworm.com/index.php?rid=5450699&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%3D22090086%26dopt%3DAbstract Authors: PMID: 22090086 [PubMed - in process] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5450699 Mon, 28 Nov 2011 16:38:06 +0100 5450699 http://www.medworm.com/index.php?rid=5450692&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%3D22114317%26dopt%3DAbstract Authors: Sim S, Yao J, Weinberg DE, Niessen S, Yates JR, Wolin SL Abstract The Ro 60-kDa autoantigen, a ring-shaped RNA-binding protein, traffics between the nucleus and cytoplasm in vertebrate cells. In some vertebrate nuclei, Ro binds misfolded noncoding RNAs and may function in quality control. In the cytoplasm, Ro binds noncoding RNAs called Y RNAs. Y RNA binding blocks a nuclear accumulation signal, retaining Ro in the cytoplasm. Following UV irradiation, this signal becomes accessible, allowing Ro to accumulate in nuclei. To investigate how other cellular components influence the function and subcellular location of Ro, we identified several proteins that copurify with the mouse Ro protein. Here, we report that the zipcode-binding protein ZBP1 influences the subcellular local... RNA journals http://www.medworm.com/rss/comments.php?id=5450692 Wed, 23 Nov 2011 05:00:00 +0100 5450692 http://www.medworm.com/index.php?rid=5450691&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%3D22114318%26dopt%3DAbstract Authors: Keel AY, Jha BK, Kieft JS Abstract Activation of RNase L endonuclease activity is part of the mammalian innate immune response to viral infection. The poliovirus RNA genome contains a sequence in its protein-coding region that can act as a competitive inhibitor of RNase L. Mutation, sequence, and functional analysis of this competitive inhibitor RNA (ciRNA) revealed that its activity depends on specific sequences, showed that a loop-loop hairpin interaction forms in the ciRNA, and suggested the presence of a loop E motif. These features lead to the hypothesis that the ciRNA's function is conferred in part by a specific three-dimensional folded RNA architecture. By using a combination of biophysical, mutational, and functional studies, we have mapped features of the three-d... RNA journals http://www.medworm.com/rss/comments.php?id=5450691 Wed, 23 Nov 2011 05:00:00 +0100 5450691 http://www.medworm.com/index.php?rid=5450690&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%3D22114319%26dopt%3DAbstract Authors: Halbach F, Rode M, Conti E Abstract Ski2 is a cytoplasmic RNA helicase that functions together with the exosome in the turnover and quality control of mRNAs. Ski2 is conserved in eukaryotes and is related to the helicase Mtr4, a cofactor of the nuclear exosome involved in the processing and quality control of a variety of structured RNAs. We have determined the 2.4 Å resolution crystal structure of the 113 kDa helicase region of Saccharomyces cerevisiae Ski2. The structure shows that Ski2 has an overall architecture similar to that of Mtr4, with a core DExH region and an extended insertion domain. The insertion is not required for the formation of the Ski2-Ski3-Ski8 complex, but is instead an RNA-binding domain. While this is reminiscent of the Mtr4 insertion, there are s... RNA journals http://www.medworm.com/rss/comments.php?id=5450690 Wed, 23 Nov 2011 05:00:00 +0100 5450690 http://www.medworm.com/index.php?rid=5450689&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%3D22114320%26dopt%3DAbstract Authors: Postic G, Danchin A, Mechold U Abstract Processive RNases are unable to degrade efficiently very short oligonucleotides, and they are complemented by specific enzymes, nanoRNases, that assist in this process. We previously identified NrnA (YtqI) from Bacillus subtilis as a bifunctional protein with the ability to degrade nanoRNA (RNA oligos ≤5 nucleotides) and to dephosphorylate 3'-phosphoadenosine 5'-phosphate (pAp) to AMP. While the former activity is analogous to that of oligoribonuclease (Orn) from Escherichia coli, the latter corresponds to CysQ. NrnA homologs are widely present in bacterial and archaeal genomes. They are found preferably in genomes that lack Orn or CysQ homologs. Here, we characterize NrnA homologs from important human pathogens, Mpn140 from Mycopl... RNA journals http://www.medworm.com/rss/comments.php?id=5450689 Wed, 23 Nov 2011 05:00:00 +0100 5450689 http://www.medworm.com/index.php?rid=5450688&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%3D22114321%26dopt%3DAbstract Authors: Robson JE, Eaton SA, Underhill P, Williams D, Peters J Abstract Genomic imprinting is the phenomenon whereby a subset of genes is differentially expressed according to parental origin. Imprinted genes tend to occur in clusters, and microRNAs are associated with the majority of well-defined clusters of imprinted genes. We show here that two microRNAs, miR-296 and miR-298, are part of the imprinted Gnas/GNAS clusters in both mice and humans. Both microRNAs show imprinted expression and are expressed from the paternally derived allele, but not the maternal allele. They arise from a long, noncoding antisense transcript, Nespas, with a promoter more than 27 kb away. Nespas had been shown previously to act in cis to regulate imprinted gene expression within the Gnas cluster. Usi... RNA journals http://www.medworm.com/rss/comments.php?id=5450688 Wed, 23 Nov 2011 05:00:00 +0100 5450688 http://www.medworm.com/index.php?rid=5450693&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%3D22109839%26dopt%3DAbstract Authors: Martin JS, Halvorsen M, Davis-Neulander L, Ritz J, Gopinath C, Beauregard A, Laederach A Abstract A majority of SNPs (single nucleotide polymorphisms) map to noncoding and intergenic regions of the genome. Noncoding SNPs are often identified in genome wide association studies (GWAS) as strongly associated with human disease. Two such disease-associated SNPs in the 5' UTR of the human FTL (Ferritin Light Chain) gene are predicted to alter the ensemble of structures adopted by the mRNA. High-accuracy single nucleotide resolution chemical mapping reveals that these SNPs result in substantial changes in the structural ensemble in agreement with the computational prediction. Furthermore six rescue mutations are correctly predicted to restore the mRNA to its wild-type ensemble. ... RNA journals http://www.medworm.com/rss/comments.php?id=5450693 Tue, 22 Nov 2011 05:00:00 +0100 5450693 http://www.medworm.com/index.php?rid=5450694&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%3D22106413%26dopt%3DAbstract Authors: Betancur JG, Tomari Y Abstract In flies, asymmetric loading of small RNA duplexes into Argonaute2-containing RNA-induced silencing complex (Ago2-RISC) requires Dicer-2/R2D2 heterodimer, which acts as a protein sensor for the thermodynamic stabilities of the ends of small RNA duplexes. However, the mechanism of small RNA asymmetry sensing in mammalian RISC assembly remains obscure. Here, we quantitatively examined RISC assembly and target silencing activity in the presence or absence of Dicer in mammals. Our data show that, unlike the well-characterized fly Ago2-RISC assembly pathway, mammalian Dicer is dispensable for asymmetric RISC loading in vivo and in vitro. PMID: 22106413 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5450694 Mon, 21 Nov 2011 05:00:00 +0100 5450694 http://www.medworm.com/index.php?rid=5450697&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%3D22101241%26dopt%3DAbstract Authors: Wang DO, Matsuno H, Ikeda S, Nakamura A, Yanagisawa H, Hayashi Y, Okamoto A Abstract Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO-FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO-FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO-FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resol... RNA journals http://www.medworm.com/rss/comments.php?id=5450697 Fri, 18 Nov 2011 05:00:00 +0100 5450697 http://www.medworm.com/index.php?rid=5450696&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%3D22101242%26dopt%3DAbstract We report that the RNA repair phase of the bacterial virus-host dynamic is also portable to yeast, where coexpression of the T4 enzymes Pnkp and Rnl1 ameliorated the toxicity of NmePrrC-R316W. Plant tRNA ligase AtRNL also countered NmePrrC-R316W toxicity, in a manner that depended on AtRNL's 5'-kinase and ligase functions. PMID: 22101242 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5450696 Fri, 18 Nov 2011 05:00:00 +0100 5450696 http://www.medworm.com/index.php?rid=5450695&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%3D22101243%26dopt%3DAbstract Authors: Mihailovich M, Wurth L, Zambelli F, Abaza I, Militti C, Mancuso FM, Roma G, Pavesi G, Gebauer F Abstract Upstream of N-ras (UNR) is a conserved RNA-binding protein that regulates mRNA translation and stability by binding to sites generally located in untranslated regions (UTRs). In Drosophila, sex-specific binding of UNR to msl2 mRNA and the noncoding RNA roX is believed to play key roles in the control of X-chromosome dosage compensation in both sexes. To investigate broader sex-specific functions of UNR, we have identified its RNA targets in adult male and female flies by high-throughput RNA binding and transcriptome analysis. Here we show that UNR binds to a large set of protein-coding transcripts and to a smaller set of noncoding RNAs in a sex-specific fashion. The ana... RNA journals http://www.medworm.com/rss/comments.php?id=5450695 Fri, 18 Nov 2011 05:00:00 +0100 5450695 http://www.medworm.com/index.php?rid=5450698&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%3D22096018%26dopt%3DAbstract Authors: Muerdter F, Olovnikov I, Molaro A, Rozhkov NV, Czech B, Gordon A, Hannon GJ, Aravin AA Abstract In animals a discrete class of small RNAs, the piwi-interacting RNAs (piRNAs), guard germ cell genomes against the activity of mobile genetic elements. piRNAs are generated, via an unknown mechanism, from apparently single-stranded precursors that arise from discrete genomic loci, termed piRNA clusters. Presently, little is known about the signals that distinguish a locus as a source of piRNAs. It is also unknown how individual piRNAs are selected from long precursor transcripts. To address these questions, we inserted new artificial sequence information into piRNA clusters and introduced these marked clusters as transgenes into heterologous genomic positions in mice and flies. ... RNA journals http://www.medworm.com/rss/comments.php?id=5450698 Thu, 17 Nov 2011 05:00:00 +0100 5450698 http://www.medworm.com/index.php?rid=5374874&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%3D22045228%26dopt%3DAbstract Authors: Stadler M, Fire A Abstract In the universal genetic code, most amino acids can be encoded by multiple trinucleotide codons, and the choice among available codons can influence position-specific translation elongation rates. By using sequence-based ribosome profiling, we obtained transcriptome-wide profiles of in vivo ribosome occupancy as a function of codon identity in Caenorhabditis elegans and human cells. Particularly striking in these profiles was a universal trend of higher ribosome occupancy for codons translated via G:U wobble base-pairing compared with synonymous codons that pair with the same tRNA family using G:C base-pairing. These data support a model in which ribosomal translocation is slowed at wobble codon positions. PMID: 22045228 [PubMed - as supplied... RNA journals http://www.medworm.com/rss/comments.php?id=5374874 Tue, 01 Nov 2011 04:00:00 +0100 5374874 http://www.medworm.com/index.php?rid=5374879&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%3D22033329%26dopt%3DAbstract Authors: Saraiya AA, Li W, Wang CC Abstract We have previously shown that a snoRNA-derived microRNA, miR2, in Giardia lamblia potentially regulates the expression of 22 variant surface protein (VSP) genes. Here, we identified another miRNA, miR4, also capable of regulating the expression of several VSPs but derived from an unannotated open reading frame (ORF) rather than a snoRNA, suggesting a canonical miRNA biogenesis pathway in Giardia. miR4 represses expression of a reporter containing two miR4 antisense sequences at the 3' UTR without causing a corresponding decrease in the mRNA level. This repression requires the presence of the Giardia Argonaute protein (GlAgo) and is reversed by 2' O-methylated antisense oligo to miR4, suggesting an RNA-induced silencing complex (RISC)-medi... RNA journals http://www.medworm.com/rss/comments.php?id=5374879 Thu, 27 Oct 2011 04:00:00 +0100 5374879 http://www.medworm.com/index.php?rid=5374878&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%3D22033330%26dopt%3DAbstract Authors: Quiroga C, Kronstad L, Ritlop C, Filion A, Cousineau B Abstract Group II introns are mobile genetic elements that self-splice from pre-mRNA transcripts. Some fragmented group II introns found in chloroplastic and mitochondrial genomes are able to assemble and splice in trans. The Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis was shown to splice in trans when fragmented at various locations throughout its structure. Here we used Ll.LtrB to assess the contribution of base-pairing interactions between intron fragments during trans-splicing in vivo. By comparing closely located fragmentation sites, we show that Ll.LtrB trans-splices more efficiently when base-pairing interactions can occur between the two intron fragments. Disruptions and stepwise... RNA journals http://www.medworm.com/rss/comments.php?id=5374878 Thu, 27 Oct 2011 04:00:00 +0100 5374878 http://www.medworm.com/index.php?rid=5374877&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%3D22033331%26dopt%3DAbstract Authors: Ma L, Tan Z, Teng Y, Hoersch S, Horvitz HR Abstract The in vivo analysis of the roles of splicing factors in regulating alternative splicing in animals remains a challenge. Using a microarray-based screen, we identified a Caenorhabditis elegans gene, tos-1, that exhibited three of the four major types of alternative splicing: intron retention, exon skipping, and, in the presence of U2AF large subunit mutations, the use of alternative 3' splice sites. Mutations in the splicing factors U2AF large subunit and SF1/BBP altered the splicing of tos-1. 3' splice sites of the retained intron or before the skipped exon regulate the splicing pattern of tos-1. Our study provides in vivo evidence that intron retention and exon skipping can be regulated largely by the identities of 3' s... RNA journals http://www.medworm.com/rss/comments.php?id=5374877 Thu, 27 Oct 2011 04:00:00 +0100 5374877 http://www.medworm.com/index.php?rid=5374876&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%3D22033332%26dopt%3DAbstract Authors: Sharwood RE, Halpert M, Luro S, Schuster G, Stern DB Abstract Ribonuclease J is an essential enzyme, and the Bacillus subtilis ortholog possesses both endoribonuclease and 5' → 3' exoribonuclease activities. Chloroplasts also contain RNase J, which has been postulated to participate, as both an exo- and endonuclease, in the maturation of polycistronic mRNAs. Here we have examined recombinant Arabidopsis RNase J and found both 5' → 3' exoribonuclease and endonucleolytic activities. Virus-induced gene silencing was used to reduce RNase J expression in Arabidopsis and Nicotiana benthamiana, leading to chlorosis but surprisingly few disruptions in the cleavage of polycistronic rRNA and mRNA precursors. In contrast, antisense RNAs accumulated massively, suggesting that the ... RNA journals http://www.medworm.com/rss/comments.php?id=5374876 Thu, 27 Oct 2011 04:00:00 +0100 5374876 http://www.medworm.com/index.php?rid=5374875&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%3D22033333%26dopt%3DAbstract Authors: Wang L, Altman RB, Blanchard SC Abstract Translocation, the directional movement of transfer RNA (tRNA) and messenger RNA (mRNA) substrates on the ribosome during protein synthesis, is regulated by dynamic processes intrinsic to the translating particle. Using single-molecule fluorescence resonance energy transfer (smFRET) imaging, in combination with site-directed mutagenesis of the ribosome and tRNA substrates, we show that peptidyl-tRNA within the aminoacyl site of the bacterial pretranslocation complex can adopt distinct hybrid tRNA configurations resulting from uncoupled motions of the 3'-CCA terminus and the tRNA body. As expected for an on-path translocation intermediate, the hybrid configuration where both the 3'-CCA end and body of peptidyl-tRNA have moved in the ... RNA journals http://www.medworm.com/rss/comments.php?id=5374875 Thu, 27 Oct 2011 04:00:00 +0100 5374875 http://www.medworm.com/index.php?rid=5374886&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%3D22028360%26dopt%3DAbstract Authors: Jambor H, Brunel C, Ephrussi A Abstract mRNA localization coupled with translational control is a highly conserved and widespread mechanism for restricting protein expression to specific sites within eukaryotic cells. In Drosophila, patterning of the embryo requires oskar mRNA transport to the posterior pole of the oocyte and translational repression prior to localization. oskar RNA splicing and the 3' untranslated region (UTR) are required for posterior enrichment of the mRNA. However, reporter RNAs harboring the oskar 3' UTR can localize by hitchhiking with endogenous oskar transcripts. Here we show that the oskar 3' UTR contains a stem-loop structure that promotes RNA dimerization in vitro and hitchhiking in vivo. Mutations in the loop that abolish in vitro dimerization... RNA journals http://www.medworm.com/rss/comments.php?id=5374886 Tue, 25 Oct 2011 04:00:00 +0100 5374886 http://www.medworm.com/index.php?rid=5374885&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%3D22028361%26dopt%3DAbstract Authors: Cao S, Chen SJ Abstract We develop a statistical mechanical model to predict the structure and folding stability of the RNA/RNA kissing-loop complex. One of the key ingredients of the theory is the conformational entropy for the RNA/RNA kissing complex. We employ the recently developed virtual bond-based RNA folding model (Vfold model) to evaluate the entropy parameters for the different types of kissing loops. A benchmark test against experiments suggests that the entropy calculation is reliable. As an application of the model, we apply the model to investigate the structure and folding thermodynamics for the kissing complex of the HIV-1 dimerization initiation signal. With the physics-based energetic parameters, we compute the free energy landscape for the HIV-1 dimer. F... RNA journals http://www.medworm.com/rss/comments.php?id=5374885 Tue, 25 Oct 2011 04:00:00 +0100 5374885 http://www.medworm.com/index.php?rid=5374884&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%3D22028362%26dopt%3DAbstract Authors: Yepiskoposyan H, Aeschimann F, Nilsson D, Okoniewski M, Mühlemann O Abstract Nonsense-mediated mRNA decay (NMD) is traditionally portrayed as a quality-control mechanism that degrades mRNAs with truncated open reading frames (ORFs). However, it is meanwhile clear that NMD also contributes to the post-transcriptional gene regulation of numerous physiological mRNAs. To identify endogenous NMD substrate mRNAs and analyze the features that render them sensitive to NMD, we performed transcriptome profiling of human cells depleted of the NMD factors UPF1, SMG6, or SMG7. It revealed that mRNAs up-regulated by NMD abrogation had a greater median 3'-UTR length compared with that of the human mRNAome and were also enriched for 3'-UTR introns and uORFs. Intriguingly, most mRNAs codi... RNA journals http://www.medworm.com/rss/comments.php?id=5374884 Tue, 25 Oct 2011 04:00:00 +0100 5374884 http://www.medworm.com/index.php?rid=5374883&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%3D22028363%26dopt%3DAbstract Authors: de Turris V, Nicholson P, Orozco RZ, Singer RH, Mühlemann O Abstract Aberrant mRNAs with premature translation termination codons (PTCs) are recognized and eliminated by the nonsense-mediated mRNA decay (NMD) pathway in eukaryotes. We employed a novel live-cell imaging approach to investigate the kinetics of mRNA synthesis and release at the transcription site of PTC-containing (PTC+) and PTC-free (PTC-) immunoglobulin-μ reporter genes. Fluorescence recovery after photobleaching (FRAP) and photoconversion analyses revealed that PTC+ transcripts are specifically retained at the transcription site. Remarkably, the retained PTC+ transcripts are mainly unspliced, and this RNA retention is dependent upon two important NMD factors, UPF1 and SMG6, since their depletion led to t... RNA journals http://www.medworm.com/rss/comments.php?id=5374883 Tue, 25 Oct 2011 04:00:00 +0100 5374883 http://www.medworm.com/index.php?rid=5374882&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%3D22028364%26dopt%3DAbstract Authors: Pendrak ML, Roberts DD Abstract Ribosome assembly begins with conversion of a polycistronic precursor into 18S, 5.8S, and 25S rRNAs. In the ascomycete fungus Candida albicans, rRNA transcription starts 604 nt upstream of the 18S rRNA junction (site A1). One major internal processing site in the 5' external transcribed spacer (A0) occurs 108 nt from site A1. The A0-A1 fragment persists as a stable species during log phase growth and can be used to assess proliferation rates. Separation of the small and large subunit pre-rRNAs occurs at sites A2 and A3 in internal transcribed spacer-1 Saccharomyces cerevisiae pre-rRNA. However, the 5' end of the 5.8S rRNA is represented by only a 5.8S (S) form, and a 7S rRNA precursor of the 5.8S rRNA extends into internal transcribed spacer... RNA journals http://www.medworm.com/rss/comments.php?id=5374882 Tue, 25 Oct 2011 04:00:00 +0100 5374882 http://www.medworm.com/index.php?rid=5374881&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%3D22028365%26dopt%3DAbstract Authors: Rackham O, Shearwood AM, Mercer TR, Davies SM, Mattick JS, Filipovska A Abstract Human mitochondrial long noncoding RNAs (lncRNAs) have not been described to date. By analysis of deep-sequencing data we have identified three lncRNAs generated from the mitochondrial genome and confirmed their expression by Northern blotting and strand-specific qRT-PCR. We show that the abundance of these lncRNAs is comparable to their complementary mRNAs and that nuclear-encoded mitochondrial proteins involved in RNA processing regulate their expression. We also identify the 5' and 3' transcript ends of the three lncRNAs and show that mitochondrial RNase P protein 1 (MRPP1) is important for the processing of these transcripts. Finally, we show that mitochondrial lncRNAs form intermolecular ... RNA journals http://www.medworm.com/rss/comments.php?id=5374881 Tue, 25 Oct 2011 04:00:00 +0100 5374881 http://www.medworm.com/index.php?rid=5374880&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%3D22028366%26dopt%3DAbstract Authors: Allnér O, Nilsson L Abstract We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo(5)U34 and m(6)A37. In tRNA(Val), these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural a... RNA journals http://www.medworm.com/rss/comments.php?id=5374880 Tue, 25 Oct 2011 04:00:00 +0100 5374880 http://www.medworm.com/index.php?rid=5374888&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%3D22025736%26dopt%3DAbstract Authors: Haim-Vilmovsky L, Gadir N, Herbst RH, Gerst JE Abstract Protein localization within cells can be achieved by the targeting and localized translation of mRNA. Yet, our understanding of the dynamics of mRNA targeting and protein localization, and of how general this phenomenon is, is not clear. Plasmid-based expression systems have been used to visualize exogenously expressed mRNAs and proteins; however, these methods typically produce them at levels greater than endogenous and can result in mislocalization. Hence, a method that allows for the simultaneous visualization of endogenous mRNAs and their translation products in living cells is needed. We previously developed a method (m-TAG) to localize endogenously expressed mRNAs in yeast by chromosomal insertion of the MS2 apt... RNA journals http://www.medworm.com/rss/comments.php?id=5374888 Mon, 24 Oct 2011 04:00:00 +0100 5374888 http://www.medworm.com/index.php?rid=5374887&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%3D22025737%26dopt%3DAbstract Authors: Rüdinger M, Fritz-Laylin L, Polsakiewicz M, Knoop V Abstract RNA editing converts hundreds of cytidines into uridines in plant mitochondrial and chloroplast transcripts. Recognition of the RNA editing sites in the organelle transcriptomes requires numerous specific, nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins with characteristic carboxy-terminal protein domain extensions (E/DYW) previously thought to be unique to plants. However, a small gene family of such plant-like PPR proteins of the DYW-type was recently discovered in the genome of the protist Naegleria gruberi. This raised the possibility that plant-like RNA editing may occur in this amoeboflagellate. Accordingly, we have investigated the mitochondrial transcriptome of Naegleria gruberi and h... RNA journals http://www.medworm.com/rss/comments.php?id=5374887 Mon, 24 Oct 2011 04:00:00 +0100 5374887 http://www.medworm.com/index.php?rid=5374891&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%3D22020973%26dopt%3DAbstract In this study, by comparing ovary- and testis-derived piRNAs, we identified numerous female-enriched piRNAs. Our data indicated that female-enriched piRNAs are derived from the W chromosome. Moreover, comparative analyses on piRNA profiles from a series of W chromosome mutant strains revealed a striking enrichment of a specific set of transposon-derived piRNAs in the putative sex-determining region. Collectively, we revealed the nature of the silkworm W chromosome as a source of piRNAs. PMID: 22020973 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5374891 Fri, 21 Oct 2011 04:00:00 +0100 5374891 http://www.medworm.com/index.php?rid=5374890&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%3D22020974%26dopt%3DAbstract Authors: Görnemann J, Barrandon C, Hujer K, Rutz B, Rigaut G, Kotovic KM, Faux C, Neugebauer KM, Séraphin B Abstract Complex cellular functions involve large networks of interactions. Pre-mRNA splicing and transcription are thought to be coupled by the C-terminal domain (CTD) of the large subunit of RNA polymerase II (Pol II). In yeast, the U1 snRNP subunit Prp40 was proposed to mediate cotranscriptional recruitment of early splicing factors through binding of its WW domains to the Pol II CTD. Here we investigate the role of Prp40 in splicing with an emphasis on the role of the WW domains, which might confer protein-protein interactions among the splicing and transcriptional machineries. Affinity purification revealed that Prp40 and Snu71 form a stable heterodimer that stably ass... RNA journals http://www.medworm.com/rss/comments.php?id=5374890 Fri, 21 Oct 2011 04:00:00 +0100 5374890 http://www.medworm.com/index.php?rid=5374889&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%3D22020975%26dopt%3DAbstract Authors: Melanson BD, Bose R, Hamill JD, Marcellus KA, Pan EF, McKay BC Abstract The p53 tumor suppressor is a DNA-damage-responsive sequence-specific transcriptional activator. The sustained activation of the p53 response is incompatible with cell growth and viability. To circumvent this issue, a variety of negative feedback loops exist to limit the duration of p53 activation. Despite our understanding of p53 regulation, very little is known about the effect of transient p53 activation on the long-term expression of p53 target genes. Here we used a temperature-sensitive variant of p53 and oligonucleotide microarrays to monitor gene expression during and following reversible p53 activation. The expression of most p53-induced transcripts was rapidly reversible, consistent with activ... RNA journals http://www.medworm.com/rss/comments.php?id=5374889 Fri, 21 Oct 2011 04:00:00 +0100 5374889 http://www.medworm.com/index.php?rid=5374892&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%3D22016383%26dopt%3DAbstract Authors: Sun G, Wu X, Wang J, Li H, Li X, Gao H, Rossi J, Yen Y Abstract Small RNAs (smRNAs) encompass several different classes of short noncoding RNAs. Progress in smRNA research and applications has coincided with the advance of techniques to detect them. Next-generation sequencing technologies are becoming the preferred smRNA profiling method because of their high-throughput capacity and digitized results. In our small RNA profiling study using Solexa, we observed serious biases introduced by the 5' adaptors in small RNA species coverage and abundance; therefore, the results cannot reveal the accurate composition of the small RNAome. We found that the profiling results can be significantly optimized by using an index pool of 64 customized 5' adaptors. This pool of 64 adaptors c... RNA journals http://www.medworm.com/rss/comments.php?id=5374892 Thu, 20 Oct 2011 04:00:00 +0100 5374892 http://www.medworm.com/index.php?rid=5323336&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%3D21998096%26dopt%3DAbstract Authors: Wright JR, Keffer-Wilkes LC, Dobing SR, Kothe U Abstract Pseudouridine synthases catalyze formation of the most abundant modification of functional RNAs by site-specifically isomerizing uridines to pseudouridines. While the structure and substrate specificity of these enzymes have been studied in detail, the kinetic and the catalytic mechanism of pseudouridine synthases remain unknown. Here, the first pre-steady-state kinetic analysis of three Escherichia coli pseudouridine synthases is presented. A novel stopped-flow absorbance assay revealed that substrate tRNA binding by TruB takes place in two steps with an overall rate of 6 sec(-1). In order to observe catalysis of pseudouridine formation directly, the traditional tritium release assay was adapted for the quench-flow ... RNA journals http://www.medworm.com/rss/comments.php?id=5323336 Thu, 13 Oct 2011 04:00:00 +0100 5323336 http://www.medworm.com/index.php?rid=5238658&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%3D21930692%26dopt%3DAbstract Authors: PMID: 21930692 [PubMed - in process] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5238658 Thu, 22 Sep 2011 09:40:12 +0100 5238658 http://www.medworm.com/index.php?rid=5224447&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%3D21914842%26dopt%3DAbstract Authors: Montanari A, De Luca C, Di Micco P, Morea V, Frontali L, Francisci S Abstract Previous work has demonstrated the usefulness of the yeast model to investigate the molecular mechanisms underlying defects due to base substitutions in mitochondrial tRNA genes, and to identify suppressing molecules endowed with potential clinical relevance. The present paper extends these investigations to two human equivalent yeast mutations located at positions 32 and 33 in the anticodon loop of tRNA(Ile). Notwithstanding the proximity of the two T>C base substitutions, the effects of these mutations have been found to be quite different in yeast, as they are in human. The T32C substitution has a very severe effect in yeast, consisting in a complete inhibition of growth on nonfermentable s... RNA journals http://www.medworm.com/rss/comments.php?id=5224447 Tue, 13 Sep 2011 04:00:00 +0100 5224447 http://www.medworm.com/index.php?rid=5184152&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%3D21880780%26dopt%3DAbstract Authors: Karve R, Liu W, Willet SG, Torii KU, Shpak ED Abstract Gene expression in eukaryotes is often enhanced by the presence of introns. Depending on the specific gene, this enhancement can be minor or very large and occurs at both the transcriptional and post-transcriptional levels. The Arabidopsis ERECTA gene contains 27 exons encoding a receptor-like kinase that promotes cell proliferation and inhibits cell differentiation in above-ground plant organs. The expression of ERECTA very strongly depends on the presence of introns. The intronless ERECTA gene does not rescue the phenotype of erecta mutant plants and produces about 500-900 times less protein compared with the identical construct containing introns. This result is somewhat surprising as the region upstream of the EREC... RNA journals http://www.medworm.com/rss/comments.php?id=5184152 Tue, 30 Aug 2011 23:00:00 +0100 5184152 http://www.medworm.com/index.php?rid=5184156&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%3D21878546%26dopt%3DAbstract Authors: Perederina A, Khanova E, Quan C, Berezin I, Esakova O, Krasilnikov AS Abstract Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding ... RNA journals http://www.medworm.com/rss/comments.php?id=5184156 Mon, 29 Aug 2011 23:00:00 +0100 5184156 http://www.medworm.com/index.php?rid=5184155&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%3D21878547%26dopt%3DAbstract We report that, in cultured human HeLa cells and mouse embryonic fibroblasts, Argonaute1 (Ago1), Ago3, and Ago4 act cooperatively to silence both perfectly and partially complementary target RNAs bearing multiple small RNA-binding sites. Our data suggest that for Ago1, Ago3, and Ago4, multiple, adjacent small RNA-binding sites facilitate cooperative interactions that stabilize Argonaute binding. In contrast, small RNAs bound to Ago2 and pairing perfectly to an mRNA target act independently to silence expression. Noncooperative silencing by Ago2 does not require the endoribonuclease activity of the protein: A mutant Ago2 that cannot cleave its mRNA target also silences noncooperatively. We propose that Ago2 binds its targets by a mechanism fundamentally distinct from that used by the three ... RNA journals http://www.medworm.com/rss/comments.php?id=5184155 Mon, 29 Aug 2011 23:00:00 +0100 5184155 http://www.medworm.com/index.php?rid=5184154&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%3D21878548%26dopt%3DAbstract Authors: Mooers BH, Singh A Abstract Guide RNAs bind antiparallel to their target pre-mRNAs to form editing substrates in reaction cycles that insert or delete uridylates (Us) in most mitochondrial transcripts of trypanosomes. The 5' end of each guide RNA has an anchor sequence that binds to the pre-mRNA by base-pair complementarity. The template sequence in the middle of the guide RNA directs the editing reactions. The 3' ends of most guide RNAs have ∼15 contiguous Us that bind to the purine-rich unedited pre-mRNA upstream of the editing site. The resulting U-helix is rich in G·U wobble base pairs. To gain insights into the structure of the U-helix, we crystallized 8 bp of the U-helix in one editing substrate for the A6 mRNA of Trypanosoma brucei. The fragment provides three sa... RNA journals http://www.medworm.com/rss/comments.php?id=5184154 Mon, 29 Aug 2011 23:00:00 +0100 5184154 http://www.medworm.com/index.php?rid=5184153&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%3D21878549%26dopt%3DAbstract Authors: Noton SL, Fearns R Abstract There is limited knowledge regarding how the RNA-dependent RNA polymerases of the nonsegmented negative-strand RNA viruses initiate genome replication. In a previous study of respiratory syncytial virus (RSV) RNA replication, we found evidence that the polymerase could select the 5'-ATP residue of the genome RNA independently of the 3' nucleotide of the template. To investigate if a similar mechanism is used during antigenome synthesis, a study of initiation from the RSV leader (Le) promoter was performed using an intracellular minigenome assay in which RNA replication was restricted to a single step, so that the products examined were derived only from input mutant templates. Templates in which Le nucleotides 1U, or 1U and 2G, were deleted dire... RNA journals http://www.medworm.com/rss/comments.php?id=5184153 Mon, 29 Aug 2011 23:00:00 +0100 5184153 http://www.medworm.com/index.php?rid=5184159&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%3D21873461%26dopt%3DAbstract This study illustrates previously unappreciated molecular plasticity and biological diversity of the tRNA-isopentenyltransferase system of eukaryotes. PMID: 21873461 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5184159 Thu, 25 Aug 2011 23:00:00 +0100 5184159 http://www.medworm.com/index.php?rid=5184158&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%3D21873462%26dopt%3DAbstract Authors: Lin L, Caton-Williams J, Kaur M, Patino AM, Sheng J, Punetha J, Huang Z Abstract Phosphoroselenoate RNA (PSe-RNA) is nuclease resistant and has great potentials in X-ray crystal structure and function studies of noncoding RNAs and protein-RNA interactions. In order to conveniently synthesize PSe-RNA via transcription, we have developed a one-pot synthetic method for the nucleoside 5'-(α-P-seleno)-triphosphates (NTPαSe) analogs without protecting any functionality of the ribonucleosides. The NTPαSe diastereomers have been purified, fully characterized, and incorporated into RNAs by T7 RNA polymerase. The transcribed RNAs are diastereomerically pure, and the Se-derivatized ribozymes are generally active. Furthermore, we have established an affinity purification strategy b... RNA journals http://www.medworm.com/rss/comments.php?id=5184158 Thu, 25 Aug 2011 23:00:00 +0100 5184158 http://www.medworm.com/index.php?rid=5184157&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%3D21873463%26dopt%3DAbstract In this study, we analyze 51 RNAs with tertiary structure, including aptamers, riboswitches, ribozymes, and ribosomal RNAs, for number, location, and properties of syn nucleobases. These RNAs represent the set of nonoverlapping, moderate- to high-resolution structures available at present. We find that syn nucleobases are much more common among purines than pyrimidines, and that they favor C2'-endo-like conformations especially among those nucleobases in the intermediate syn conformation. Strikingly, most syn nucleobases participate in tertiary stacking and base-pairing interactions: Inspection of RNA structures revealed that the majority of the syn nucleobases are in regions assigned to function, with many syn nucleobases interacting directly with a ligand or ribozyme active site. These o... RNA journals http://www.medworm.com/rss/comments.php?id=5184157 Thu, 25 Aug 2011 23:00:00 +0100 5184157 http://www.medworm.com/index.php?rid=5170213&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%3D21868483%26dopt%3DAbstract Authors: Berezhna SY, Supekova L, Sever MJ, Schultz PG, Deniz AA Abstract The antiviral role of RNA interference (RNAi) in humans remains to be better understood. In RNAi, Ago2 proteins and microRNAs (miRNAs) or small interfering RNAs (siRNAs) form endonucleolytically active complexes which down-regulate expression of target mRNAs. P-bodies, cytoplasmic centers of mRNA decay, are involved in these pathways. Evidence exists that hepatitis C virus (HCV) utilizes host cellular RNAi machinery, including miRNA-122, Ago1-4, and Dicer proteins for replication and viral genome translation in Huh7 cells by, so far, nebulous mechanisms. Conversely, synthetic siRNAs have been used to suppress HCV replication. Here, using a combination of biochemical, transfection, confocal imaging, and digita... RNA journals http://www.medworm.com/rss/comments.php?id=5170213 Wed, 24 Aug 2011 23:00:00 +0100 5170213 http://www.medworm.com/index.php?rid=5170214&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%3D21865603%26dopt%3DAbstract Authors: Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE Abstract RNA sequence elements involved in the regulation of pre-mRNA splicing previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5' and 3' splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates... RNA journals http://www.medworm.com/rss/comments.php?id=5170214 Tue, 23 Aug 2011 23:00:00 +0100 5170214 http://www.medworm.com/index.php?rid=5170215&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%3D21862638%26dopt%3DAbstract Authors: Assenholt J, Mouaikel J, Saguez C, Rougemaille M, Libri D, Jensen TH Abstract Production of messenger ribonucleoprotein particles (mRNPs) is subjected to quality control (QC). In Saccharomyces cerevisiae, the RNA exosome and its cofactors are part of the nuclear QC machinery that removes, or stalls, aberrant molecules, thereby ensuring that only correctly formed mRNPs are exported to the cytoplasm. The Ccr4-Not complex, which constitutes the major S. cerevisiae cytoplasmic deadenylase, has recently been implied in nuclear exosome-related processes. Consistent with a possible nuclear function of the complex, the deletion or mutation of Ccr4-Not factors also elicits transcription phenotypes. Here we use genetic depletion of the Mft1p protein of the THO transcription/mRNP pac... RNA journals http://www.medworm.com/rss/comments.php?id=5170215 Mon, 22 Aug 2011 23:00:00 +0100 5170215 http://www.medworm.com/index.php?rid=5147046&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%3D21849429%26dopt%3DAbstract Authors: Newman MA, Mani V, Hammond SM Abstract MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate gene expression. An emerging mechanism to control miRNA production is the addition of an oligo-uridine tail to the 3' end of the precursor miRNA. This has been demonstrated for the Let-7 family of miRNAs in embryonic cells. Additionally, nontemplated nucleotides have been found on mature miRNA species, though in most cases it is not known if nucleotide addition occurs at the precursor step or at the mature miRNA. To examine the diversity of nucleotide addition we have developed a high-throughput sequencing method specific for miRNA precursors. Here we report that nontemplated addition is a widespread phenomenon occurring in many miRNA families. As previo... RNA journals http://www.medworm.com/rss/comments.php?id=5147046 Tue, 16 Aug 2011 23:00:00 +0100 5147046 http://www.medworm.com/index.php?rid=5134493&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%3D21810935%26dopt%3DAbstract We report the identification and functional characterization of a close homolog of editing endonucleases, mRPN1 (mitochondrial RNA precursor-processing endonuclease 1), which is involved in gRNA biogenesis. Recombinant mRPN1 is a dimeric dsRNA-dependent endonuclease that requires Mg(2+), a critical catalytic carboxylate, and generates 2-nucleotide 3' overhangs. The cleavage specificity of mRPN1 is reminiscent of bacterial RNase III and thus is fundamentally distinct from editing endonucleases, which target a single scissile bond just 5' of short duplexes. An inducible knockdown of mRPN1 in T. brucei results in loss of gRNA and accumulation of precursor transcripts (pre-gRNAs), consistent with a role of mRPN1 in processing. mRPN1 stably associates with three proteins previously identified i... RNA journals http://www.medworm.com/rss/comments.php?id=5134493 Mon, 01 Aug 2011 23:00:00 +0100 5134493 http://www.medworm.com/index.php?rid=5134492&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%3D21810936%26dopt%3DAbstract This study suggests that sncRNAs including miRNAs contribute to lifespan regulation in C. elegans, and indicates new connections between aging, stress responses, and the small RNA world. PMID: 21810936 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5134492 Mon, 01 Aug 2011 23:00:00 +0100 5134492 http://www.medworm.com/index.php?rid=5086979&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%3D21803972%26dopt%3DAbstract Authors: Masquida B, Westhof E Apart from the ribosome, the crystal structure of the bacterial RNase P in complex with a tRNA, reported by Reiter and colleagues recently, constitutes the first example of a multiple turnover RNA enzyme. Except in rare exceptions, RNase P is ubiquitous and, like the ribosome, is older than the initial branch point of the phylogenetic tree. Importantly, the structure shows how the RNA and the protein moieties cooperate to process the pre-tRNA substrates. The catalytic site comprises some critical RNA residues spread over the secondary structure but gathered in a compact volume next to the protein, which helps recognize and orient the substrate. The discussion here outlines some important aspects of that crystal structure, some of which could apply to RNA ... RNA journals http://www.medworm.com/rss/comments.php?id=5086979 Thu, 28 Jul 2011 23:00:00 +0100 5086979 http://www.medworm.com/index.php?rid=5087003&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%3D21799029%26dopt%3DAbstract Authors: Stammler SN, Cao S, Chen SJ, Giedroc DP The 3'-untranslated region (UTR) of the group 2 coronavirus mouse hepatitis virus (MHV) genome contains a predicted bulged stem-loop (designated P0ab), a conserved cis-acting pseudoknot (PK), and a more distal stem-loop (designated P2). Base-pairing to create the pseudoknot-forming stem (P1(pk)) is mutually exclusive with formation of stem P0a at the base of the bulged stem-loop; as a result, the two structures cannot be present simultaneously. Herein, we use thermodynamic methods to evaluate the ability of individual subdomains of the 3' UTR to adopt a pseudoknotted conformation. We find that an RNA capable of forming only the predicted PK (58 nt; 3' nucleotides 241-185) adopts the P2 stem-loop with little evidence for P1(pk) pairing in... RNA journals http://www.medworm.com/rss/comments.php?id=5087003 Wed, 27 Jul 2011 23:00:00 +0100 5087003 http://www.medworm.com/index.php?rid=5087031&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%3D21795410%26dopt%3DAbstract Authors: Miller MR, Liu Z, Cazier DJ, Gebhard GM, Herron SR, Zaher HS, Green R, Buskirk AR In bacteria, stalled ribosomes are recycled by a hybrid transfer-messenger RNA (tmRNA). Like tRNA, tmRNA is aminoacylated with alanine and is delivered to the ribosome by EF-Tu, where it reacts with the growing polypeptide chain. tmRNA entry into stalled ribosomes poses a challenge to our understanding of ribosome function because it occurs in the absence of a codon-anticodon interaction. Instead, tmRNA entry is licensed by the binding of its protein partner, SmpB, to the ribosomal decoding center. We analyzed a series of SmpB mutants and found that its C-terminal tail is essential for tmRNA accommodation but not for EF-Tu activation. We obtained evidence that the tail likely functions as a helix... RNA journals http://www.medworm.com/rss/comments.php?id=5087031 Tue, 26 Jul 2011 23:00:00 +0100 5087031 http://www.medworm.com/index.php?rid=5087049&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%3D21788334%26dopt%3DAbstract Authors: Rammelt C, Bilen B, Zavolan M, Keller W PAPD5 is one of the seven members of the family of noncanonical poly(A) polymerases in human cells. PAPD5 was shown to polyadenylate aberrant pre-ribosomal RNAs in vivo, similar to degradation-mediating polyadenylation by the noncanonical poly(A) polymerase Trf4p in yeast. PAPD5 has been reported to be also involved in the uridylation-dependent degradation of histone mRNAs. To test whether PAPD5 indeed catalyzes adenylation as well as uridylation of RNA substrates, we analyzed the in vitro properties of recombinant PAPD5 expressed in mammalian cells as well as in bacteria. Our results show that PAPD5 catalyzes the polyadenylation of different types of RNA substrates in vitro. Interestingly, PAPD5 is active without a protein cofactor, whe... RNA journals http://www.medworm.com/rss/comments.php?id=5087049 Sun, 24 Jul 2011 23:00:00 +0100 5087049 http://www.medworm.com/index.php?rid=5087040&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%3D21788335%26dopt%3DAbstract Authors: Qiu ZR, Schwer B, Shuman S Meiosis-specific pre-mRNA splicing in budding yeast embraces multiple pre-mRNA targets grouped into regulons defined by their genetic requirements for vegetatively optional splicing factors (e.g., splicing enhancer Mer1 and the U1 snRNP subunit Nam8) or snRNA modifications (trimethylguanosine caps). Here, we genetically demarcate a complete meiotic splicing regulon by the criterion of cDNA bypass of the requirement for the governing splicing regulators to execute sporulation. We thereby show that the Mer1 and Nam8 regulons embrace four essential pre-mRNAs: MER2, MER3, SPO22, and AMA1. Whereas Nam8 also regulates PCH2 splicing, PCH2 cDNA is not needed for sporulation by nam8Δ diploids. Our results show that there are no essential intron-containing RN... RNA journals http://www.medworm.com/rss/comments.php?id=5087040 Sun, 24 Jul 2011 23:00:00 +0100 5087040 http://www.medworm.com/index.php?rid=5087061&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%3D21784868%26dopt%3DAbstract Authors: Mori S, Kajita T, Endo T, Yoshihisa T A part of eukaryotic tRNA genes harbor an intron at one nucleotide 3' to the anticodon, so that removal of the intron is an essential processing step for tRNA maturation. While some tRNA introns have important roles in modification of certain nucleotides, essentiality of the tRNA intron in eukaryotes has not been tested extensively. This is partly because most of the eukaryotic genomes have multiple genes encoding an isoacceptor tRNA. Here, we examined whether the intron of tRNA-Trp(CCA) genes, six copies of which are scattered on the genome of yeast, Saccharomyces cerevisiae, is essential for growth or translation of the yeast in vivo. We devised a procedure to remove all of the tRNA introns from the yeast genome iteratively with marker c... RNA journals http://www.medworm.com/rss/comments.php?id=5087061 Thu, 21 Jul 2011 23:00:00 +0100 5087061 http://www.medworm.com/index.php?rid=5087055&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%3D21784869%26dopt%3DAbstract Authors: Liu S, Ghalei H, Lührmann R, Wahl MC Human proteins 15.5K and hPrp31 are components of the major spliceosomal U4 snRNP and of the minor spliceosomal U4atac snRNP. The two proteins bind to related 5'-stem loops (5'SLs) of the U4 and U4atac snRNAs in a strictly sequential fashion. The primary binding 15.5K protein binds at K-turns that exhibit identical sequences in the two snRNAs. However, RNA sequences contacted by the secondary binding hPrp31 differ in U4 and U4atac snRNAs, and the mechanism by which hPrp31 achieves its dual specificity is presently unknown. We show by crystal structure analysis that the capping pentaloops of the U4 and U4atac 5'SLs adopt different structures in the ternary hPrp31-15.5K-snRNA complexes. In U4atac snRNA, a noncanonical base pair forms across ... RNA journals http://www.medworm.com/rss/comments.php?id=5087055 Thu, 21 Jul 2011 23:00:00 +0100 5087055 http://www.medworm.com/index.php?rid=5087067&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%3D21778280%26dopt%3DAbstract Authors: Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared wi... RNA journals http://www.medworm.com/rss/comments.php?id=5087067 Wed, 20 Jul 2011 23:00:00 +0100 5087067 http://www.medworm.com/index.php?rid=5087078&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%3D21775473%26dopt%3DAbstract Authors: Hafner M, Renwick N, Brown M, Mihailovic A, Holoch D, Lin C, Pena JT, Nusbaum JD, Morozov P, Ludwig J, Ojo T, Luo S, Schroth G, Tuschl T Sequencing of small RNA cDNA libraries is an important tool for the discovery of new RNAs and the analysis of their mutational status as well as expression changes across samples. It requires multiple enzyme-catalyzed steps, including sequential oligonucleotide adapter ligations to the 3' and 5' ends of the small RNAs, reverse transcription (RT), and PCR. We assessed biases in representation of miRNAs relative to their input concentration, using a pool of 770 synthetic miRNAs and 45 calibrator oligoribonucleotides, and tested the influence of Rnl1 and two variants of Rnl2, Rnl2(1-249) and Rnl2(1-249)K227Q, for 3'-adapter ligation. The use of ... RNA journals http://www.medworm.com/rss/comments.php?id=5087078 Tue, 19 Jul 2011 23:00:00 +0100 5087078 http://www.medworm.com/index.php?rid=5087073&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%3D21775474%26dopt%3DAbstract Authors: Harris KA, Jones V, Bilbille Y, Swairjo MA, Agris PF The post-transcriptional nucleoside modifications of tRNA's anticodon domain form the loop structure and dynamics required for effective and accurate recognition of synonymous codons. The N(6)-threonylcarbamoyladenosine modification at position 37 (t(6)A(37)), 3'-adjacent to the anticodon, of many tRNA species in all organisms ensures the accurate recognition of ANN codons by increasing codon affinity, enhancing ribosome binding, and maintaining the reading frame. However, biosynthesis of this complex modification is only partially understood. The synthesis requires ATP, free threonine, a single carbon source for the carbamoyl, and an enzyme yet to be identified. Recently, the universal protein family Sua5/YciO/YrdC was asso... RNA journals http://www.medworm.com/rss/comments.php?id=5087073 Tue, 19 Jul 2011 23:00:00 +0100 5087073 http://www.medworm.com/index.php?rid=5087084&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%3D21768221%26dopt%3DAbstract In this study, several of the leading biocomputational tools, which use different methodologies, were investigated. The performance of the tools, both individually and in combination, was evaluated on ten sets of benchmark data, including data from a novel RNA-seq experiment conducted in this study. The results of this study offer insight into the utility as well as the limitations of the leading biocomputational tools for sRNA identification and provide practical guidance for users of the tools. PMID: 21768221 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=5087084 Sun, 17 Jul 2011 23:00:00 +0100 5087084 http://www.medworm.com/index.php?rid=5037423&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%3D21757508%26dopt%3DAbstract Authors: De S, Varsally W, Falciani F, Brogna S Ribosomal proteins (RPs) are essential components of ribosomes, but several RPs are also present at transcription sites of eukaryotic chromosomes. Here, we report a genome-wide ChIP-on-chip analysis of the association of three representative 60S RPs with sites in the Schizosaccharomyces pombe chromosomes. All three proteins tend to bind at the same subset of coding and noncoding loci. The data demonstrate selective RNA-dependent interactions between RPs and many transcription sites and suggest that the RPs bind as components of a preassembled multiprotein complex, perhaps 60S or pre-60S subunits. These findings further indicate that the presence of RPs complexes at transcription sites might be a general feature of eukaryotic cells and fun... RNA journals http://www.medworm.com/rss/comments.php?id=5037423 Wed, 13 Jul 2011 23:00:00 +0100 5037423 http://www.medworm.com/index.php?rid=5037424&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%3D21752927%26dopt%3DAbstract Authors: Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, Pritt MJ, Le Grice SF, Shapiro BA Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structu... RNA journals http://www.medworm.com/rss/comments.php?id=5037424 Tue, 12 Jul 2011 23:00:00 +0100 5037424 http://www.medworm.com/index.php?rid=5037425&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%3D21750099%26dopt%3DAbstract Authors: Zheng D, Chen CY, Shyu AB The cellular factors involved in mRNA degradation and translation repression can aggregate into cytoplasmic domains known as GW bodies or mRNA processing bodies (P-bodies). However, current understanding of P-bodies, especially the regulatory aspect, remains relatively fragmentary. To provide a framework for studying the mechanisms and regulation of P-body formation, maintenance, and disassembly, we compiled a list of P-body proteins found in various species and further grouped both reported and predicted human P-body proteins according to their functions. By analyzing protein-protein interactions of human P-body components, we found that many P-body proteins form complex interaction networks with each other and with other cellular proteins that are n... RNA journals http://www.medworm.com/rss/comments.php?id=5037425 Mon, 11 Jul 2011 23:00:00 +0100 5037425 http://www.medworm.com/index.php?rid=4993743&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%3D21712399%26dopt%3DAbstract Authors: Wang X, Xu X, Ma Z, Huo Y, Xiao Z, Li Y, Wang Y The biogenesis and function of mature microRNAs (miRNAs) is dependent on the nuclear export of miRNA precursors (pre-miRNA) by Exportin-5 (Exp5). To characterize the molecular mechanisms of how pre-miRNA is recognized and transported by Exp5, we have performed 21 molecular dynamic (MD) simulations of RNA-bound Exp5 (Exp5-RanGTP-premiRNA, Exp5-RanGDP-premiRNA, Exp5-premiRNA), RNA-unbound Exp5 (Exp5-RanGTP, Exp5-RanGDP, apo-Exp5), and pre-miRNA. Our simulations with standard MD, steered molecular dynamics (SMD), and energy analysis have shown that (1) Free Exp5 undergoes extensive opening motion, and in this way facilitates the RanGTP binding. (2) RanGTP efficiently regulates the association/dissociation of pre-miRNA to its complex... RNA journals http://www.medworm.com/rss/comments.php?id=4993743 Mon, 27 Jun 2011 23:00:00 +0100 4993743 http://www.medworm.com/index.php?rid=4993742&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%3D21712400%26dopt%3DAbstract Authors: Mitra S, Laederach A, Golden BL, Altman RB, Brenowitz M Functional and kinetic constraints must be efficiently balanced during the folding process of all biopolymers. To understand how homologous RNA molecules with different global architectures fold into a common core structure we determined, under identical conditions, the folding mechanisms of three phylogenetically divergent group I intron ribozymes. These ribozymes share a conserved functional core defined by topologically equivalent tertiary motifs but differ in their primary sequence, size, and structural complexity. Time-resolved hydroxyl radical probing of the backbone solvent accessible surface and catalytic activity measurements integrated with structural-kinetic modeling reveal that each ribozyme adopts a unique st... RNA journals http://www.medworm.com/rss/comments.php?id=4993742 Mon, 27 Jun 2011 23:00:00 +0100 4993742 http://www.medworm.com/index.php?rid=4993741&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%3D21712401%26dopt%3DAbstract Authors: Babiarz JE, Hsu R, Melton C, Thomas M, Ullian EM, Blelloch R Noncanonical microRNAs (miRNAs) and endogenous small interfering RNAs (endo-siRNAs) are distinct subclasses of small RNAs that bypass the DGCR8/DROSHA Microprocessor but still require DICER1 for their biogenesis. What role, if any, they have in mammals remains unknown. To identify potential functional properties for these subclasses, we compared the phenotypes resulting from conditional deletion of Dgcr8 versus Dicer1 in post-mitotic neurons. The loss of Dicer1 resulted in an earlier lethality, more severe structural abnormalities, and increased apoptosis relative to that from Dgcr8 loss. Deep sequencing of small RNAs from the hippocampus and cortex of the conditional knockouts and control littermates identified mult... RNA journals http://www.medworm.com/rss/comments.php?id=4993741 Mon, 27 Jun 2011 23:00:00 +0100 4993741 http://www.medworm.com/index.php?rid=4993744&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%3D21708909%26dopt%3DAbstract Authors: Eipper-Mains JE, Kiraly DD, Palakodeti D, Mains RE, Eipper BA, Graveley BR MicroRNAs (miRNAs) are small RNAs that modulate gene expression by binding target mRNAs. The hundreds of miRNAs expressed in the brain are critical for synaptic development and plasticity. Drugs of abuse cause lasting changes in the limbic regions of the brain that process reward, and addiction is viewed as a form of aberrant neuroplasticity. Using next-generation sequencing, we cataloged miRNA expression in the nucleus accumbens and at striatal synapses in control and chronically cocaine-treated mice. We identified cocaine-responsive miRNAs, synaptically enriched and depleted miRNA families, and confirmed cocaine-induced changes in protein expression for several predicted synaptic target genes. The miR... RNA journals http://www.medworm.com/rss/comments.php?id=4993744 Sun, 26 Jun 2011 23:00:00 +0100 4993744 http://www.medworm.com/index.php?rid=4993753&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%3D21705430%26dopt%3DAbstract Authors: Januszyk K, Liu Q, Lima CD The eukaryotic RNA exosome is a highly conserved multi-subunit complex that catalyzes degradation and processing of coding and noncoding RNA. A noncatalytic nine-subunit exosome core interacts with Rrp44 and Rrp6, two subunits that possess processive and distributive 3'-5' exoribonuclease activity, respectively. While both Rrp6 and Rrp44 are responsible for RNA processing in budding yeast, Rrp6 may play a more prominent role in processing, as it has been demonstrated to be inhibited by stable RNA secondary structure in vitro and because the null allele in budding yeast leads to the buildup of specific structured RNA substrates. Human RRP6, otherwise known as PM/SCL-100 or EXOSC10, shares sequence similarity to budding yeast Rrp6 and is proposed to ca... RNA journals http://www.medworm.com/rss/comments.php?id=4993753 Thu, 23 Jun 2011 23:00:00 +0100 4993753 http://www.medworm.com/index.php?rid=4993749&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%3D21705431%26dopt%3DAbstract Authors: Soper TJ, Doxzen K, Woodson SA Bacterial small RNAs (sRNAs) modulate gene expression by base-pairing with target mRNAs. Many sRNAs require the Sm-like RNA binding protein Hfq as a cofactor. Well-characterized interactions between DsrA sRNA and the rpoS mRNA leader were used to understand how Hfq stimulates sRNA pairing with target mRNAs. DsrA annealing stimulates expression of rpoS by disrupting a secondary structure in the rpoS leader, which otherwise prevents translation. Both RNAs bind Hfq with similar affinity but interact with opposite faces of the Hfq hexamer. Using mutations that block interactions between two of the three components, we demonstrate that Hfq binding to a functionally critical (AAN)(4) motif in rpoS mRNA rescues DsrA binding to a hyperstable rpoS mutant.... RNA journals http://www.medworm.com/rss/comments.php?id=4993749 Thu, 23 Jun 2011 23:00:00 +0100 4993749 http://www.medworm.com/index.php?rid=4993745&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%3D21705432%26dopt%3DAbstract We examined the specific determinants of ATP2 and OXA1 mRNA localization and found a mutual dependency on the 3' UTR, Puf3, Tom7, and Tom70, but not Tom20, for localization. Tom6 may facilitate the localization of specific mRNAs as OXA1, but not ATP2, mRNA was mislocalized in tom6Δ cells. Interestingly, a substantial fraction of OXA1 and ATP2 RNA granules colocalized with the endoplasmic reticulum (ER) and a deletion in MDM10, which mediates mitochondria-ER tethering, resulted in a significant loss of OXA1 mRNA localization with ER. Finally, neither ATP2 nor OXA1 mRNA targeting was affected by a block in translation initiation, indicating that translation may not be essential for mRNA anchoring. Thus, endogenously expressed mRNAs are targeted to the mitochondria in vivo, and multiple fact... RNA journals http://www.medworm.com/rss/comments.php?id=4993745 Thu, 23 Jun 2011 23:00:00 +0100 4993745 http://www.medworm.com/index.php?rid=4993759&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%3D21700725%26dopt%3DAbstract Authors: Korostelev AA Translation of genetic information encoded in messenger RNAs into polypeptide sequences is carried out by ribosomes in all organisms. When a full protein is synthesized, a stop codon positioned in the ribosomal A site signals termination of translation and protein release. Translation termination depends on class I release factors. Recently, atomic-resolution crystal structures were determined for bacterial 70S ribosome termination complexes bound with release factors RF1 or RF2. In combination with recent biochemical studies, the structures resolve long-standing questions about translation termination. They bring insights into the mechanisms of recognition of all three stop codons, peptidyl-tRNA hydrolysis, and coordination of stop-codon recognition with peptidy... RNA journals http://www.medworm.com/rss/comments.php?id=4993759 Wed, 22 Jun 2011 23:00:00 +0100 4993759 http://www.medworm.com/index.php?rid=4993754&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%3D21700726%26dopt%3DAbstract Authors: Pélissier T, Clavel M, Chaparro C, Pouch-Pélissier MN, Vaucheret H, Deragon JM Biogenesis of the vast majority of plant siRNAs depends on the activity of the plant-specific RNA polymerase IV (PolIV) enzyme. As part of the RNA-dependent DNA methylation (RdDM) process, PolIV-dependent siRNAs (p4-siRNAs) are loaded onto an ARGONAUTE4-containing complex and guide de novo DNA methyltransferases to target loci. Here we show that the double-stranded RNA binding proteins DRB2 and DRB4 are required for proper accumulation of p4-siRNAs. In flowers, loss of DRB2 results in increased accumulation of p4-siRNAs but not ta-siRNAs, inverted repeat (IR)-derived siRNAs, or miRNA. Loss of DRB2 does not impair uniparental expression of p4-dependent siRNAs in developing endosperm, indicating tha... RNA journals http://www.medworm.com/rss/comments.php?id=4993754 Wed, 22 Jun 2011 23:00:00 +0100 4993754 http://www.medworm.com/index.php?rid=4993760&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%3D21697354%26dopt%3DAbstract Authors: Bergkessel M, Whitworth GB, Guthrie C Gene expression in eukaryotic cells is profoundly influenced by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways. These processes have the potential to affect both the steady-state levels and the kinetics of changes to levels of intron-containing transcripts. Here we report the use of a splicing isoform-specific microarray platform to investigate the effects of diverse stress conditions on pre-mRNA processing. Interestingly, we find that diverse stresses cause distinct patterns of changes at this level. The responses we observed are most dramatic for the RPGs and can be categorized into three major classes. The first is characterized by accu... RNA journals http://www.medworm.com/rss/comments.php?id=4993760 Tue, 21 Jun 2011 23:00:00 +0100 4993760 http://www.medworm.com/index.php?rid=4993762&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%3D21693620%26dopt%3DAbstract Authors: Dang Y, Schneider-Poetsch T, Eyler DE, Jewett JC, Bhat S, Rawal VH, Green R, Liu JO Mycalamide B (MycB) is a marine sponge-derived natural product with potent antitumor activity. Although it has been shown to inhibit protein synthesis, the molecular mechanism of action by MycB remains incompletely understood. We verified the inhibition of translation elongation by in vitro HCV IRES dual luciferase assays, ribosome assembly, and in vivo [(35)S]methinione labeling experiments. Similar to cycloheximide (CHX), MycB inhibits translation elongation through blockade of eEF2-mediated translocation without affecting the eEF1A-mediated loading of tRNA onto the ribosome, AUG recognition, or dipeptide synthesis. Using chemical footprinting, we identified the MycB binding site proximal to ... RNA journals http://www.medworm.com/rss/comments.php?id=4993762 Mon, 20 Jun 2011 23:00:00 +0100 4993762 http://www.medworm.com/index.php?rid=4993761&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%3D21693621%26dopt%3DAbstract Authors: Yang CS, Li Z, Rana TM Although induced pluripotent stem cells (iPSCs) hold great promise for customized regenerative medicine, the molecular basis of reprogramming is largely unknown. Overcoming barriers that maintain cell identities is a critical step in the reprogramming of differentiated cells. Since microRNAs (miRNAs) modulate target genes tissue-specifically, we reasoned that distinct mouse embryonic fibroblast (MEF)-enriched miRNAs post-transcriptionally modulate proteins that function as reprogramming barriers. Inhibiting these miRNAs should influence cell signaling to lower those barriers. Here we show that depleting miR-21 and miR-29a enhances reprogramming efficiency in MEFs. We also show that the p53 and ERK1/2 pathways are regulated by miR-21 and miR-29a and funct... RNA journals http://www.medworm.com/rss/comments.php?id=4993761 Mon, 20 Jun 2011 23:00:00 +0100 4993761 http://www.medworm.com/index.php?rid=4993763&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%3D21685478%26dopt%3DAbstract This study expands the repertoire of cis elements bound by PUF proteins and suggests new modes by which PUF proteins recognize their mRNA targets. PMID: 21685478 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=4993763 Thu, 16 Jun 2011 23:00:00 +0100 4993763 http://www.medworm.com/index.php?rid=4944838&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%3D21673105%26dopt%3DAbstract Authors: Pastor T, Dal Mas A, Talotti G, Bussani E, Pagani F We previously showed that the insertion of a hammerhead ribozyme (Rz) in a critical intronic position between the EDA exon and a downstream regulatory element affects alternative splicing. Here we evaluate the effect of other intronic cotranscriptional cleavage events on alternative pre-mRNA processing using different ribozymes (Rz) and Microprocessor target sequences (MTSs). In the context of the fibronectin EDA minigene, intronic MTSs were cleaved very inefficiently and did not affect alternative splicing or the level of mature transcripts. On the contrary, all hammerhead Rz derivatives and hepatitis δ Rz were completely cleaved before a splicing decision and able to affect alternative splicing. Despite the very efficient ... RNA journals http://www.medworm.com/rss/comments.php?id=4944838 Mon, 13 Jun 2011 23:00:00 +0100 4944838 http://www.medworm.com/index.php?rid=4944841&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%3D21665995%26dopt%3DAbstract Authors: Marvin MC, Clauder-Münster S, Walker SC, Sarkeshik A, Yates JR, Steinmetz LM, Engelke DR Ribonuclease P (RNase P) is an essential endoribonuclease that catalyzes the cleavage of the 5' leader of pre-tRNAs. In addition, a growing number of non-tRNA substrates have been identified in various organisms. RNase P varies in composition, as bacterial RNase P contains a catalytic RNA core and one protein subunit, while eukaryotic nuclear RNase P retains the catalytic RNA but has at least nine protein subunits. The additional eukaryotic protein subunits most likely provide additional functionality to RNase P, with one possibility being additional RNA recognition capabilities. To investigate the possible range of additional RNase P substrates in vivo, a strand-specific, high-density mi... RNA journals http://www.medworm.com/rss/comments.php?id=4944841 Thu, 09 Jun 2011 23:00:00 +0100 4944841 http://www.medworm.com/index.php?rid=4944840&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%3D21665996%26dopt%3DAbstract Authors: Shcherbik N, Pestov DG Rsp5p is a conserved HECT-domain ubiquitin ligase with diverse roles in cellular physiology. Here we report a previously unknown role of Rsp5p in facilitating the stability of the cytoplasmic ribosome pool in budding yeast. Yeast strains carrying temperature-sensitive mutations in RSP5 showed a progressive decline in levels of 18S and 25S rRNAs and accumulation of rRNA decay fragments when cells grown in rich medium were shifted to restrictive temperature. This was accompanied by a decreased number of translating ribosomes and the appearance of ribosomal subunits with an abnormally low sedimentation rate in polysome analysis. Abrogating Rsp5p function affected stability of other tested noncoding RNA species (tRNA and snoRNA), but to a lower extent than t... RNA journals http://www.medworm.com/rss/comments.php?id=4944840 Thu, 09 Jun 2011 23:00:00 +0100 4944840 http://www.medworm.com/index.php?rid=4944839&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%3D21665997%26dopt%3DAbstract Authors: Marvin MC, Walker SC, Fierke CA, Engelke DR Ribonuclease P (RNase P) is an essential endoribonuclease for which the best-characterized function is processing the 5' leader of pre-tRNAs. Compared to bacterial RNase P, which contains a single small protein subunit and a large catalytic RNA subunit, eukaryotic nuclear RNase P is more complex, containing nine proteins and an RNA subunit in Saccharomyces cerevisiae. Consistent with this, nuclear RNase P has been shown to possess unique RNA binding capabilities. To understand the unique molecular recognition of nuclear RNase P, the interaction of S. cerevisiae RNase P with single-stranded RNA was characterized. Unstructured, single-stranded RNA inhibits RNase P in a size-dependent manner, suggesting that multiple interactions are re... RNA journals http://www.medworm.com/rss/comments.php?id=4944839 Thu, 09 Jun 2011 23:00:00 +0100 4944839 http://www.medworm.com/index.php?rid=4894245&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%3D21628430%26dopt%3DAbstract Authors: Blaby IK, Majumder M, Chatterjee K, Jana S, Grosjean H, de Crécy-Lagard V, Gupta R Pseudouridine (Ψ), the isomer of uridine, is commonly found at various positions of noncoding RNAs of all organisms. Ψ residues are formed by a number of single- or multisite specific Ψ synthases, which generally act as stand-alone proteins. In addition, in Eukarya and Archaea, specific ribonucleoprotein complexes, each containing a distinct box H/ACA guide RNA and four core proteins, can produce Ψ at many sites of different cellular RNAs. Cbf5 is the core Ψ synthase in these complexes. Using Haloferax volcanii as an archaeal model organism, we show that, contrary to eukaryotes, the Cbf5 homolog (HVO_2493) is not essential in this archaeon. The Cbf5-deleted strain of H. volcanii completely... RNA journals http://www.medworm.com/rss/comments.php?id=4894245 Mon, 30 May 2011 23:00:00 +0100 4894245 http://www.medworm.com/index.php?rid=4894244&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%3D21628431%26dopt%3DAbstract Authors: Schudoma C, Larhlimi A, Walther D RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence... RNA journals http://www.medworm.com/rss/comments.php?id=4894244 Mon, 30 May 2011 23:00:00 +0100 4894244 http://www.medworm.com/index.php?rid=4894243&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%3D21628432%26dopt%3DAbstract Authors: Kawaoka S, Arai Y, Kadota K, Suzuki Y, Hara K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S PIWI-interacting RNAs (piRNAs) are 23-30-nucleotide-long small RNAs that act as sequence-specific silencers of transposable elements in animal gonads. In flies, genetics and deep sequencing data have led to a hypothesis for piRNA biogenesis called the ping-pong cycle, where antisense primary piRNAs initiate an amplification loop to generate sense secondary piRNAs. However, to date, the process of the ping-pong cycle has never been monitored at work. Here, by large-scale profiling of piRNAs from silkworm ovary and embryos of different developmental stages, we demonstrate that maternally inherited antisense-biased piRNAs trigger acute amplification of secondary sense piRNA producti... RNA journals http://www.medworm.com/rss/comments.php?id=4894243 Mon, 30 May 2011 23:00:00 +0100 4894243 http://www.medworm.com/index.php?rid=4894242&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%3D21628433%26dopt%3DAbstract Authors: Kaur J, Raj M, Cooperman BS Dihydrouridine (DHU) positions within tRNAs have long been used as sites to covalently attach fluorophores, by virtue of their unique chemical reactivity toward reduction by NaBH(4), their abundance within prokaryotic and eukaryotic tRNAs, and the biochemical functionality of the labeled tRNAs so produced. Interpretation of experiments employing labeled tRNAs can depend on knowing the distribution of dye among the DHU positions present in a labeled tRNA. Here we combine matrix-assisted laser desorption/ionization mass spectroscopy (MALDI-MS) analysis of oligonucleotide fragments and thin layer chromatography to resolve and quantify sites of DHU labeling by the fluorophores Cy3, Cy5, and proflavin in Escherichia coli tRNA(Phe) and E. coli tRNA(Arg). ... RNA journals http://www.medworm.com/rss/comments.php?id=4894242 Mon, 30 May 2011 23:00:00 +0100 4894242 http://www.medworm.com/index.php?rid=4894248&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%3D21622899%26dopt%3DAbstract Authors: Koutmou KS, Day-Storms JJ, Fierke CA Ribonuclease P (RNase P) catalyzes the metal-dependent 5' end maturation of precursor tRNAs (pre-tRNAs). In Bacteria, RNase P is composed of a catalytic RNA (PRNA) and a protein subunit (P protein) necessary for function in vivo. The P protein enhances pre-tRNA affinity, selectivity, and cleavage efficiency, as well as modulates the cation requirement for RNase P function. Bacterial P proteins share little sequence conservation although the protein structures are homologous. Here we combine site-directed mutagenesis, affinity measurements, and single turnover kinetics to demonstrate that two residues (R60 and R62) in the most highly conserved region of the P protein, the RNR motif (R60-R68 in Bacillus subtilis), stabilize PRNA complexes wit... RNA journals http://www.medworm.com/rss/comments.php?id=4894248 Thu, 26 May 2011 23:00:00 +0100 4894248 http://www.medworm.com/index.php?rid=4894247&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%3D21622900%26dopt%3DAbstract Authors: Yao C, Müller UF The RNA world hypothesis states that the early evolution of life went through a stage where RNA served as genome and as catalyst. The replication of RNA world organisms would have been facilitated by ribozymes that catalyze RNA polymerization. To recapitulate an RNA world in the laboratory, a series of RNA polymerase ribozymes was developed previously. However, these ribozymes have a polymerization efficiency that is too low for self-replication, and the most efficient ribozymes prefer one specific template sequence. The limiting factor for polymerization efficiency is the weak sequence-independent binding to its primer/template substrate. Most of the known polymerase ribozymes bind an RNA heptanucleotide to form the P2 duplex on the ribozyme. By modifying th... RNA journals http://www.medworm.com/rss/comments.php?id=4894247 Thu, 26 May 2011 23:00:00 +0100 4894247 http://www.medworm.com/index.php?rid=4894246&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%3D21622901%26dopt%3DAbstract In this study, the inactivation of the vapBC6 operon by targeted gene disruption produced two recessive phenotypes related to fitness, HS sensitivity and a heat-dependent reduction in the rate of growth. In-frame vapBC6 deletion mutants were analyzed to examine the respective roles of each protein. Since vapB6 transcript abundance was elevated in the vapC6 deletion, the VapC6 toxin appears to regulate abundance of its cognate antitoxin. In contrast, vapC6 transcript abundance was reduced in the vapB6 deletion. A putative intergenic terminator may underlie these observations by coordinating vapBC6 expression. As predicted by structural modeling, recombinant VapC6 produced using chaperone cosynthesis exhibited heat-dependent ribonucleolytic activity toward S. solfataricus total RNA. This act... RNA journals http://www.medworm.com/rss/comments.php?id=4894246 Thu, 26 May 2011 23:00:00 +0100 4894246 http://www.medworm.com/index.php?rid=4894251&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%3D21613530%26dopt%3DAbstract Authors: Li CF, Costa M, Bassi G, Lai YK, Michel F A survey of sequence databases revealed 10 instances of subgroup IIB1 mitochondrial ribosomal introns with 1 to 33 additional nucleotides inserted between the 5' exon and the consensus sequence at the intron 5' end. These 10 introns depart further from the IIB1 consensus in their predicted domain VI structure: In contrast to its basal helix and distal GNRA terminal loop, the middle part of domain VI is highly variable and lacks the bulging A that serves as the branchpoint in lariat formation. In vitro experiments using two closely related IIB1 members inserted at the same ribosomal RNA site in the basidiomycete fungi Grifola frondosa and Pycnoporellus fulgens revealed that both ribozymes are capable of efficient self-splicing. However,... RNA journals http://www.medworm.com/rss/comments.php?id=4894251 Tue, 24 May 2011 23:00:00 +0100 4894251 http://www.medworm.com/index.php?rid=4894250&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%3D21613531%26dopt%3DAbstract Authors: Strong CL, Lanchy JM, Lodmell JS The 5' UTR of HIV-2 genomic RNA contains signaling motifs that regulate specific steps of the replication cycle. Two motifs of interest are the C-box and the G-box. The C-box is found in the 5' untranslated region upstream of the primer binding site, while the G-box is found downstream from the major splice donor site, encompassing the gag start codon and flanking nucleotides. Together the C-box and the G-box form a long-range base-pairing interaction called the CGI. We and others have previously shown that formation of the CGI affects RNA dimerization in vitro and the positions of the C-box and the G-box are suggestive of potential roles of the CGI in other steps of HIV-2 replication. Therefore, we attempted to elucidate the role of the CGI us... RNA journals http://www.medworm.com/rss/comments.php?id=4894250 Tue, 24 May 2011 23:00:00 +0100 4894250 http://www.medworm.com/index.php?rid=4894249&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%3D21613532%26dopt%3DAbstract Authors: Coyle JH, Bor YC, Rekosh D, Hammarskjold ML Post-transcriptional regulation of mRNA includes restriction mechanisms to prevent export and expression of mRNAs that are incompletely spliced. Here we present evidence that the mammalian protein Tpr is involved in this restriction. To study the role of Tpr in export of mRNA with retained introns, we used reporters in which the mRNA was exported either via the Nxf1/Nxt1 pathway using a CTE or via the Crm1 pathway using Rev/RRE. Our data show that even modest knockdown of Tpr using RNAi leads to a significant increase in export and translation from the mRNA containing the CTE. In contrast, Tpr perturbation has no effect on export of mRNA containing the RRE, either in the absence or presence of Rev. Also, no effects were observed on e... RNA journals http://www.medworm.com/rss/comments.php?id=4894249 Tue, 24 May 2011 23:00:00 +0100 4894249 http://www.medworm.com/index.php?rid=4894255&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%3D21610211%26dopt%3DAbstract Authors: Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS New deep RNA sequencing methodologies in transcriptome analyses identified a wealth of novel nonprotein-coding RNAs (npcRNAs). Recently, deep sequencing was used to delineate the small npcRNA transcriptome of the human pathogen Vibrio cholerae and 627 novel npcRNA candidates were identified. Here, we report the detection of 223 npcRNA candidates in V. cholerae by different cDNA library construction and conventional sequencing methods. Remarkably, only 39 of the candidates were common to both surveys. We therefore examined possible biasing influences in the transcriptome analyses. Key steps, including tailing and adapter ligations for generating cDNA, contribute qualitatively and quantitatively to the discrepanci... RNA journals http://www.medworm.com/rss/comments.php?id=4894255 Mon, 23 May 2011 23:00:00 +0100 4894255 http://www.medworm.com/index.php?rid=4894254&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%3D21610212%26dopt%3DAbstract Authors: Rocca-Serra P, Bellaousov S, Birmingham A, Chen C, Cordero P, Das R, Davis-Neulander L, Duncan CD, Halvorsen M, Knight R, Leontis NB, Mathews DH, Ritz J, Stombaugh J, Weeks KM, Zirbel CL, Laederach A Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public... RNA journals http://www.medworm.com/rss/comments.php?id=4894254 Mon, 23 May 2011 23:00:00 +0100 4894254 http://www.medworm.com/index.php?rid=4894253&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%3D21610213%26dopt%3DAbstract Authors: Jain R, Poulos MG, Gros J, Chakravarty AK, Shuman S tRNA anticodon damage inflicted by the Kluyveromyces lactis γ-toxin underlies an RNA-based innate immune system that distinguishes self from nonself species. γ-toxin arrests the growth of Saccharomyces cerevisiae by incising a single phosphodiester 3' of the wobble base of tRNA(Glu(UUC)) to generate a break with 2',3'-cyclic phosphate and 5'-OH ends. Recombinant γ-toxin cleaves oligonucleotide substrates in vitro that mimic the anticodon stem-loop of tRNA(Glu). A single 2'-deoxy sugar substitution at the wobble nucleoside abolishes anticodon nuclease activity. To gain further insights to γ-toxin's substrate specificity, we tested deoxynucleoside effects at positions other than the site of transesterification. The results ... RNA journals http://www.medworm.com/rss/comments.php?id=4894253 Mon, 23 May 2011 23:00:00 +0100 4894253 http://www.medworm.com/index.php?rid=4894252&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%3D21610214%26dopt%3DAbstract Authors: Rispal D, Henri J, van Tilbeurgh H, Graille M, Séraphin B In Saccharomyces cerevisiae, the putative 2-OG-Fe(II) dioxygenase Tpa1 and its partner Ett1 have been shown to impact mRNA decay and translation. Hence, inactivation of these factors was shown to influence stop codon read-though. In addition, Tpa1 represses, by an unknown mechanism, genes regulated by Hap1, a transcription factor involved in the response to levels of heme and O(2). The Schizosaccharomyces pombe orthologs of Tpa1 and Ett1, Ofd1, and its partner Nro1, respectively, have been shown to regulate the stability of the Sre1 transcription factor in response to oxygen levels. To gain insight into the function of Nro1/Ett1, we have solved the crystal structure of the S. pombe Nro1 protein deleted of its 54 N-term... RNA journals http://www.medworm.com/rss/comments.php?id=4894252 Mon, 23 May 2011 23:00:00 +0100 4894252 http://www.medworm.com/index.php?rid=4894256&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%3D21606179%26dopt%3DAbstract Authors: Filbin ME, Kieft JS Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem-loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem-loop domain (domain IIb) located far fr... RNA journals http://www.medworm.com/rss/comments.php?id=4894256 Sun, 22 May 2011 23:00:00 +0100 4894256 http://www.medworm.com/index.php?rid=4894259&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%3D21602302%26dopt%3DAbstract Authors: Ragone FL, Spears JL, Wohlgamuth-Benedum JM, Kreel N, Papavasiliou FN, Alfonzo JD Adenosine to inosine editing at the wobble position allows decoding of multiple codons by a single tRNA. This reaction is catalyzed by adenosine deaminases acting on tRNA (ADATs) and is essential for viability. In bacteria, the anticodon-specific enzyme is a homodimer that recognizes a single tRNA substrate (tRNA(Arg)(ACG)) and can efficiently deaminate short anticodon stem-loop mimics of this tRNA in vitro. The eukaryal enzyme is composed of two nonidentical subunits, ADAT2 and ADAT3, which upon heterodimerization, recognize seven to eight different tRNAs as substrates, depending on the organism, and require a full-length tRNA for activity. Although crystallographic data have provided clues to w... RNA journals http://www.medworm.com/rss/comments.php?id=4894259 Thu, 19 May 2011 23:00:00 +0100 4894259 http://www.medworm.com/index.php?rid=4894258&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%3D21602303%26dopt%3DAbstract Authors: Lahoud G, Goto-Ito S, Yoshida KI, Ito T, Yokoyama S, Hou YM Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N(1) of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis expo... RNA journals http://www.medworm.com/rss/comments.php?id=4894258 Thu, 19 May 2011 23:00:00 +0100 4894258 http://www.medworm.com/index.php?rid=4894257&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%3D21602304%26dopt%3DAbstract In this study, we first profiled the expression of small RNAs in type A spermatogonia, pachytene spermatocytes, and round spermatids by deep sequencing. We then focused on the computational analysis of the potential piRNAs generated in the present study as well as other published sets. piRNAs mapping to retrotransposons, mRNAs, and intergenic regions had different length distributions and were differentially regulated in spermatogenesis. piRNA-generating mRNAs (PRMRs), whose expression positively correlated with their piRNA products, constituted one-third of the protein-coding genes and were evolutionarily conserved and enriched with splicing isoforms and antisense transcripts. PRMRs with piRNAs preferentially mapped to CDSs and 3' UTRs partitioned into three clusters differentially expres... RNA journals http://www.medworm.com/rss/comments.php?id=4894257 Thu, 19 May 2011 23:00:00 +0100 4894257 http://www.medworm.com/index.php?rid=4849238&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%3D21576381%26dopt%3DAbstract Authors: Smith RW, Anderson RC, Smith JW, Brook M, Richardson WA, Gray NK DAZ-associated protein 1 (DAZAP1) is an RNA-binding protein required for normal growth, development, and fertility in mice. However, its molecular functions have not been elucidated. Here we find that Xenopus laevis and human DAZAP1, which are each expressed as short and long forms, act as mRNA-specific activators of translation in a manner that is sensitive to the number of binding sites present within the 3' UTR. Domain mapping suggests that this conserved function is mainly associated with C-terminal regions of DAZAP1. Interestingly, we find that the expression of xDAZAP1 and its polysome association are developmentally controlled, the latter suggesting that the translational activator function of DAZAP1 is re... RNA journals http://www.medworm.com/rss/comments.php?id=4849238 Sun, 15 May 2011 23:00:00 +0100 4849238 http://www.medworm.com/index.php?rid=4795254&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%3D21536710%26dopt%3DAbstract Authors: Moss WN, Priore SF, Turner DH Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for conserved secondary structure. The predictions are based on identifying regions of unusual thermodynamic stabilities and are correlated with studies of suppression of synonymous codon usage (SSCU). The results indicate that secondary structure is favored in the (+) sense influenza RNA. Twenty regions with putative conserved RNA structure have been identified, ... RNA journals http://www.medworm.com/rss/comments.php?id=4795254 Sun, 01 May 2011 23:00:00 +0100 4795254 http://www.medworm.com/index.php?rid=4795256&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%3D21531919%26dopt%3DAbstract Authors: Valli A, Oliveros JC, Molnar A, Baulcombe D, García JA RNA silencing mediated by siRNAs plays an important role as an anti-viral defense mechanism in plants and other eukaryotic organisms, which is usually counteracted by viral RNA silencing suppressors (RSSs). The ipomovirus Cucumber vein yellowing virus (CVYV) lacks the typical RSS of members of the family Potyviridae, HCPro, which is replaced by an unrelated RSS, P1b. CVYV P1b resembles potyviral HCPro in forming complexes with synthetic siRNAs in vitro. Electrophoretic mobility shift assays showed that P1b, like potyviral HCPro, interacts with double-stranded siRNAs, but is not able to bind single-stranded small RNAs or small DNAs. These assays also showed a preference of CVYV P1b for binding to 21-nt siRNAs, a feature al... RNA journals http://www.medworm.com/rss/comments.php?id=4795256 Thu, 28 Apr 2011 23:00:00 +0100 4795256 http://www.medworm.com/index.php?rid=4795255&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%3D21531920%26dopt%3DAbstract Authors: Kazantsev AV, Rambo RP, Karimpour S, Santalucia J, Tainer JA, Pace NR The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: the RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Ag... RNA journals http://www.medworm.com/rss/comments.php?id=4795255 Thu, 28 Apr 2011 23:00:00 +0100 4795255 http://www.medworm.com/index.php?rid=4795258&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%3D21527671%26dopt%3DAbstract Authors: De Lay N, Gottesman S In Escherichia coli, many small noncoding regulatory RNAs (sRNAs) post-transcriptionally regulate gene expression by base-pairing to mRNAs in a process that is mediated by the RNA chaperone Hfq. Binding of the sRNA to the mRNA can lead to increased or decreased mRNA stability and/or translation. It is not known if proteins other than Hfq are necessary for this process. In order to identify additional genes required for the post-transcriptional regulation of gene expression by Hfq-dependent sRNAs, we developed a novel combined genetic selection and screen for mutants defective in sRNA regulation. In our combined genetic selection and screen, we isolated hfq mutants and mutants in pnp, encoding polynucleotide phosphorylase (PNPase). We show that loss-of-fun... RNA journals http://www.medworm.com/rss/comments.php?id=4795258 Wed, 27 Apr 2011 23:00:00 +0100 4795258 http://www.medworm.com/index.php?rid=4795257&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%3D21527672%26dopt%3DAbstract Authors: Saks ME, Sanderson LE, Choi DS, Crosby CM, Uhlenbeck OC The binding affinities between Escherichia coli EF-Tu and 34 single and double base-pair changes in the T stem of E. coli tRNA(Thr)(UGU) were compared with similar data obtained previously for several aa-tRNAs binding to Thermus thermophilus EF-Tu. With a single exception, the two proteins bound to mutations in three T-stem base pairs in a quantitatively identical manner. However, tRNA(Thr) differs from other tRNAs by also using its rare A52-C62 pair as a negative specificity determinant. Using a plasmid-based tRNA gene replacement strategy, we show that many of the tRNA(Thr)(UGU) T-stem changes are either unable to support growth of E. coli or are less effective than the wild-type sequence. Since the inviable T-stem sequ... RNA journals http://www.medworm.com/rss/comments.php?id=4795257 Wed, 27 Apr 2011 23:00:00 +0100 4795257 http://www.medworm.com/index.php?rid=4795260&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%3D21525145%26dopt%3DAbstract In this study, we describe the establishment of a mouse embryo fibroblast cell line (MEF), THOC5 flox/flox. Four days after infection of MEF THOC5 flox/flox with adenovirus carrying Cre-recombinase gene (Ad-GFP-Cre), THOC5 is down-regulated >95% at the protein level, and cell growth is strongly suppressed. Transcriptome analysis using cytoplasmic RNA isolated from cells lacking functional THOC5 reveals that only 2.9% of all genes were down-regulated more than twofold. Although we examined these genes in fibroblasts, one-fifth of all down-regulated genes (including HoxB3 and polycomb CBX2) are known to play a key role in hematopoietic development. We further identified 10 genes that are spliced but not exported to the cytoplasm in the absence of THOC5. These mRNAs were copurified with TH... RNA journals http://www.medworm.com/rss/comments.php?id=4795260 Tue, 26 Apr 2011 23:00:00 +0100 4795260 http://www.medworm.com/index.php?rid=4795259&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%3D21525146%26dopt%3DAbstract Authors: Burch BD, Godfrey AC, Gasdaska PY, Salzler HR, Duronio RJ, Marzluff WF, Dominski Z Metazoan replication-dependent histone mRNAs are the only nonpolyadenylated cellular mRNAs. Formation of the histone mRNA 3' end requires the U7 snRNP, which contains Lsm10 and Lsm11, and FLASH, a processing factor that binds Lsm11. Here, we identify sequences in Drosophila FLASH (dFLASH) that bind Drosophila Lsm11 (dLsm11), allow localization of dFLASH to the nucleus and histone locus body (HLB), and participate in histone pre-mRNA processing in vivo. Amino acids 105-154 of dFLASH bind to amino acids 1-78 of dLsm11. A two-amino acid mutation of dLsm11 that prevents dFLASH binding but does not affect localization of U7 snRNP to the HLB cannot rescue the lethality or histone pre-mRNA processing d... RNA journals http://www.medworm.com/rss/comments.php?id=4795259 Tue, 26 Apr 2011 23:00:00 +0100 4795259 http://www.medworm.com/index.php?rid=4795261&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%3D21521828%26dopt%3DAbstract Authors: Bernauer J, Huang X, Sim AY, Levitt M RNA molecules play integral roles in gene regulation, and understanding their structures gives us important insights into their biological functions. Despite recent developments in template-based and parameterized energy functions, the structure of RNA-in particular the nonhelical regions-is still difficult to predict. Knowledge-based potentials have proven efficient in protein structure prediction. In this work, we describe two differentiable knowledge-based potentials derived from a curated data set of RNA structures, with all-atom or coarse-grained representation, respectively. We focus on one aspect of the prediction problem: the identification of native-like RNA conformations from a set of near-native models. Using a variety of near-n... RNA journals http://www.medworm.com/rss/comments.php?id=4795261 Mon, 25 Apr 2011 23:00:00 +0100 4795261 http://www.medworm.com/index.php?rid=4795266&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%3D21518803%26dopt%3DAbstract Authors: Chen D, Meng Y, Yuan C, Bai L, Huang D, Lv S, Wu P, Chen LL, Chen M Small RNAs (sRNAs), largely known as microRNAs (miRNAs) and short interfering RNAs (siRNAs), emerged as the critical components of genetic and epigenetic regulation in eukaryotic genomes. In animals, a sizable portion of miRNAs reside within the introns of protein-coding genes, designated as mirtron genes. Recently, high-throughput sequencing (HTS) revealed a huge amount of sRNAs that derived from introns in plants, such as the monocot rice (Oryza sativa). However, the biogenesis and the biological functions of this kind of sRNAs remain elusive. Here, we performed a genome-scale survey of intron-derived sRNAs in rice based on HTS data. Several introns were found to have great potential to form internal hairpin... RNA journals http://www.medworm.com/rss/comments.php?id=4795266 Sun, 24 Apr 2011 23:00:00 +0100 4795266 http://www.medworm.com/index.php?rid=4795265&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%3D21518804%26dopt%3DAbstract Authors: D'Silva S, Haider SJ, Phizicky EM The 3-methylcytidine (m(3)C) modification is widely found in eukaryotic species of tRNA(Ser), tRNA(Thr), and tRNA(Arg); at residue 32 in the anti-codon loop; and at residue e2 in the variable stem of tRNA(Ser). Little is known about the function of this modification or about the specificity of the corresponding methyltransferase, since the gene has not been identified. We have used a primer extension assay to screen a battery of methyltransferase candidate knockout strains in the yeast Saccharomyces cerevisiae, and find that tRNA(Thr(IGU)) from abp140-Δ strains lacks m(3)C. Curiously, Abp140p is composed of a poorly conserved N-terminal ORF fused by a programed +1 frameshift in budding yeasts to a C-terminal ORF containing an S-adenosylmethio... RNA journals http://www.medworm.com/rss/comments.php?id=4795265 Sun, 24 Apr 2011 23:00:00 +0100 4795265 http://www.medworm.com/index.php?rid=4795264&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%3D21518805%26dopt%3DAbstract Authors: Noma A, Yi S, Katoh T, Takai Y, Suzuki T, Suzuki T Transfer RNAs contain various modified nucleotides that are introduced enzymatically at the post-transcriptional level. In Saccharomyces cerevisiae, 3-methylcytidine (m(3)C) is found at position 32 of the tRNAs for Thr and Ser. We used a systematic reverse genetic approach combined with mass spectrometry (ribonucleome analysis), and identified the actin-binding protein ABP140 as the protein responsible for m(3)C formation in both tRNA(Thr1) and tRNA(Ser1). ABP140 consists of an N-terminal actin-binding sequence and a C-terminal S-adenosylmethionine (Ado-Met) binding motif. Deletion of the actin-binding sequence in ABP140 did not affect m(3)C formation, indicating that subcellular localization of ABP140 to actin filaments is no... RNA journals http://www.medworm.com/rss/comments.php?id=4795264 Sun, 24 Apr 2011 23:00:00 +0100 4795264 http://www.medworm.com/index.php?rid=4795263&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%3D21518806%26dopt%3DAbstract Authors: Kafasla P, Lin H, Curry S, Jackson RJ Polypyrimidine tract binding protein (PTB) is an RNA-binding protein with four RNA-binding domains (RBDs). It is a major regulator of alternative splicing and also stimulates translation initiation at picornavirus IRESs (internal ribosome entry sites). The sites of interaction of each RBD with two picornaviral IRESs have previously been mapped. To establish which RBD-IRES interactions are essential for IRES activation, point mutations were introduced into the RNA-binding surface of each RBD. Three such mutations were sufficient to inactivate RNA-binding by any one RBD, but the sites of the other three RBD-IRES interactions remained unperturbed. Poliovirus IRES activation was abrogated by inactivation of RBD1, 2, or 4, but the RBD3-IRES int... RNA journals http://www.medworm.com/rss/comments.php?id=4795263 Sun, 24 Apr 2011 23:00:00 +0100 4795263 http://www.medworm.com/index.php?rid=4795262&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%3D21518807%26dopt%3DAbstract This study is the first intense characterization of pre-miR-886 as well as the initial report on its function as a PKR regulator, which suggests a critical role in tumorigenesis. PMID: 21518807 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=4795262 Sun, 24 Apr 2011 23:00:00 +0100 4795262 http://www.medworm.com/index.php?rid=4795267&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%3D21515829%26dopt%3DAbstract We report a more widespread expression of a limited set of piRNAs and particularly focus on their expression in the hippocampus. Deep sequencing of extracted RNA from the mouse hippocampus revealed a set of small RNAs in the size range of piRNAs. These were confirmed by their presence in the piRNA database as well as coimmunoprecipitation with MIWI. Their expression was validated by Northern blot and in situ hybridization in cultured hippocampal neurons, where signal from one piRNA extended to the dendritic compartment. Antisense suppression of this piRNA suggested a role in spine morphogenesis. Possible targets include genes, which control spine shape by a distinctive mechanism in comparison to microRNAs. PMID: 21515829 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=4795267 Thu, 21 Apr 2011 23:00:00 +0100 4795267 http://www.medworm.com/index.php?rid=4795268&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%3D21493786%26dopt%3DAbstract Authors: Lapierre J, Salomon W, Cardia J, Bulock K, Lam JT, Stanney WJ, Ford G, Smith-Anzures B, Woolf T, Kamens J, Khvorova A, Samarsky D RNA interference (RNAi) has been established as an important tool for functional genomics studies and has great promise as a therapeutic intervention for human diseases. In mammalian cells, RNAi is conventionally induced by 19-27-bp RNA duplexes generated by hybridization of two complementary oligonucleotide strands (oligos). Here we describe a novel class of RNAi molecules composed of a single 25-28-nucleotide (nt) oligo. The oligo has a 16-nt mRNA targeting region, followed by an additional 8-10 nt to enable self-dimerization into a partially complementary duplex. Analysis of numerous diverse structures demonstrates that molecules composed of two ... RNA journals http://www.medworm.com/rss/comments.php?id=4795268 Wed, 13 Apr 2011 23:00:00 +0100 4795268 http://www.medworm.com/index.php?rid=4795269&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%3D21474576%26dopt%3DAbstract Authors: Shih JD, Hunter CP Systemic RNAi in Caenorhabditis elegans requires the widely conserved transmembrane protein SID-1 to transport RNAi silencing signals between cells. When expressed in Drosophila S2 cells, C. elegans SID-1 enables passive dsRNA uptake from the culture medium, suggesting that SID-1 functions as a channel for the transport of double-stranded RNA (dsRNA). Here we show that nucleic acid transport by SID-1 is specific for dsRNA and that addition of dsRNA to SID-1 expressing cells results in changes in membrane conductance, which indicate that SID-1 is a dsRNA gated channel protein. Consistent with passive bidirectional transport, we find that the RNA induced silencing complex (RISC) is required to prevent the export of imported dsRNA and that retention of dsRNA by... RNA journals http://www.medworm.com/rss/comments.php?id=4795269 Wed, 06 Apr 2011 23:00:00 +0100 4795269 http://www.medworm.com/index.php?rid=4685039&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%3D21467217%26dopt%3DAbstract Authors: Clancy JL, Wei GH, Echner N, Humphreys DT, Beilharz TH, Preiss T Reporter-based studies support inhibition of translation at the level of initiation as a substantial component of the miRNA mechanism, yet recent global analyses have suggested that they predominantly act through decreasing target mRNA stability. Cells commonly coexpress several processing isoforms of an mRNA, which may also differ in their regulatory untranslated regions (UTR). In particular, cancer cells are known to express high levels of short 3' UTR isoforms that evade miRNA-mediated regulation, whereas longer 3' UTRs predominate in nontransformed cells. To test whether mRNA isoform diversity can obscure detection of miRNA-mediated control at the level of translation, we assayed the responses of 11 endogenou... RNA journals http://www.medworm.com/rss/comments.php?id=4685039 Mon, 04 Apr 2011 23:00:00 +0100 4685039 http://www.medworm.com/index.php?rid=4685045&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%3D21460234%26dopt%3DAbstract Authors: Yang X, Tan SH, Teh YJ, Yuan YA Rice Hoja Blanca Tenuivirus (RHBV), a negative strand RNA virus, has been identified to infect rice and is widely transmitted by the insect vector. NS3 protein encoded by RHBV RNA3 was reported to be a potent RNAi suppressor to counterdefense RNA silencing in plants, insect cells, and mammalian cells. Here, we report the crystal structure of the N-terminal domain of RHBV NS3 (residues 21-114) at 2.0 Å. RHBV NS3 N-terminal domain forms a dimer by two pairs of α-helices in an anti-parallel mode, with one surface harboring a shallow groove at the dimension of 20 Å × 30 Å for putative dsRNA binding. In vitro RNA binding assay and RNA silencing suppression assay have demonstrated that the structural conserved residues located along this shallow ... RNA journals http://www.medworm.com/rss/comments.php?id=4685045 Thu, 31 Mar 2011 23:00:00 +0100 4685045 http://www.medworm.com/index.php?rid=4685044&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%3D21460235%26dopt%3DAbstract Authors: Andrews S, Snowflack DR, Clark IE, Gavis ER Translational control of gene expression is essential for development in organisms that rely on maternal mRNAs. In Drosophila, translation of maternal nanos (nos) mRNA must be restricted to the posterior of the early embryo for proper patterning of the anterior-posterior axis. Spatial control of nos translation is coordinated through the localization of a small subset of nos mRNA to the posterior pole late in oogenesis, activation of this localized mRNA, and repression of the remaining unlocalized nos mRNA throughout the bulk cytoplasm. Translational repression is mediated by the interaction of a cis-acting element in the nos 3' untranslated region with two proteins, Glorund (Glo) and Smaug (Smg), that function in the oocyte and embr... RNA journals http://www.medworm.com/rss/comments.php?id=4685044 Thu, 31 Mar 2011 23:00:00 +0100 4685044 http://www.medworm.com/index.php?rid=4685043&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%3D21460236%26dopt%3DAbstract Authors: Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME, Mattick JS Long noncoding RNAs (lncRNAs) are increasingly recognized to play major regulatory roles in development and disease. To identify novel regulators in breast biology, we identified differentially regulated lncRNAs during mouse mammary development. Among the highest and most differentially expressed was a transcript (Zfas1) antisense to the 5' end of the protein-coding gene Znfx1. In vivo, Zfas1 RNA is localized within the ducts and alveoli of the mammary gland. Zfas1 intronically hosts three previously undescribed C/D box snoRNAs (SNORDs): Snord12, Snord12b, and Snord12c. In contrast to the general assumption th... RNA journals http://www.medworm.com/rss/comments.php?id=4685043 Thu, 31 Mar 2011 23:00:00 +0100 4685043 http://www.medworm.com/index.php?rid=4685042&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%3D21460237%26dopt%3DAbstract Authors: Heinicke LA, Nallagatla SR, Hull CM, Bevilacqua PC The protein kinase, PKR, is activated by long stretches of double-stranded (ds) RNA. Viruses often make long dsRNA elements with imperfections that still activate PKR. However, due to the complexity of the RNA structure, prediction of whether a given RNA is an activator of PKR is difficult. Herein, we systematically investigated how various RNA secondary structure defects contained within model dsRNA affect PKR activation. We find that bulges increasingly disfavor activation as they are moved toward the center of a duplex and as they are increased in size. Model RNAs designed to conform to cis, trans, or bent global geometries through strategic positioning of one or more bulges decreased activation of PKR relative to perfect d... RNA journals http://www.medworm.com/rss/comments.php?id=4685042 Thu, 31 Mar 2011 23:00:00 +0100 4685042 http://www.medworm.com/index.php?rid=4685041&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%3D21460238%26dopt%3DAbstract Authors: Balagopal V, Parker R The control of translation is a critical aspect of gene regulation. It is often inversely related to mRNA degradation and is typically controlled during initiation. The Stm1 protein in Saccharomyces cerevisiae has been shown to interact with ribosomes, affect the interaction of eEF3 with ribosomes, and promote the decapping of a subclass of mRNAs. We demonstrate that in vitro Stm1 inhibits translation after formation of an 80S complex. This suggests that Stm1 modulates translation and mRNA decapping by controlling translation elongation. PMID: 21460238 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=4685041 Thu, 31 Mar 2011 23:00:00 +0100 4685041 http://www.medworm.com/index.php?rid=4685040&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%3D21460239%26dopt%3DAbstract Authors: Shen K, Zhang X, Shan SO During cotranslational protein targeting by the Signal Recognition Particle (SRP), the correct cargo accelerates stable complex assembly between the SRP and SRP receptor (FtsY) by several orders of magnitude, thus enabling rapid and faithful cargo delivery to the target membrane. The molecular mechanism underlying this cargo-induced rate acceleration has been unclear. Here we show that the SRP RNA allows assembly of the SRP-FtsY complex to be specifically stimulated by a correct cargo, and, reciprocally, a correct cargo enables the SRP RNA to optimize its electrostatic interactions with FtsY. These results combined with recent structural work led us to suggest a "conformational selection" model that explains the synergistic action of the SRP RNA with t... RNA journals http://www.medworm.com/rss/comments.php?id=4685040 Thu, 31 Mar 2011 23:00:00 +0100 4685040 http://www.medworm.com/index.php?rid=4685046&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%3D21451155%26dopt%3DAbstract In this study we examined the function of the MRB1 protein, Tb927.5.3010, which we term MRB3010. We show that MRB3010 is essential for growth of both procyclic form and bloodstream form life-cycle stages of T. brucei. Down-regulation of MRB3010 by RNAi leads to a dramatic inhibition of RNA editing, yet its depletion does not impact total gRNA levels. Rather, it appears to affect the editing process at an early stage, as indicated by the accumulation of pre-edited and small partially edited RNAs. MRB3010 is present in large (>20S) complexes and exhibits both RNA-dependent and RNA-independent interactions with other MRB1 complex proteins. Comparison of proteins isolated with MRB3010 tagged at its endogenous locus to those reported from other MRB1 complex purifications strongly suggests th... RNA journals http://www.medworm.com/rss/comments.php?id=4685046 Tue, 29 Mar 2011 23:00:00 +0100 4685046 http://www.medworm.com/index.php?rid=4685047&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%3D21447710%26dopt%3DAbstract Authors: Su W, Slepenkov S, Grudzien-Nogalska E, Kowalska J, Kulis M, Zuberek J, Lukaszewicz M, Darzynkiewicz E, Jemielity J, Rhoads RE Decapping is an essential step in multiple pathways of mRNA degradation. Previously, we synthesized mRNAs containing caps that were resistant to decapping, both to dissect the various pathways for mRNA degradation and to stabilize mRNA for more sustained protein expression. mRNAs containing an α-β CH(2) group are resistant to in vitro cleavage by the decapping enzyme hDcp2 but poorly translated. mRNAs containing an S substitution at the β-phosphate are well translated but only partially resistant to hDcp2. We now describe seven new cap analogs substituted at the β-phosphate with BH(3) or Se, or substituted at either the α-β or β-γ O with NH. Th... RNA journals http://www.medworm.com/rss/comments.php?id=4685047 Mon, 28 Mar 2011 23:00:00 +0100 4685047 http://www.medworm.com/index.php?rid=4685048&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%3D21444632%26dopt%3DAbstract Authors: Vishnu MR, Sumaroka M, Klein PS, Liebhaber SA Post-transcriptional control of mRNA stability and translation is central to multiple developmental pathways. This control can be linked to cytoplasmic polyadenylation in certain settings. In maturing Xenopus oocytes, specific mRNAs are targeted for polyadenylation via recruitment of the Cytoplasmic Polyadenylation Element (CPE) binding protein (CPEB) to CPE(s) within the 3' UTR. Cytoplasmic polyadenylation is also critical to early embryonic events, although corresponding determinants are less defined. Here, we demonstrate that the Xenopus ortholog of the poly(rC) binding protein αCP2 can recruit cytoplasmic poly(A) polymerase activity to mRNAs in Xenopus post-fertilization embryos, and that this recruitment relies on cis sequenc... RNA journals http://www.medworm.com/rss/comments.php?id=4685048 Sun, 27 Mar 2011 23:00:00 +0100 4685048 http://www.medworm.com/index.php?rid=4685052&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%3D21441346%26dopt%3DAbstract Authors: Torres AG, Fabani MM, Vigorito E, Gait MJ MicroRNAs (miRNAs) are small non-coding RNAs involved in fine-tuning of gene regulation. Antisense oligonucleotides (ONs) are promising tools as anti-miRNA (anti-miR) agents toward therapeutic applications and to uncover miRNA function. Such anti-miR ONs include 2'-O-methyl (OMe), cationic peptide nucleic acids like K-PNA-K3, and locked nucleic acid (LNA)-based anti-miRs such as LNA/DNA or LNA/OMe. Northern blotting is a widely used and robust technique to detect miRNAs. However, miRNA quantification in the presence of anti-miR ONs has proved to be challenging, due to detection artifacts, which has led to poor understanding of miRNA fate upon anti-miR binding. Here we show that anti-miR ON bound to miR-122 can prevent the miRNA from be... RNA journals http://www.medworm.com/rss/comments.php?id=4685052 Fri, 25 Mar 2011 00:00:00 +0100 4685052 http://www.medworm.com/index.php?rid=4685051&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%3D21441347%26dopt%3DAbstract Authors: Kowarsch A, Preusse M, Marr C, Theis FJ MicroRNAs (miRNAs) are an important class of post-transcriptional regulators of gene expression that are involved in various cellular and phenotypic processes. A number of studies have shown that miRNA expression is induced by signaling pathways. Moreover, miRNAs emerge as regulators of signaling pathways. Here, we present the miTALOS web resource, which provides insight into miRNA-mediated regulation of signaling pathways. As a novel feature, miTALOS considers the tissue-specific expression signatures of miRNAs and target transcripts to improve the analysis of miRNA regulation in biological pathways. MiTALOS identifies potential pathway regulation by (i) an enrichment analysis of miRNA targets genes and (ii) by using a proximity score t... RNA journals http://www.medworm.com/rss/comments.php?id=4685051 Fri, 25 Mar 2011 00:00:00 +0100 4685051 http://www.medworm.com/index.php?rid=4685050&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%3D21441348%26dopt%3DAbstract Authors: Dlakic M, Mushegian A Prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. Despite all evidence that Prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. By analyzing sequence and structure similarities between Prp8 and other protein domains, we show that its N-terminal region contains a putative bromodomain. The central conserved domain of Prp8 is related to the catalytic domain of reverse transcriptases (RTs) and is most similar to homologous enzymes encoded by prokaryotic retroelements. However, putative catalytic residues in this RT domain are only partially conserved and may n... RNA journals http://www.medworm.com/rss/comments.php?id=4685050 Fri, 25 Mar 2011 00:00:00 +0100 4685050 http://www.medworm.com/index.php?rid=4685049&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%3D21441349%26dopt%3DAbstract Authors: Rakauskaite R, Dinman JD Molecular dynamics simulation identified three highly conserved rRNA bases in the large subunit of the ribosome that form a three-dimensional (3D) "gate" that induces pausing of the aa-tRNA acceptor stem during accommodation into the A-site. A nearby fourth base contacting the "tryptophan finger" of yeast protein L3, which is involved in the coordinating elongation factor recruitment to the ribosome with peptidyltransfer, is also implicated in this process. To better understand the functional importance of these bases, single base substitutions as well as deletions at all four positions were constructed and expressed as the sole forms of ribosomes in yeast Saccharomyces cerevisiae. None of the mutants had strong effects on cell growth, translational fi... RNA journals http://www.medworm.com/rss/comments.php?id=4685049 Fri, 25 Mar 2011 00:00:00 +0100 4685049 http://www.medworm.com/index.php?rid=4630107&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%3D21415141%26dopt%3DAbstract Authors: Calarco JA, Zhen M, Blencowe BJ Recent genome-wide analyses have indicated that almost all primary transcripts from multi-exon human genes undergo alternative pre-mRNA splicing (AS). Given the prevalence of AS and its importance in expanding proteomic complexity, a major challenge that lies ahead is to determine the functional specificity of isoforms in a cellular context. A significant fraction of alternatively spliced transcripts are regulated in a tissue- or cell-type-specific manner, suggesting that these mRNA variants likely function in the generation of cellular diversity. Complementary to these observations, several tissue-specific splicing factors have been identified, and a number of methodological advances have enabled the identification of large repertoires of targe... RNA journals http://www.medworm.com/rss/comments.php?id=4630107 Thu, 17 Mar 2011 00:00:00 +0100 4630107 http://www.medworm.com/index.php?rid=4630106&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%3D21415142%26dopt%3DAbstract We report that yeast ribosomes do not respond to mismatches in the P site by loss of fidelity in subsequent substrate recognition events. We conclude that retrospective editing, as initially characterized in Escherichia coli, does not occur in S. cerevisiae. These results highlight potential mechanistic differences in the functional core of highly conserved ribosomes. PMID: 21415142 [PubMed - as supplied by publisher] (Source: RNA) RNA journals http://www.medworm.com/rss/comments.php?id=4630106 Thu, 17 Mar 2011 00:00:00 +0100 4630106