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 'Genome Research' source. Tue, 16 Mar 2010 17:23:29 +0100 http://www.medworm.com/index.php?rid=3353244&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099044.109v1%3Frss%3D1 The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the sex chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1 element density, respectively. Second, we analyze sex chromosome vs. autosome TE densities corrected for regional genomic effects. We discover that sex-chromosome bias in Alu... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353244 Wed, 10 Mar 2010 21:55:41 +0100 3353244 http://www.medworm.com/index.php?rid=3353242&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100594.109v1%3Frss%3D1 Mammalian preimplantation embryonic development (PED) is thought to be governed by highly conserved processes. While it had been suggested that some plasticity of conserved signaling networks exists among different mammalian species, it was not known to what extent modulation of the genomes and the regulatory proteins could "rewire" the gene regulatory networks (GRN) that control PED. We therefore generated global transcriptional profiles from three mammalian species (human, mouse and bovine) at representative stages of PED, including: zygote, 2-cell, 4-cell, 8-cell, 16-cell, morula and blastocyst. Co-expression network analysis suggested that 40.2% orthologous gene triplets exhibited different expression patterns among these species. Combining the expression data with genomic sequences an... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353242 Wed, 10 Mar 2010 21:55:41 +0100 3353242 http://www.medworm.com/index.php?rid=3353243&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100479.109v1%3Frss%3D1 The cohesin protein complex holds sister chromatids in dividing cells together, and is essential for chromosome segregation. Recently, cohesin has been implicated in mediating transcriptional insulation, via its interactions with CTCF. Here, we show in different cell types that cohesin functionally behaves as a tissue-specific transcriptional regulator, independent of CTCF binding. By performing matched genome-wide binding assays (ChIP-seq) in human breast cancer cells (MCF7), we discovered thousands of genomic sites that share cohesin and estrogen receptor alpha (ER), yet lack CTCF binding. Using human hepatocellular carcinoma cells (HepG2), we found that liver-specific transcription factors co-localize with cohesin independently of CTCF at liver-specific targets that are distinct from th... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353243 Wed, 10 Mar 2010 21:55:40 +0100 3353243 http://www.medworm.com/index.php?rid=3353241&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.102764.109v1%3Frss%3D1 We describe the DNA replication timing programs of fourteen yeast mutants with an extended S phase identified by a novel genome-wide screen. These mutants are associated with the DNA replication machinery, cell-cycle control and dNTP synthesis and affect different parts of S phase. In thirteen of the mutants, origin activation time scales with the duration of S phase. A limited number of origins becomes inactive in these strains, with inactive origins characterized by small replicons and are distributed throughout S phase. In sharp contrast, cells deleted of MRC1, a gene implicated in replication fork stabilization and in the replication checkpoint pathway, maintained wild-type firing times despite over two-fold lengthening of S phase. Numerous dormant origins were activated in this mutant... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353241 Wed, 10 Mar 2010 17:37:02 +0100 3353241 http://www.medworm.com/index.php?rid=3353245&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096305.109v1%3Frss%3D1 Information about the binding preferences of many transcription factors is known and characterized by a sequence binding motif. However, determining regions of the genome in which a transcription factor binds based on its motif is a challenging problem, particularly in species with large genomes, since there are often many sequences containing matches to the motif but are not bound. Several rules based on sequence conservation or location, relative to a transcription start site, have been proposed to help differentiate true binding sites from random ones. Other evidence sources may also be informative for this task. We developed a method for integrating multiple evidence sources using logistic regression classifiers. Our method works in two steps. First, we infer a score quantifying the ge... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353245 Wed, 10 Mar 2010 17:36:12 +0100 3353245 http://www.medworm.com/index.php?rid=3353239&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.103606.109v1%3Frss%3D1 Polycomb group proteins (PCGs) are involved in repression of genes that are required for stem cell differentiation. Recently, it was shown that promoters of PCG target genes (PCGTs) are 12-fold more likely to be methylated in cancer than non-PCGTs. Age is the most important demographic risk factor for cancer, and we hypothesized that its carcinogenic potential may be referred by irreversibly stabilizing stem cell features. To test this, we analyzed the methylation status of over 27,000 CpGs mapping to promoters of ~14,000 genes in whole blood samples from 261 postmenopausal women. We demonstrate that stem cell PCGTs are far more likely to become methylated with age than non-targets (odds ratio = 5.3 [3.8–7.4], P < 10–10), independently of sex, tissue type, disease state, and... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353239 Wed, 10 Mar 2010 17:36:12 +0100 3353239 http://www.medworm.com/index.php?rid=3353240&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.103101.109v1%3Frss%3D1 There is a growing realization that some aging-associated phenotypes/diseases have an epigenetic basis. Here, we report the first genome-scale study of epigenomic dynamics during normal human aging. We identify aging-associated differentially methylated regions (aDMRs) in whole blood in a discovery cohort, and then replicate these aDMRs in sorted CD4+ T-cells and CD14+ monocytes in an independent cohort, suggesting that aDMRs occur in precursor haematopoietic cells. Further replication of the aDMRs in buccal cells, representing a tissue that originates from a different germ layer compared with blood, demonstrates that the aDMR signature is a multitissue phenomenon. Moreover, we demonstrate that aging-associated DNA hypermethylation occurs predominantly at bivalent chromatin domain promoter... Genome Research journals http://www.medworm.com/rss/comments.php?id=3353240 Wed, 10 Mar 2010 17:36:11 +0100 3353240 http://www.medworm.com/index.php?rid=3345632&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100271.109v1%3Frss%3D1 Pre-mRNA 5' spliced-leader (SL) trans-splicing occurs in some metazoan groups, e.g. tunicate chordates, but not in others, e.g. vertebrates. Functional and evolutionary aspects of SL trans-splicing remain poorly understood and although genome-wide characterization of the trans-spliced mRNA subpopulation would give useful insight, this has not yet been reported for any metazoan. We carried out a high-throughput analysis of the SL trans-spliced mRNA population of the ascidian tunicate Ciona intestinalis by Roche/454 pyrosequencing of SL-PCR-amplified random-primed reverse transcripts of tailbud embryo RNA. We obtained ~250,000 high-quality reads corresponding to 8,790 genes, ~58% of the Ciona total gene number. The great depth of this data revealed new aspects of trans-splicing, including th... Genome Research journals http://www.medworm.com/rss/comments.php?id=3345632 Mon, 08 Mar 2010 16:15:50 +0100 3345632 http://www.medworm.com/index.php?rid=3345630&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.103622.109v1%3Frss%3D1 Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here we have studied the effect of balanced chromosomal rearrangements on gene expression by comparing the transcriptomes of cell lines from controls and individuals with the t(11;22)(q23;q11) translocation. The number of differentially expressed transcripts between translocation carrying and control cohorts is significantly higher than that observed between control samples alone, suggesting that balanced rearrangements have a greater effect on gene expression than normal variation. Many of the affected genes are located along the length ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3345630 Mon, 08 Mar 2010 16:15:50 +0100 3345630 http://www.medworm.com/index.php?rid=3345629&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.105403.110v1%3Frss%3D1 Genomic structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The array CGH panel included 90 animals from 11 Bos taurus, 3 Bos indicus and 3 composite breeds for beef, dairy or dual purpose. We identified over 200 candidate CNV regions (CNVRs) in total and 177 within known chromosomes, which harbor or are adjacent to gains or losses. These 177 high-confidence CNVRs cover 28.1 mega bases or ~1.07% of the genome. Over 50% of the CNVRs (89/177) were found in multiple animals or breeds and analysis reve... Genome Research journals http://www.medworm.com/rss/comments.php?id=3345629 Mon, 08 Mar 2010 16:15:50 +0100 3345629 http://www.medworm.com/index.php?rid=3345631&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101469.109v2%3Frss%3D1 Trophoblast stem cells (TS cells), derived from the trophectoderm (TE) of blastocysts, require transcription factors (TFs) and external signals (FGF4, INHBA/NODAL/TGFB1) for self-renewal. While many reports have focused on TF networks that regulate embryonic stem cell (ES cell) self-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells. To further understand transcriptional networks in TS cells, we used chromatin immunoprecipitation with DNA microarray hybridization (ChIP-chip) analysis to investigate targets of the TFs—TCFAP2C, EOMES, ETS2, and GATA3—and a chromatin remodeling factor, SMARCA4. We then evaluated the transcriptional states of target genes using transcriptome analysis and genome-wide analysis of histone H3 acetylation (... Genome Research journals http://www.medworm.com/rss/comments.php?id=3345631 Mon, 08 Mar 2010 16:12:30 +0100 3345631 http://www.medworm.com/index.php?rid=3337525&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.103226.109v2%3Frss%3D1 Eukaryotic transcriptional regulation is mediated by the organization of nucleosomes in promoter regions. Most Saccharomyces cerevisiae promoters have a highly stereotyped chromatin organization, where nucleosome-free regions (NFR) are flanked by well-ordered nucleosomes. We have found that yeast promoters fall into two classes differing in NFR sharpness, and that this distinction follows a known transcriptional dichotomy in yeast genes. A class of yeast promoters having well-defined NFRs are characterized by positioned patterns of poly(dA:dT) tracts with several novel features. First, poly(dA:dT) tracts are localized in a strand-dependent manner, with poly(dA) tracts lying proximal to transcriptional start sites and poly(dT) tracts lying distal, and collectively define a symmetry axis tha... Genome Research journals http://www.medworm.com/rss/comments.php?id=3337525 Fri, 05 Mar 2010 15:52:34 +0100 3337525 http://www.medworm.com/index.php?rid=3337526&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100040.109v2%3Frss%3D1 Next-generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for single nucleotide polymorphism (SNP) detection are designed to detect SNPs from single individual sequence data sets. Here, we describe a novel method SNIP-Seq (single nucleotide polymorphism identification from population sequence data) that leverages sequence data from a population of individuals to detect SNPs and assign genotypes to individuals. To evaluate our method, we utilized sequence data from a 200-kilobase (kb) region on chromosome 9p21 of the human genome. This re... Genome Research journals http://www.medworm.com/rss/comments.php?id=3337526 Fri, 05 Mar 2010 15:52:33 +0100 3337526 http://www.medworm.com/index.php?rid=3334069&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.102129.109v2%3Frss%3D1 Accurate profiling of minute quantities of RNA in a global manner can enable key advances in many scientific and clinical disciplines. Here, we present low-quantity RNA sequencing (LQ-RNAseq), a high-throughput sequencing-based technique allowing whole transcriptome surveys from subnanogram RNA quantities in an amplification/ligation-free manner. LQ-RNAseq involves first-strand cDNA synthesis from RNA templates, followed by 3' polyA tailing of the single-stranded cDNA products and direct single molecule sequencing. We applied LQ-RNAseq to profile S. cerevisiae polyA+ transcripts, demonstrate the reproducibility of the approach across different sample preparations and independent instrument runs, and establish the absolute quantitative power of this method through comparisons with other rep... Genome Research journals http://www.medworm.com/rss/comments.php?id=3334069 Thu, 04 Mar 2010 15:33:04 +0100 3334069 http://www.medworm.com/index.php?rid=3325835&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F393%3Frss%3D1 We present a likelihood method for detecting selective sweeps that involves jointly modeling the multilocus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on single nucleotide polymorphisms (SNPs) in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325835 Tue, 02 Mar 2010 21:45:40 +0100 3325835 http://www.medworm.com/index.php?rid=3325834&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F381%3Frss%3D1 We describe a strategy to systematically identify tissue-specific cis-regulatory elements that share combinations of sequence motifs. Using heart development as an experimental framework, we employed a combination of Gibbs sampling and linear regression to build a classifier that identifies heart enhancers based on the presence and/or absence of various sequence features, including known and putative transcription factor (TF) binding specificities. In distinguishing heart enhancers from a large pool of random noncoding sequences, the performance of our classifier is vastly superior to four commonly used methods, with an accuracy reaching 92% in cross-validation. Furthermore, most of the binding specificities learned by our method resemble the specificities of TFs widely recognized as key p... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325834 Tue, 02 Mar 2010 21:45:40 +0100 3325834 http://www.medworm.com/index.php?rid=3325833&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F372%3Frss%3D1 Biological networks are highly complex systems, consisting largely of enzymes that act as molecular switches to activate/inhibit downstream targets via post-translational modification. Computational techniques have been developed to perform signaling network inference using some high-throughput data sources, such as those generated from transcriptional and proteomic studies, but comparable methods have not been developed to use high-content morphological data, which are emerging principally from large-scale RNAi screens, to these ends. Here, we describe a systematic computational framework based on a classification model for identifying genetic interactions using high-dimensional single-cell morphological data from genetic screens, apply it to RhoGAP/GTPase regulation in Drosophila, and ev... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325833 Tue, 02 Mar 2010 21:45:40 +0100 3325833 http://www.medworm.com/index.php?rid=3325832&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F361%3Frss%3D1 Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here, we describe the short-term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chr... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325832 Tue, 02 Mar 2010 21:45:40 +0100 3325832 http://www.medworm.com/index.php?rid=3325831&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F351%3Frss%3D1 ATRX (alpha thalassemia/mental retardation syndrome X-linked) belongs to the SWI2/SNF2 family of chromatin remodeling proteins. Besides the ATPase/helicase domain at its C terminus, it contains a PHD-like zinc finger at the N terminus. Mutations in the ATRX gene are associated with X-linked mental retardation (XLMR) often accompanied by alpha thalassemia (ATRX syndrome). Although ATRX has been postulated to be a transcriptional regulator, its precise roles remain undefined. We demonstrate ATRX localization at the telomeres in interphase mouse embryonic stem (ES) cells in synchrony with the incorporation of H3.3 during telomere replication at S phase. Moreover, we found that chromobox homolog 5 (CBX5) (also known as heterochromatin protein 1 alpha, or HP1 alpha) is also present at the telom... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325831 Tue, 02 Mar 2010 21:45:40 +0100 3325831 http://www.medworm.com/index.php?rid=3325830&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F341%3Frss%3D1 Human colorectal cancer (CRC) is one of the better-understood systems for studying the genetics of cancer initiation and progression. To develop a cross-species comparison strategy for identifying CRC causative gene or genomic alterations, we performed array comparative genomic hybridization (aCGH) to investigate copy number abnormalities (CNAs), one of the most prominent lesion types reported for human CRCs, in 10 spontaneously occurring canine CRCs. The results revealed for the first time a strong degree of genetic homology between sporadic canine and human CRCs. First, we saw that between 5% and 22% of the canine genome was amplified/deleted in these tumors, and that, reminiscent of human CRCs, the total altered sequences directly correlated to the tumor's progression stage, origin, and... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325830 Tue, 02 Mar 2010 21:45:40 +0100 3325830 http://www.medworm.com/index.php?rid=3325829&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F332%3Frss%3D1 Aberrant methylation of promoter CpG islands in cancer is associated with silencing of tumor-suppressor genes, and age-dependent hypermethylation in normal appearing mucosa may be a risk factor for human colon cancer. It is not known whether this age-related DNA methylation phenomenon is specific to human tissues. We performed comprehensive DNA methylation profiling of promoter regions in aging mouse intestine using methylated CpG island amplification in combination with microarray analysis. By comparing C57BL/6 mice at 3-mo-old versus 35-mo-old for 3627 detectable autosomal genes, we found 774 (21%) that showed increased methylation and 466 (13%) that showed decreased methylation. We used pyrosequencing to quantitatively validate the microarray data and confirmed linear age-related methyl... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325829 Tue, 02 Mar 2010 21:45:40 +0100 3325829 http://www.medworm.com/index.php?rid=3325828&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F320%3Frss%3D1 DNA methylation is a critical epigenetic regulator in mammalian development. Here, we present a whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation: human embryonic stem cells (hESCs), a fibroblastic differentiated derivative of the hESCs, and neonatal fibroblasts. As a reference, we compared our maps with a methylome map of a fully differentiated adult cell type, mature peripheral blood mononuclear cells (monocytes). We observed many notable common and cell-type-specific features among all cell types. Promoter hypomethylation (both CG and CA) and higher levels of gene body methylation were positively correlated with transcription in all cell types. Exons were more highly methylated than... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325828 Tue, 02 Mar 2010 21:45:40 +0100 3325828 http://www.medworm.com/index.php?rid=3325827&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F311%3Frss%3D1 Noncoding DNA, particularly intronic DNA, harbors important functional elements that affect gene expression and RNA splicing. Yet, it is unclear which specific noncoding sites are essential for gene function and regulation. To identify functional elements in noncoding DNA, we characterized genetic variation within introns using ethnically diverse human polymorphism data from three public databases—PMT, NIEHS, and SeattleSNPs. We demonstrate that positions within introns corresponding to known functional elements involved in pre-mRNA splicing, including the branch site, splice sites, and polypyrimidine tract show reduced levels of genetic variation. Additionally, we observed regions of reduced genetic variation that are candidates for distance-dependent localization sites of functiona... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325827 Tue, 02 Mar 2010 21:45:40 +0100 3325827 http://www.medworm.com/index.php?rid=3325825&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F301%3Frss%3D1 Here, we demonstrate how comparative sequence analysis facilitates genome-wide base-pair-level interpretation of individual genetic variation and address two questions of importance for human personal genomics: first, whether an individual's functional variation comes mostly from noncoding or coding polymorphisms; and, second, whether population-specific or globally-present polymorphisms contribute more to functional variation in any given individual. Neither has been definitively answered by analyses of existing variation data because of a focus on coding polymorphisms, ascertainment biases in favor of common variation, and a lack of base-pair-level resolution for identifying functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionar... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325825 Tue, 02 Mar 2010 21:45:40 +0100 3325825 http://www.medworm.com/index.php?rid=3325824&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F3%2F291%3Frss%3D1 Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are currently under way. And in light of the falling costs of next-generation sequencing technologies, such studies will soon become common in many other organisms as well. Here, we assess the challenges to analyzing whole-genome sequence polymorphism data, and we discuss the potential of these data to yield new insights concerning population history and the genomic prevalence of natural selection. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3325824 Tue, 02 Mar 2010 21:45:40 +0100 3325824 http://www.medworm.com/index.php?rid=3325821&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101956.109v1%3Frss%3D1 We performed integrated gene coexpression network analysis on two large microarray-based brain gene expression data sets generated from the prefrontal cortex obtained post-mortem from 101 subjects, 47 subjects with schizophrenia and 54 normal control subjects, ranging in age from 19 to 81 years. Twenty-eight modules of coexpressed genes with functional interpretations were detected in both normal subjects and those with schizophrenia. Significant overlap of "case" and "control" module composition was observed, indicating that extensive differences in underlying molecular connectivity are not likely driving pathology in schizophrenia. Modules of coexpressed genes were characterized according to disease association, cell type specificity, and the effects of aging. We find that genes with alt... Genome Research journals http://www.medworm.com/rss/comments.php?id=3325821 Tue, 02 Mar 2010 09:00:44 +0100 3325821 http://www.medworm.com/index.php?rid=3321252&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096719.109v1%3Frss%3D1 We have produced an evolutionary model for promoters, analogous to the commonly used synonymous/nonsynonymous mutation models for protein-coding sequence. Although our model, called Sunflower, relies on some simple assumptions, it captures enough of the biology of transcription factor action to show clear correlation with other biological features. Sunflower predicts a binding profile of transcription factors to DNA sequence, in which different factors compete for the same potential binding sites. The parametrized model simultaneously estimates a continuous measurement of binding occupancy across the genomic sequence for each factor. We can then introduce a localized mutation, rerun the binding model and record the difference in binding profiles. A single mutation can alter interactions bo... Genome Research journals http://www.medworm.com/rss/comments.php?id=3321252 Mon, 01 Mar 2010 22:32:56 +0100 3321252 http://www.medworm.com/index.php?rid=3305525&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.102038.109v1%3Frss%3D1 The global diabetes epidemic poses a major challenge. Epigenetic events contribute to the etiology of diabetes; however, the lack of epigenomic analysis has limited the elucidation of the mechanistic basis for this link. To determine the epigenetic architecture of human pancreatic islets we mapped the genome-wide locations of four histone marks: three associated with gene activation—H3K4me1, H3K4me2, and H3K4me3—and one associated with gene repression, H3K27me3. Interestingly, the promoters of the highly transcribed insulin and glucagon genes are occupied only sparsely by H3K4me2 and H3K4me3. Globally, we identified important relationships between promoter structure, histone modification, and gene expression. We demonstrated co-occurrences of histone modifications including biv... Genome Research journals http://www.medworm.com/rss/comments.php?id=3305525 Wed, 24 Feb 2010 21:07:35 +0100 3305525 http://www.medworm.com/index.php?rid=3300941&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.103697.109v1%3Frss%3D1 Global studies of transcript structure and abundance in cancer cells enable the systematic discovery of aberrations that contribute to carcinogenesis, including gene fusions, alternative splice isoforms, and somatic mutations. We developed a systematic approach to characterize the spectrum of cancer-associated mRNA alterations through integration of transcriptomic and structural genomic data, and we applied this approach to generate new insights into melanoma biology. Using paired-end massively parallel sequencing of cDNA (RNA-seq) together with analyses of high-resolution chromosomal copy number data, we identified 11 novel melanoma gene fusions produced by underlying genomic rearrangements, as well as 12 novel readthrough transcripts. We mapped these chimeric transcripts to base-pair res... Genome Research journals http://www.medworm.com/rss/comments.php?id=3300941 Tue, 23 Feb 2010 09:00:46 +0100 3300941 http://www.medworm.com/index.php?rid=3297481&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101469.109v1%3Frss%3D1 Trophoblast stem cells (TS cells), derived from the trophectoderm (TE) of blastocysts, require transcription factors (TFs) and external signals (FGF4, INHBA/NODAL/TGFB1) for self-renewal. While many reports have focused on TF networks that regulate embryonic stem cell (ES cell) self-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells. To further understand transcriptional networks in TS cells we used chromatin immunopreciptiation and DNA microarray analysis (ChIP-chip) to investigate targets of TFs TCFAP2C, EOMES, ETS2, and GATA3, and a chromatin remodeling factor, SMARCA4. We then evaluated the transcriptional states of target genes using transcriptome analysis and genome-wide analysis of histone H3 acetylation (AcH3). Our results describe pre... Genome Research journals http://www.medworm.com/rss/comments.php?id=3297481 Mon, 22 Feb 2010 15:36:28 +0100 3297481 http://www.medworm.com/index.php?rid=3286640&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098947.109v2%3Frss%3D1 Neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. Here, we study the role of replication in the neutral substitution pattern. We obtained a high-resolution replication timing profile of the whole human genome by massively parallel sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates increase monotonously with replication timing even after controlling for local or regional nucleotide composition, crossover rate, distance to telomeres, and chromatin... Genome Research journals http://www.medworm.com/rss/comments.php?id=3286640 Thu, 18 Feb 2010 22:06:03 +0100 3286640 http://www.medworm.com/index.php?rid=3265881&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101246.109v2%3Frss%3D1 Low complexity and homopolymer sequences within coding regions are known to evolve rapidly. While their expansion may be deleterious, there is increasing evidence for a functional role associated with these amino acid sequences. Homopolymer sequences are thought to evolve mostly through replication slippage and, therefore, they may be expected to be longer in regions with relaxed selective constraint. Within the coding sequences of eukaryotes, alternatively spliced exons are known to evolve under relaxed constraints in comparison to those exons that are constitutively spliced because they are not included in all of the mature mRNA of a gene. This relaxed exposure to selection leads to faster rates of evolution for alternatively spliced exons in comparison to constitutively spliced exons. H... Genome Research journals http://www.medworm.com/rss/comments.php?id=3265881 Thu, 11 Feb 2010 15:41:40 +0100 3265881 http://www.medworm.com/index.php?rid=3265882&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100545.109v2%3Frss%3D1 We present a likelihood method for detecting selective sweeps that involves jointly modeling the multilocus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on single nucleotide polymorphisms (SNPs) in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than... Genome Research journals http://www.medworm.com/rss/comments.php?id=3265882 Thu, 11 Feb 2010 15:41:39 +0100 3265882 http://www.medworm.com/index.php?rid=3265883&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100040.109v1%3Frss%3D1 Next generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for SNP detection are designed to detect SNPs from single individual sequence datasets. Here we describe a novel method SNIP-Seq (Single Nucleotide polymorphism Identification from Population Sequence data) that leverages sequence data from a population of individuals to detect SNPs and assign genotypes to individuals. To evaluate our method, we utilized sequence data from a 200 kilobase region on chromosome 9p21 of the human genome. This region was sequenced in 48 individuals (5 ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3265883 Thu, 11 Feb 2010 15:38:45 +0100 3265883 http://www.medworm.com/index.php?rid=3257735&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.079509.108v2%3Frss%3D1 Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are currently under way. And in light of the falling costs of next-generation sequencing technologies, such studies will soon become common in many other organisms as well. Here, we assess the challenges to analyzing whole-genome sequence polymorphism data, and we discuss the potential of these data to yield new insights concerning population history and the genomic prevalence of natural selection. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3257735 Tue, 09 Feb 2010 20:36:53 +0100 3257735 http://www.medworm.com/index.php?rid=3257734&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098657.109v2%3Frss%3D1 We describe a strategy to systematically identify tissue-specific cis-regulatory elements that share combinations of sequence motifs. Using heart development as an experimental framework, we employed a combination of Gibbs sampling and linear regression to build a classifier that identifies heart enhancers based on the presence and/or absence of various sequence features, including known and putative transcription factor (TF) binding specificities. In distinguishing heart enhancers from a large pool of random noncoding sequences, the performance of our classifier is vastly superior to four commonly used methods, with an accuracy reaching 92% in cross-validation. Furthermore, most of the binding specificities learned by our method resemble the specificities of TFs widely recognized as key p... Genome Research journals http://www.medworm.com/rss/comments.php?id=3257734 Tue, 09 Feb 2010 20:36:53 +0100 3257734 http://www.medworm.com/index.php?rid=3257732&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.102210.109v2%3Frss%3D1 Here, we demonstrate how comparative sequence analysis facilitates genome-wide base-pair-level interpretation of individual genetic variation and address two questions of importance for human personal genomics: first, whether an individual's functional variation comes mostly from noncoding or coding polymorphisms; and, second, whether population-specific or globally-present polymorphisms contribute more to functional variation in any given individual. Neither has been definitively answered by analyses of existing variation data because of a focus on coding polymorphisms, ascertainment biases in favor of common variation, and a lack of base-pair-level resolution for identifying functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionar... Genome Research journals http://www.medworm.com/rss/comments.php?id=3257732 Tue, 09 Feb 2010 20:36:53 +0100 3257732 http://www.medworm.com/index.php?rid=3257733&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100248.109v1%3Frss%3D1 Biological networks are highly complex systems, consisting largely of enzymes that act as molecular switches to activate/inhibit downstream targets via post-translational modification. Computational techniques have been developed to perform signaling network inference using some high-throughput data sources, such as those generated from transcriptional and proteomic studies, but comparable methods have not been developed to use high-content morphological data, which are emerging principally from large-scale RNAi screens, to these ends. Here, we describe a systematic computational framework based on a classification model for identifying genetic interactions using high-dimensional single-cell morphological data from genetic screens, apply it to RhoGAP/GTPase regulation in Drosophila, and ev... Genome Research journals http://www.medworm.com/rss/comments.php?id=3257733 Tue, 09 Feb 2010 09:00:46 +0100 3257733 http://www.medworm.com/index.php?rid=3253524&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.092726.109v2%3Frss%3D1 Human colorectal cancer (CRC) is one of the better-understood systems for studying the genetics of cancer initiation and progression. To develop a cross-species comparison strategy for identifying CRC causative gene or genomic alterations, we performed array comparative genomic hybridization (aCGH) to investigate copy number abnormalities (CNAs), one of the most prominent lesion types reported for human CRCs, in 10 spontaneously occurring canine CRCs. The results revealed for the first time a strong degree of genetic homology between sporadic canine and human CRCs. First, we saw that between 5% and 22% of the canine genome was amplified/deleted in these tumors, and that, reminiscent of human CRCs, the total altered sequences directly correlated to the tumor's progression stage, origin, and... Genome Research journals http://www.medworm.com/rss/comments.php?id=3253524 Mon, 08 Feb 2010 19:08:58 +0100 3253524 http://www.medworm.com/index.php?rid=3253523&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098558.109v2%3Frss%3D1 Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady-state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here, we describe the short-term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chr... Genome Research journals http://www.medworm.com/rss/comments.php?id=3253523 Mon, 08 Feb 2010 19:08:58 +0100 3253523 http://www.medworm.com/index.php?rid=3242707&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.103226.109v1%3Frss%3D1 Eukaryotic transcriptional regulation is mediated by the organization of nucleosomes in promoter regions. Most S. cerevisiae promoters have a highly stereotyped chromatin organization, where nucleosome-free regions (NFR) are flanked by well-ordered nucleosomes. We have found that yeast promoters fall into two classes differing in NFR sharpness, and that this distinction follows a known transcriptional dichotomy in yeast genes. A class of yeast promoters having well-defined NFRs are characterized by positioned patterns of poly(dA:dT) tracts with several novel features. First, poly(dA:dT) tracts are localized in a strand-dependent manner, with poly(dA) tracts lying proximal to transcriptional start sites and poly(dT) tracts lying distal, and collectively define a symmetry axis that is coinci... Genome Research journals http://www.medworm.com/rss/comments.php?id=3242707 Thu, 04 Feb 2010 19:48:31 +0100 3242707 http://www.medworm.com/index.php?rid=3242708&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.102129.109v1%3Frss%3D1 Accurate profiling of minute quantities of RNA in a global manner can enable key advances in many scientific and clinical disciplines. Here we present low quantity RNA sequencing (LQ-RNAseq), a high-throughput sequencing-based technique allowing whole transcriptome surveys from subnanogram RNA quantities in an amplification/ligation-free manner. LQ-RNAseq involves first-strand cDNA synthesis from RNA templates, followed by 3' polyA tailing of the single-stranded cDNA products and direct single molecule sequencing. We applied LQ-RNAseq to profile S. cerevisiae polyA+ transcripts and demonstrate the reproducibility of the approach across different sample preparations and independent instrument runs, and establish the absolute quantitative power of this method through comparisons with other r... Genome Research journals http://www.medworm.com/rss/comments.php?id=3242708 Thu, 04 Feb 2010 15:19:28 +0100 3242708 http://www.medworm.com/index.php?rid=3242709&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101907.109v1%3Frss%3D1 DNA methylation is a critical epigenetic regulator in mammalian development. Here, we present a whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation: human embryonic stem cells (hESCs), a fibroblastic differentiated derivative of the hESCs, and neonatal fibroblasts. As a reference, we compared our maps with a methylome map of a fully differentiated adult cell type, mature peripheral blood mononuclear cells (monocytes). We observed many notable common and cell-type-specific features among all cell types. Promoter hypomethylation (both CG and CA) and higher levels of gene body methylation were positively correlated with transcription in all cell types. Exons were more highly methylated than... Genome Research journals http://www.medworm.com/rss/comments.php?id=3242709 Thu, 04 Feb 2010 09:00:39 +0100 3242709 http://www.medworm.com/index.php?rid=3226817&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F281%3Frss%3D1 We report a novel strategy for association mapping that combines classic inbred strains for mapping resolution and recombinant inbred strains for mapping power. Using a mixed model algorithm to correct for population structure, we validate the approach by mapping over 2500 cis-expression QTL with a resolution an order of magnitude narrower than traditional QTL analysis. We also report the fine mapping of metabolic traits such as plasma lipids. This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3226817 Mon, 01 Feb 2010 15:02:44 +0100 3226817 http://www.medworm.com/index.php?rid=3226816&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F273%3Frss%3D1 Accurate identification of genetic variants from next-generation sequencing (NGS) data is essential for immediate large-scale genomic endeavors such as the 1000 Genomes Project, and is crucial for further genetic analysis based on the discoveries. The key challenge in single nucleotide polymorphism (SNP) discovery is to distinguish true individual variants (occurring at a low frequency) from sequencing errors (often occurring at frequencies orders of magnitude higher). Therefore, knowledge of the error probabilities of base calls is essential. We have developed Atlas-SNP2, a computational tool that detects and accounts for systematic sequencing errors caused by context-related variables in a logistic regression model learned from training data sets. Subsequently, it estimates the posterior... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226816 Mon, 01 Feb 2010 15:02:44 +0100 3226816 http://www.medworm.com/index.php?rid=3226815&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F265%3Frss%3D1 Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3226815 Mon, 01 Feb 2010 15:02:44 +0100 3226815 http://www.medworm.com/index.php?rid=3226814&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F257%3Frss%3D1 MicroRNAs (miRNAs) are short (20–23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In cont... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226814 Mon, 01 Feb 2010 15:02:44 +0100 3226814 http://www.medworm.com/index.php?rid=3226813&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F249%3Frss%3D1 We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we appli... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226813 Mon, 01 Feb 2010 15:02:44 +0100 3226813 http://www.medworm.com/index.php?rid=3226812&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F239%3Frss%3D1 The biological impact of transposons on the physiology of the host depends greatly on the frequency and position of integration. Previous studies of Tf1, a long terminal repeat retrotransposon in Schizosaccharomyces pombe, showed that integration occurs at the promoters of RNA polymerase II (Pol II) transcribed genes. To determine whether specific promoters are preferred targets of integration, we sequenced large numbers of insertions using high-throughput pyrosequencing. In four independent experiments we identified a total of 73,125 independent integration events. These data provided strong support for the conclusion that Pol II promoters are the targets of Tf1 integration. The size and number of the integration experiments resulted in reproducible measures of integration for each interg... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226812 Mon, 01 Feb 2010 15:02:44 +0100 3226812 http://www.medworm.com/index.php?rid=3226811&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F228%3Frss%3D1 In eukaryotic cells, chromatin reorganizes within promoters of active genes to allow the transcription machinery and various transcription factors to access DNA. In this model, promoter-specific transcription factors bind DNA to initiate the production of mRNA in a tightly regulated manner. In the case of the human malaria parasite, Plasmodium falciparum, specific transcription factors are apparently underrepresented with regards to the size of the genome, and mechanisms underlying transcriptional regulation are controversial. Here, we investigate the modulation of DNA accessibility by chromatin remodeling during the parasite infection cycle. We have generated genome-wide maps of nucleosome occupancy across the parasite erythrocytic cycle using two complementary assays—the formaldehy... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226811 Mon, 01 Feb 2010 15:02:44 +0100 3226811 http://www.medworm.com/index.php?rid=3226810&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F212%3Frss%3D1 Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) pi... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226810 Mon, 01 Feb 2010 15:02:44 +0100 3226810 http://www.medworm.com/index.php?rid=3226809&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F201%3Frss%3D1 The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Although no clear sequence motif emerged, we were able to use machine learning approaches to accurately discriminate between ORC-associated sequences and ORC-free sequences based solely on primary sequence. The complex sequence features that define ORC binding sites are highly correlated with nucleosome positioning signals and likely represent a p... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226809 Mon, 01 Feb 2010 15:02:44 +0100 3226809 http://www.medworm.com/index.php?rid=3226808&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F190%3Frss%3D1 In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226808 Mon, 01 Feb 2010 15:02:44 +0100 3226808 http://www.medworm.com/index.php?rid=3226807&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F180%3Frss%3D1 Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here, we used recently developed RNA sequencing protocols, which sidestep this limitation, to assess intra- and interspecies variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNA-seq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evol... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226807 Mon, 01 Feb 2010 15:02:44 +0100 3226807 http://www.medworm.com/index.php?rid=3226806&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F170%3Frss%3D1 Monozygotic (MZ) twins are partially concordant for most complex diseases, including autoimmune disorders. Whereas phenotypic concordance can be used to study heritability, discordance suggests the role of non-genetic factors. In autoimmune diseases, environmentally driven epigenetic changes are thought to contribute to their etiology. Here we report the first high-throughput and candidate sequence analyses of DNA methylation to investigate discordance for autoimmune disease in twins. We used a cohort of MZ twins discordant for three diseases whose clinical signs often overlap: systemic lupus erythematosus (SLE), rheumatoid arthritis, and dermatomyositis. Only MZ twins discordant for SLE featured widespread changes in the DNA methylation status of a significant number of genes. Gene ontolo... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226806 Mon, 01 Feb 2010 15:02:44 +0100 3226806 http://www.medworm.com/index.php?rid=3226805&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F2%2F155%3Frss%3D1 Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-reg... Genome Research journals http://www.medworm.com/rss/comments.php?id=3226805 Mon, 01 Feb 2010 15:02:43 +0100 3226805 http://www.medworm.com/index.php?rid=3219362&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101477.109v1%3Frss%3D1 ATRX (alpha thalassemia/mental retardation syndrome X-linked) belongs to the SWI2/SNF2 family of chromatin remodeling proteins. Besides the ATPase/helicase domain at its C terminus, it contains a PHD-like zinc finger at the N terminus. Mutations in the ATRX gene are associated with X-linked mental retardation (XLMR) often accompanied by alpha thalassemia (ATRX syndrome). Although ATRX has been postulated to be a transcriptional regulator, its precise roles remain undefined. We demonstrate ATRX localization at the telomeres in interphase mouse embryonic stem (ES) cells in synchrony with the incorporation of H3.3 during telomere replication at S phase. Moreover, we found that chromobox homolog 5 (CBX5) (also known as heterochromatin protein 1 alpha, or HP1 alpha) is also present at the telom... Genome Research journals http://www.medworm.com/rss/comments.php?id=3219362 Thu, 28 Jan 2010 23:19:58 +0100 3219362 http://www.medworm.com/index.php?rid=3215376&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096826.109v1%3Frss%3D1 Aberrant methylation of promoter CpG islands in cancer is associated with silencing of tumor-suppressor genes, and age-dependent hypermethylation in normal appearing mucosa may be a risk factor for human colon cancer. It is not known whether this age-related DNA methylation phenomenon is specific to human tissues. We performed comprehensive DNA methylation profiling of promoter regions in aging mouse intestine using methylated CpG island amplification in combination with microarray analysis. By comparing C57BL/6 mice at 3-mo-old versus 35-mo-old for 3627 detectable autosomal genes, we found 774 (21%) that showed increased methylation and 466 (13%) that showed decreased methylation. We used pyrosequencing to quantitatively validate the microarray data and confirmed linear age-related methyl... Genome Research journals http://www.medworm.com/rss/comments.php?id=3215376 Wed, 27 Jan 2010 20:40:28 +0100 3215376 http://www.medworm.com/index.php?rid=3211064&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098947.109v1%3Frss%3D1 Neutral nucleotide substitutions occur at varying rates along genomes and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. Here, we study the role of replication on the neutral substitution pattern. We obtained a high-resolution replication timing profile of the whole human genome by massive sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates increase monotonously with replication timing even after controlling for local or regional nucleotide composition, crossover rate, distance to telomeres and chromatin compaction. ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3211064 Tue, 26 Jan 2010 15:37:33 +0100 3211064 http://www.medworm.com/index.php?rid=3192535&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.094151.109v2%3Frss%3D1 Noncoding DNA, particularly intronic DNA, harbors important functional elements that affect gene expression and RNA splicing. Yet, it is unclear which specific noncoding sites are essential for gene function and regulation. To identify functional elements in noncoding DNA, we characterized genetic variation within introns using ethnically diverse human polymorphism data from three public databases—PMT, NIEHS, and SeattleSNPs. We demonstrate that positions within introns corresponding to known functional elements involved in pre-mRNA splicing, including the branch site, splice sites, and polypyrimidine tract show reduced levels of genetic variation. Additionally, we observed regions of reduced genetic variation that are candidates for distance-dependent localization sites of functiona... Genome Research journals http://www.medworm.com/rss/comments.php?id=3192535 Wed, 20 Jan 2010 18:50:28 +0100 3192535 http://www.medworm.com/index.php?rid=3188060&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.092726.109v1%3Frss%3D1 Human colorectal cancer (CRC) is one of the better-understood systems for studying the genetics of cancer initiation and progression. To develop a cross-species comparison strategy for identifying CRC causative gene or genomic alterations, we performed array comparative genomic hybridization (aCGH) to investigate copy number abnormalities (CNAs), one of the most prominent lesion types reported for human CRCs, in 10 spontaneously occurring canine CRCs. The results revealed for the first time a strong degree of genetic homology between sporadic canine and human CRCs. First, we saw that between 5 and 22% of the canine genome was amplified/deleted in these tumors, and that, reminiscent of human CRCs, the total altered sequences directly correlated to the tumor's progression stage, origin, and ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3188060 Tue, 19 Jan 2010 23:07:46 +0100 3188060 http://www.medworm.com/index.php?rid=3188059&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098558.109v1%3Frss%3D1 Gene transcription is associated with local changes in chromatin, both in nucleosome positions and in chemical modifications of the histones. Chromatin dynamics has mostly been studied on a single-gene basis. Those genome-wide studies that have been made primarily investigated steady state transcription. However, three studies of genome-wide changes in chromatin during the transcriptional response to heat shock in the budding yeast Saccharomyces cerevisiae revealed nucleosome eviction in promoter regions but only minor effects in coding regions. Here we describe the short term response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. Nitrogen depletion leads to a fast induction of a large number of genes in S. pombe and is thus suitable for genome-wide studies of chro... Genome Research journals http://www.medworm.com/rss/comments.php?id=3188059 Tue, 19 Jan 2010 23:07:45 +0100 3188059 http://www.medworm.com/index.php?rid=3188058&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100545.109v1%3Frss%3D1 We present a likelihood method for detecting selective sweeps that involves jointly modeling the multi-locus allele frequency differentiation between two populations. We use Brownian motion to model genetic drift under neutrality, and a deterministic model to approximate the effect of a selective sweep on SNPs in the vicinity. We test the method with extensive simulated data, and demonstrate that in some scenarios the method provides higher power than previously reported approaches to detect selective sweeps, and can provide surprisingly good localization of the position of a selected allele. A strength of our technique is that it uses allele frequency differentiation between populations, which is much more robust to ascertainment bias in SNP discovery than methods based on the allele freq... Genome Research journals http://www.medworm.com/rss/comments.php?id=3188058 Tue, 19 Jan 2010 23:07:45 +0100 3188058 http://www.medworm.com/index.php?rid=3174703&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098657.109v1%3Frss%3D1 We describe a strategy to systematically identify tissue-specific cis-regulatory elements that share combinations of sequence motifs. Using heart development as an experimental framework, we employed a combination of Gibbs sampling and linear regression to build a classifier that identifies heart enhancers based on the presence and/or absence of various sequence features, including known and putative TF binding specificities. In distinguishing heart enhancers from a large pool of random noncoding sequences, the performance of our classifier is vastly superior to four commonly used methods, with an accuracy reaching 92% in cross-validation. Furthermore, most of the binding specificities learned by our method resemble the specificities of TFs widely recognized as key players in heart develop... Genome Research journals http://www.medworm.com/rss/comments.php?id=3174703 Thu, 14 Jan 2010 16:59:47 +0100 3174703 http://www.medworm.com/index.php?rid=3166175&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.079509.108v1%3Frss%3D1 Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole genome sequence polymorphism data are currently underway. And in light of the falling costs of next-generation sequencing technologies, such studies will soon become common in many other organisms as well. In this article, we assess the challenges to analyzing whole genome sequence polymorphism data, and we discuss the potential of this data to yield new insights concerning population history and the genomic prevalence of natural selection. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3166175 Tue, 12 Jan 2010 22:05:05 +0100 3166175 http://www.medworm.com/index.php?rid=3166174&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.102210.109v1%3Frss%3D1 We here demonstrate how comparative sequence analysis facilitates genome-wide base-pair level interpretation of individual genetic variation, and address two questions of importance for human personal genomics: First, whether an individual's functional variation comes mostly from noncoding or coding polymorphisms; second, whether population-specific or globally present polymorphisms contribute more to functional variation in any given individual. Neither has been definitively answered by analyses of existing variation data because of a focus on coding polymorphisms, ascertainment biases in favor of common variation, and a lack of base-pair level resolution for identifying functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionary con... Genome Research journals http://www.medworm.com/rss/comments.php?id=3166174 Tue, 12 Jan 2010 22:05:05 +0100 3166174 http://www.medworm.com/index.php?rid=3152304&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101246.109v1%3Frss%3D1 Low complexity and homopolymer sequences within coding regions are known to evolve rapidly. While their expansion may be deleterious, there is increasing evidence for a functional role associated with these amino acid sequences. Homopolymers sequences are thought to evolve mostly through replication slippage and therefore they may be expected to be longer in regions with relaxed selective constraint. Within the coding sequences of eukaryotes, alternatively spliced exons are known to evolve under relaxed constraints in comparison to those exons that are constitutively spliced because they are not included in all of the mature mRNA of a gene. This relaxed exposure to selection leads to faster rate of evolution of alternatively spliced exons in comparison to constitutively spliced exons. Here... Genome Research journals http://www.medworm.com/rss/comments.php?id=3152304 Thu, 07 Jan 2010 19:49:09 +0100 3152304 http://www.medworm.com/index.php?rid=3148260&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099234.109v1%3Frss%3D1 We report a novel strategy for association mapping that combines classic inbred strains for mapping resolution and recombinant inbred strains for mapping power. Using a mixed model algorithm to correct for population structure, we validate the approach by mapping over 2500 cis-expression QTL with a resolution an order of magnitude narrower than traditional QTL analysis. We also report the fine mapping of metabolic traits such as plasma lipids. This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3148260 Thu, 07 Jan 2010 00:30:46 +0100 3148260 http://www.medworm.com/index.php?rid=3148259&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.101063.109v1%3Frss%3D1 In eukaryotic cells, chromatin reorganizes within promoters of active genes to allow the transcription machinery and various transcription factors to access DNA. In this model, promoter-specific transcription factors bind DNA to initiate the production of mRNA in a tightly regulated manner. In the case of the human malaria parasite, Plasmodium falciparum, specific transcription factors are apparently underrepresented with regards to the size of the genome, and mechanisms underlying transcriptional regulation are controversial. Here, we investigate the modulation of DNA accessibility by chromatin remodeling during the parasite infection cycle. We have generated genome-wide maps of nucleosome occupancy across the parasite erythrocytic cycle using two complementary assays—the formaldehy... Genome Research journals http://www.medworm.com/rss/comments.php?id=3148259 Thu, 07 Jan 2010 00:30:45 +0100 3148259 http://www.medworm.com/index.php?rid=3144901&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.095273.109v1%3Frss%3D1 MicroRNAs (miRNAs) are short (20–23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In cont... Genome Research journals http://www.medworm.com/rss/comments.php?id=3144901 Tue, 05 Jan 2010 19:53:00 +0100 3144901 http://www.medworm.com/index.php?rid=3144900&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097873.109v2%3Frss%3D1 The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Although no clear sequence motif emerged, we were able to use machine learning approaches to accurately discriminate between ORC-associated sequences and ORC-free sequences based solely on primary sequence. The complex sequence features that define ORC binding sites are highly correlated with nucleosome positioning signals and likely represent a p... Genome Research journals http://www.medworm.com/rss/comments.php?id=3144900 Tue, 05 Jan 2010 19:52:59 +0100 3144900 http://www.medworm.com/index.php?rid=3141502&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F142%3Frss%3D1 ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The "ProPhylER Interface" displays predictive analyses in sequence space; the "CrystalPainter" maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylE... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141502 Mon, 04 Jan 2010 15:03:00 +0100 3141502 http://www.medworm.com/index.php?rid=3141501&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F133%3Frss%3D1 This study highlights transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation in Bacteria and Archaea. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3141501 Mon, 04 Jan 2010 15:03:00 +0100 3141501 http://www.medworm.com/index.php?rid=3141500&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F122%3Frss%3D1 This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141500 Mon, 04 Jan 2010 15:03:00 +0100 3141500 http://www.medworm.com/index.php?rid=3141499&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F110%3Frss%3D1 Methods for detecting nucleotide substitution rates that are faster or slower than expected under neutral drift are widely used to identify candidate functional elements in genomic sequences. However, most existing methods consider either reductions (conservation) or increases (acceleration) in rate but not both, or assume that selection acts uniformly across the branches of a phylogeny. Here we examine the more general problem of detecting departures from the neutral rate of substitution in either direction, possibly in a clade-specific manner. We consider four statistical, phylogenetic tests for addressing this problem: a likelihood ratio test, a score test, a test based on exact distributions of numbers of substitutions, and the genomic evolutionary rate profiling (GERP) test. All four ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141499 Mon, 04 Jan 2010 15:03:00 +0100 3141499 http://www.medworm.com/index.php?rid=3141498&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F101%3Frss%3D1 It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate = 4Neµ, population exponential growth rate R, and error rate , simultaneously. Using simulation, we show the combined effects of the parameters, , n, , and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of with other estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rat... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141498 Mon, 04 Jan 2010 15:03:00 +0100 3141498 http://www.medworm.com/index.php?rid=3141497&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F90%3Frss%3D1 Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression, and has led to mechanistic hypotheses regarding the rules by which chromatin structure is established. High-throughput sequencing has recently become the technology of choice for chromatin mapping studies, yet analysis of these experiments is still in its infancy. Here, we introduce a pipeline for analyzing deep sequencing maps of chromatin structure and apply it to data from S. cerevisiae. We analyze a digestion series where nucleosomes are isolated from under- and overdigested chromatin. We find that certain classes of nucleosomes are unusually susceptible or resistant to overdigestion, with promoter nucleosomes easily digested and mid-coding re... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141497 Mon, 04 Jan 2010 15:03:00 +0100 3141497 http://www.medworm.com/index.php?rid=3141496&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F81%3Frss%3D1 We present a novel approach for generating targeted deletions of genomic segments in human and other eukaryotic cells using engineered zinc finger nucleases (ZFNs). We found that ZFNs designed to target two different sites in a human chromosome could introduce two concurrent DNA double-strand breaks (DSBs) in the chromosome and give rise to targeted deletions of the genomic segment between the two sites. Using this method in human cells, we were able to delete predetermined genomic DNA segments in the range of several-hundred base pairs (bp) to 15 mega-bp at frequencies of 10–3 to 10–1. These high frequencies allowed us to isolate clonal populations of cells, in which the target chromosomal segments were deleted, by limiting dilution. Sequence analysis revealed that many of the... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141496 Mon, 04 Jan 2010 15:03:00 +0100 3141496 http://www.medworm.com/index.php?rid=3141495&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F68%3Frss%3D1 Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subp... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141495 Mon, 04 Jan 2010 15:03:00 +0100 3141495 http://www.medworm.com/index.php?rid=3141494&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F59%3Frss%3D1 Numerous studies of chromatin structure showed that nucleosome free regions (NFRs) located at 5' gene ends contribute to transcription initiation regulation. Here, we determine the role of intragenic chromatin structure on gene expression regulation. We show that, along Saccharomyces cerevisiae genes, nucleosomes are highly organized following two types of architecture that depend only on the distance between the NFRs located at the 5' and 3' gene ends. In the first type, this distance constrains in vivo the positioning of n nucleosomes regularly organized in a "crystal-like" array. In the second type, this distance is such that the corresponding genes can accommodate either n or (n + 1) nucleosomes, thereby displaying two possible crystal-like arrays of n weakly compacted or n + 1 highly ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141494 Mon, 04 Jan 2010 15:03:00 +0100 3141494 http://www.medworm.com/index.php?rid=3141493&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F45%3Frss%3D1 Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least ~42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirm... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141493 Mon, 04 Jan 2010 15:03:00 +0100 3141493 http://www.medworm.com/index.php?rid=3141492&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F36%3Frss%3D1 Embryonic stem (ES) cells are under precise control of both intrinsic self-renewal gene regulatory network and extrinsic growth factor-triggered signaling cascades. How external signaling pathways connect to core self-renewal transcriptional circuits is largely unknown. To probe this, we chose BMP signaling, which is previously recognized as a master control for both self-renewal and lineage commitment of murine ES cells. Here, we mapped target gene promoter occupancy of SMAD1/5 and SMAD4 on a genome-wide scale and found that they associate with a large group of developmental regulators that are enriched for H3K27 trimethylation and H3K4 trimethylation bivalent marks and are repressed in the self-renewing state, whereas they are rapidly induced upon differentiation. Smad knockdown experime... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141492 Mon, 04 Jan 2010 15:03:00 +0100 3141492 http://www.medworm.com/index.php?rid=3141491&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F28%3Frss%3D1 Acetaminophen-induced liver toxicity is the most frequent precipitating cause of acute liver failure and liver transplant, but contemporary medical practice has mainly focused on patient management after a liver injury has been induced. An integrative genetic, transcriptional, and two-dimensional NMR-based metabolomic analysis performed using multiple inbred mouse strains, along with knowledge-based filtering of these data, identified betaine-homocysteine methyltransferase 2 (Bhmt2) as a diet-dependent genetic factor that affected susceptibility to acetaminophen-induced liver toxicity in mice. Through an effect on methionine and glutathione biosynthesis, Bhmt2 could utilize its substrate (S-methylmethionine [SMM]) to confer protection against acetaminophen-induced injury in vivo. Since SMM... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141491 Mon, 04 Jan 2010 15:03:00 +0100 3141491 http://www.medworm.com/index.php?rid=3141490&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F19%3Frss%3D1 This study identifies an ERV-K-type family in rats that shows obvious signs of recent activity. Ongoing retrotranspositional activity may significantly add to genomic variability among inbred rat strains. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3141490 Mon, 04 Jan 2010 15:03:00 +0100 3141490 http://www.medworm.com/index.php?rid=3141489&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F10%3Frss%3D1 We report an evolutionary analysis of the V1R gene family across 37 mammalian genomes. V1Rs comprise one of three chemosensory receptor families expressed in the vomeronasal organ, and contribute to pheromone detection. We first demonstrate that Trace Archive data can be used effectively to determine V1R family sizes and to obtain sequences of most V1R family members. Analyses of V1R sequences from trace data and genome assemblies show that species-specific expansions previously observed in only eight species were prevalent throughout mammalian evolution, resulting in "semi-private" V1R repertoires for most mammals. The largest families are found in mouse and platypus, whose V1R repertoires have been published previously, followed by mouse lemur and rabbit (~215 and ~160 intact V1Rs, respe... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141489 Mon, 04 Jan 2010 15:03:00 +0100 3141489 http://www.medworm.com/index.php?rid=3141488&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F20%2F1%2F1%3Frss%3D1 The ability to smell is governed by the largest gene family in mammalian genomes, the olfactory receptor (OR) genes. Although these genes are well annotated in the finished human and mouse genomes, we still do not understand which receptors bind specific odorants or how they fully function. Previous comparative studies have been taxonomically limited and mostly focused on the percentage of OR pseudogenes within species. No study has investigated the adaptive changes of functional OR gene families across phylogenetically and ecologically diverse mammals. To determine the extent to which OR gene repertoires have been influenced by habitat, sensory specialization, and other ecological traits, to better understand the functional importance of specific OR gene families and thus the odorants the... Genome Research journals http://www.medworm.com/rss/comments.php?id=3141488 Mon, 04 Jan 2010 15:02:59 +0100 3141488 http://www.medworm.com/index.php?rid=3128356&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099648.109v1%3Frss%3D1 The biological impact of transposons on the physiology of the host depends greatly on the frequency and position of integration. Previous studies of Tf1, a long terminal repeat retrotransposon in Schizosaccharomyces pombe, showed that integration occurs at the promoters of RNA polymerase II (Pol II) transcribed genes. To determine whether specific promoters are preferred targets of integration, we sequenced large numbers of insertions using high-throughput pyrosequencing. In four independent experiments we identified a total of 73,125 independent integration events. These data provided strong support for the conclusion that Pol II promoters are the targets of Tf1 integration. The size and number of the integration experiments resulted in reproducible measures of integration for each interg... Genome Research journals http://www.medworm.com/rss/comments.php?id=3128356 Tue, 29 Dec 2009 15:45:34 +0100 3128356 http://www.medworm.com/index.php?rid=3128355&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099796.109v2%3Frss%3D1 Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-reg... Genome Research journals http://www.medworm.com/rss/comments.php?id=3128355 Tue, 29 Dec 2009 15:45:34 +0100 3128355 http://www.medworm.com/index.php?rid=3128357&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.095406.109v2%3Frss%3D1 Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) pi... Genome Research journals http://www.medworm.com/rss/comments.php?id=3128357 Tue, 29 Dec 2009 15:45:33 +0100 3128357 http://www.medworm.com/index.php?rid=3117982&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.094151.109v1%3Frss%3D1 Non-coding DNA, particularly intronic DNA, harbors important functional elements that affect gene expression and RNA splicing. Yet, it is unclear which specific non-coding sites are essential for gene function and regulation. To identify functional elements in non-coding DNA, we characterized genetic variation within introns using ethnically diverse human polymorphism data from three public databases, PMT, NIEHS, and Seattle SNPs. We demonstrate that positions within introns corresponding to known functional elements involved in pre-mRNA splicing, including the branch site, splice sites, and polypyrimidine tract show reduced levels of genetic variation. Additionally, we observed regions of reduced genetic variation that are candidates for distance dependent localization sites of functional... Genome Research journals http://www.medworm.com/rss/comments.php?id=3117982 Wed, 23 Dec 2009 15:23:50 +0100 3117982 http://www.medworm.com/index.php?rid=3117981&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099226.109v2%3Frss%3D1 Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here, we used recently developed RNA sequencing protocols, which sidestep this limitation, to assess intra- and interspecies variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNA-seq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evol... Genome Research journals http://www.medworm.com/rss/comments.php?id=3117981 Wed, 23 Dec 2009 15:22:49 +0100 3117981 http://www.medworm.com/index.php?rid=3113978&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100289.109v1%3Frss%3D1 Monozygotic (MZ) twins are partially concordant for most complex diseases, including autoimmune disorders. Whereas phenotypic concordance can be used to study heritability, discordance suggests the role of non-genetic factors. In autoimmune diseases, environmentally driven epigenetic changes are thought to contribute to their etiology. Here we report the first high-throughput and candidate sequence analyses of DNA methylation to investigate discordance for autoimmune disease in twins. We used a cohort of MZ twins discordant for three diseases whose clinical signs often overlap: systemic lupus erythematosus (SLE), rheumatoid arthritis, and dermatomyositis. Only MZ twins discordant for SLE featured widespread changes in the DNA methylation status of a significant number of genes. Gene ontolo... Genome Research journals http://www.medworm.com/rss/comments.php?id=3113978 Tue, 22 Dec 2009 09:01:51 +0100 3113978 http://www.medworm.com/index.php?rid=3099377&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096388.109v1%3Frss%3D1 Accurate identification of genetic variants from next-generation sequencing (NGS) data is essential for immediate large-scale genomic endeavors such as the 1000 Genomes Project, and is crucial for further genetic analysis based on the discoveries. The key challenge in single nucleotide polymorphism (SNP) discovery is to distinguish true individual variants (occurring at a low frequency) from sequencing errors (often occurring at frequencies orders of magnitude higher). Therefore, knowledge of the error probabilities of base calls is essential. We have developed Atlas-SNP2, a computational tool that detects and accounts for systematic sequencing errors caused by context-related variables in a logistic regression model learned from training data sets. Subsequently, it estimates the posterior... Genome Research journals http://www.medworm.com/rss/comments.php?id=3099377 Thu, 17 Dec 2009 15:19:41 +0100 3099377 http://www.medworm.com/index.php?rid=3099376&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097261.109v1%3Frss%3D1 Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3099376 Thu, 17 Dec 2009 15:19:41 +0100 3099376 http://www.medworm.com/index.php?rid=3091705&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099226.109v1%3Frss%3D1 Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNAseq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evol... Genome Research journals http://www.medworm.com/rss/comments.php?id=3091705 Tue, 15 Dec 2009 19:51:12 +0100 3091705 http://www.medworm.com/index.php?rid=3074328&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098822.109v1%3Frss%3D1 In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-... Genome Research journals http://www.medworm.com/rss/comments.php?id=3074328 Wed, 09 Dec 2009 15:23:23 +0100 3074328 http://www.medworm.com/index.php?rid=3066021&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097873.109v1%3Frss%3D1 The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In S. cerevisiae ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Open chromatin appears to be the underlying factor that is deterministic for ORC binding. ORC-associated sequences are enriched for the histone variant, H3.3, often at transcription start sites, and depleted for bulk nucleosomes. Although no clear sequence motif emerged from the ORC binding sites, we were able to use machine learning approaches to accurately... Genome Research journals http://www.medworm.com/rss/comments.php?id=3066021 Mon, 07 Dec 2009 21:57:57 +0100 3066021 http://www.medworm.com/index.php?rid=3047157&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099796.109v1%3Frss%3D1 Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of lineage-independent early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specif... Genome Research journals http://www.medworm.com/rss/comments.php?id=3047157 Tue, 01 Dec 2009 19:56:29 +0100 3047157 http://www.medworm.com/index.php?rid=3047159&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099416.109v1%3Frss%3D1 The ability to smell is governed by the largest gene family in mammalian genomes, the olfactory receptor (OR) genes. Although these genes are well annotated in the finished human and mouse genomes, we still do not understand which receptors bind specific odorants or how they fully function. Previous comparative studies have been taxonomically limited and mostly focused on the percentage of OR pseudogenes within species. No study has investigated the adaptive changes of functional OR gene families across phylogenetically and ecologically diverse mammals. To determine the extent to which OR gene repertoires have been influenced by habitat, sensory specialization, and other ecological traits, to better understand the functional importance of specific OR gene families and thus the odorants the... Genome Research journals http://www.medworm.com/rss/comments.php?id=3047159 Tue, 01 Dec 2009 17:14:43 +0100 3047159 http://www.medworm.com/index.php?rid=3047161&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097543.109v1%3Frss%3D1 It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate = 4Neµ, population exponential growth rate R, and error rate , simultaneously. Using simulation, we show the combined effects of the parameters, , n, , and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of with other estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rat... Genome Research journals http://www.medworm.com/rss/comments.php?id=3047161 Tue, 01 Dec 2009 17:14:42 +0100 3047161 http://www.medworm.com/index.php?rid=3047162&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096644.109v2%3Frss%3D1 Numerous studies of chromatin structure showed that nucleosome free regions (NFRs) located at 5' gene ends contribute to transcription initiation regulation. Here, we determine the role of intragenic chromatin structure on gene expression regulation. We show that, along Saccharomyces cerevisiae genes, nucleosomes are highly organized following two types of architecture that depend only on the distance between the NFRs located at the 5' and 3' gene ends. In the first type, this distance constrains in vivo the positioning of n nucleosomes regularly organized in a "crystal-like" array. In the second type, this distance is such that the corresponding genes can accommodate either n or (n + 1) nucleosomes, thereby displaying two possible crystal-like arrays of n weakly compacted or n + 1 highly ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3047162 Tue, 01 Dec 2009 17:14:41 +0100 3047162 http://www.medworm.com/index.php?rid=3047160&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098913.109v1%3Frss%3D1 We report an evolutionary analysis of the V1R gene family across 37 mammalian genomes. V1Rs comprise one of three chemosensory receptor families expressed in the vomeronasal organ, and contribute to pheromone detection. We first demonstrate that Trace Archive data can be used effectively to determine V1R family sizes and to obtain sequences of most V1R family members. Analyses of V1R sequences from trace data and genome assemblies show that species-specific expansions previously observed in only eight species were prevalent throughout mammalian evolution, resulting in "semi-private" V1R repertoires for most mammals. The largest families are found in mouse and platypus, whose V1R repertoires have been published previously, followed by mouse lemur and rabbit (~215 and ~160 intact V1Rs, respe... Genome Research journals http://www.medworm.com/rss/comments.php?id=3047160 Tue, 01 Dec 2009 17:14:41 +0100 3047160 http://www.medworm.com/index.php?rid=3047158&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099747.109v1%3Frss%3D1 We present a novel approach for generating targeted deletions of genomic segments in human and other eukaryotic cells using engineered zinc finger nucleases (ZFNs). We found that ZFNs designed to target two different sites in a human chromosome could introduce two concurrent DNA double-strand breaks (DSBs) in the chromosome and give rise to targeted deletions of the genomic segment between the two sites. Using this method in human cells, we were able to delete predetermined genomic DNA segments in the range of several-hundred base pairs (bp) to 15 mega-bp at frequencies of 10–3 to 10–1. These high frequencies allowed us to isolate clonal populations of cells, in which the target chromosomal segments were deleted, by limiting dilution. Sequence analysis revealed that many of the... Genome Research journals http://www.medworm.com/rss/comments.php?id=3047158 Tue, 01 Dec 2009 17:14:40 +0100 3047158 http://www.medworm.com/index.php?rid=3043426&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2343%3Frss%3D1 (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3043426 Tue, 01 Dec 2009 15:04:07 +0100 3043426 http://www.medworm.com/index.php?rid=3043425&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2334%3Frss%3D1 Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified. To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform adapting rapid amplification of cDNA ends (RACE) for large-scale structural transcript annotation. We interrogated 2000 unverified protein-coding genes using this platform. We obtained RACE data... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043425 Tue, 01 Dec 2009 15:04:07 +0100 3043425 http://www.medworm.com/index.php?rid=3043424&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2324%3Frss%3D1 Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible with... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043424 Tue, 01 Dec 2009 15:04:07 +0100 3043424 http://www.medworm.com/index.php?rid=3043423&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2317%3Frss%3D1 The Human Microbiome Project (HMP), funded as an initiative of the NIH Roadmap for Biomedical Research (http://nihroadmap.nih.gov), is a multi-component community resource. The goals of the HMP are: (1) to take advantage of new, high-throughput technologies to characterize the human microbiome more fully by studying samples from multiple body sites from each of at least 250 "normal" volunteers; (2) to determine whether there are associations between changes in the microbiome and health/disease by studying several different medical conditions; and (3) to provide both a standardized data resource and new technological approaches to enable such studies to be undertaken broadly in the scientific community. The ethical, legal, and social implications of such research are being systematically st... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043423 Tue, 01 Dec 2009 15:04:07 +0100 3043423 http://www.medworm.com/index.php?rid=3043422&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2308%3Frss%3D1 Very high-throughput sequencing technologies need to be matched by high-throughput functional studies if we are to make full use of the current explosion in genome sequences. We have generated a very large bacterial mutant pool, consisting of an estimated 1.1 million transposon mutants and we have used genomic DNA from this mutant pool, and Illumina nucleotide sequencing to prime from the transposon and sequence into the adjacent target DNA. With this method, which we have called TraDIS (transposon directed insertion-site sequencing), we have been able to map 370,000 unique transposon insertion sites to the Salmonella enterica serovar Typhi chromosome. The unprecedented density and resolution of mapped insertion sites, an average of one every 13 base pairs, has allowed us to assay simultan... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043422 Tue, 01 Dec 2009 15:04:07 +0100 3043422 http://www.medworm.com/index.php?rid=3043421&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2300%3Frss%3D1 The genome-wide recombination rate (RR) of a species is often described by one parameter, the ratio between total genetic map length (G) and physical map length (P), measured in centimorgans per megabase (cM/Mb). The value of this parameter varies greatly between species, but the cause for these differences is not entirely clear. A constraining factor of overall RR in a species, which may cause increased RR for smaller chromosomes, is the requirement of at least one chiasma per chromosome (or chromosome arm) per meiosis. In the present study, we quantify the relative excess of recombination events on smaller chromosomes by a linear regression model, which relates the genetic length of chromosomes to their physical length. We find for several species that the two-parameter regression, G = G... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043421 Tue, 01 Dec 2009 15:04:07 +0100 3043421 http://www.medworm.com/index.php?rid=3043420&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2288%3Frss%3D1 The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replicatio... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043420 Tue, 01 Dec 2009 15:04:07 +0100 3043420 http://www.medworm.com/index.php?rid=3043419&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2279%3Frss%3D1 Whereas most nontyphoidal Salmonella (NTS) are associated with gastroenteritis, there has been a dramatic increase in reports of NTS-associated invasive disease in sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multilocus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, which currently is rarely reported outside of Africa. Whole-genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene forma... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043419 Tue, 01 Dec 2009 15:04:07 +0100 3043419 http://www.medworm.com/index.php?rid=3043418&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2271%3Frss%3D1 Fuel ethanol is now a global energy commodity that is competitive with gasoline. Using microarray-based comparative genome hybridization (aCGH), we have determined gene copy number variations (CNVs) common to five industrially important fuel ethanol Saccharomyces cerevisiae strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. These strains have significant amplifications of the telomeric SNO and SNZ genes, which are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that increased copy number of these genes confers the ability to grow more efficiently under the repressing effects of thiamin, especially in medium lacking pyridoxine and with high sugar concentrations. These genetic changes have likely been adap... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043418 Tue, 01 Dec 2009 15:04:07 +0100 3043418 http://www.medworm.com/index.php?rid=3043417&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2258%3Frss%3D1 Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (~2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043417 Tue, 01 Dec 2009 15:04:07 +0100 3043417 http://www.medworm.com/index.php?rid=3043416&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2245%3Frss%3D1 During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae. We found that meiosis-induced opening of chromatin is associated with meiotic DSB hotpots. The positive association between open chromatin and DSB hotspots is most prominent 3 h into meiosis, when the early meiotic genes DMC1 and HOP1 exhibit maximum transcription and the early recombination genes SPO11 and RAD51 are strongly up-regulated. While the degree of chromatin openness is positively assoc... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043416 Tue, 01 Dec 2009 15:04:07 +0100 3043416 http://www.medworm.com/index.php?rid=3043415&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2231%3Frss%3D1 Candida dubliniensis is the closest known relative of Candida albicans, the most pathogenic yeast species in humans. However, despite both species sharing many phenotypic characteristics, including the ability to form true hyphae, C. dubliniensis is a significantly less virulent and less versatile pathogen. Therefore, to identify C. albicans-specific genes that may be responsible for an increased capacity to cause disease, we have sequenced the C. dubliniensis genome and compared it with the known C. albicans genome sequence. Although the two genome sequences are highly similar and synteny is conserved throughout, 168 species-specific genes are identified, including some encoding known hyphal-specific virulence factors, such as the aspartyl proteinases Sap4 and Sap5 and the proposed invasi... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043415 Tue, 01 Dec 2009 15:04:07 +0100 3043415 http://www.medworm.com/index.php?rid=3043414&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2221%3Frss%3D1 In flowering plants, the accumulation of small deletions through unequal homologous recombination (UR) and illegitimate recombination (IR) is proposed to be the major process counteracting genome expansion, which is caused primarily by the periodic amplification of long terminal repeat retrotransposons (LTR-RTs). However, the full suite of evolutionary forces that govern the gain or loss of transposable elements (TEs) and their distribution within a genome remains unclear. Here, we investigated the distribution and structural variation of LTR-RTs in relation to the rates of local genetic recombination (GR) and gene densities in the rice (Oryza sativa) genome. Our data revealed a positive correlation between GR rates and gene densities and negative correlations between LTR-RT densities and ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043414 Tue, 01 Dec 2009 15:04:07 +0100 3043414 http://www.medworm.com/index.php?rid=3043413&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2214%3Frss%3D1 Genomic analyses have shown that adjacent genes are often coexpressed. However, it remains unclear whether the observed coexpression is a result of functional organization or a consequence of adjacent active chromatin or transcriptional read-through, which may be free of selective biases. Here, we compare temporal expression profiles of one-to-one orthologs in conserved or divergent genomic positions in two genetically distant nematode species—Caenorhabditis elegans and C. briggsae—that share a near-identical developmental program. We find, for all major patterns of temporal expression, a substantive amount of gene expression divergence. However, this divergence is not random: Genes that function in essential developmental processes show less divergence than genes whose functio... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043413 Tue, 01 Dec 2009 15:04:07 +0100 3043413 http://www.medworm.com/index.php?rid=3043412&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2202%3Frss%3D1 The Y centromere sequence of house mouse, Mus musculus, remains unknown despite our otherwise significant knowledge of the genome sequence of this important mammalian model organism. Here, we report the complete molecular characterization of the C57BL/6J chromosome Y centromere, which comprises a highly diverged minor satellite-like sequence (designated Ymin) with higher-order repeat (HOR) sequence organization previously undescribed at mouse centromeres. The Ymin array is ~90 kb in length and resides within a single BAC clone that provides sequence information spanning an endogenous animal centromere for the first time. By exploiting direct patrilineal inheritance of the Y chromosome, we demonstrate stability of the Y centromere DNA structure spanning at least 175 inbred generations to be... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043412 Tue, 01 Dec 2009 15:04:07 +0100 3043412 http://www.medworm.com/index.php?rid=3043411&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2193%3Frss%3D1 DNA methylation is an important epigenetic mechanism, affecting normal development and playing a key role in reprogramming epigenomes during stem cell derivation. Here we report on DNA methylation patterns in native monkey embryonic stem cells (ESCs), fibroblasts, and ESCs generated through somatic cell nuclear transfer (SCNT), identifying and comparing epigenome programming and reprogramming. We characterize hundreds of regions that are hyper- or hypomethylated in fibroblasts compared to native ESCs and show that these are conserved in human cells and tissues. Remarkably, the vast majority of these regions are reprogrammed in SCNT ESCs, leading to almost perfect correlation between the epigenomic profiles of the native and reprogrammed lines. At least 58% of these changes are correlated i... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043411 Tue, 01 Dec 2009 15:04:07 +0100 3043411 http://www.medworm.com/index.php?rid=3043410&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2185%3Frss%3D1 Proteins rely on associations to improve packing quality and thus maintain structural integrity. This makes packing deficiency a likely determinant of dosage sensitivity, that is, of the fitness impact of concentration imbalances relative to the stoichiometry of the protein complexes. This hypothesis was validated by examining evolution-related dosage imbalances: Duplicates of genes encoding for deficiently packed proteins are less likely to be retained than genes coding for well-packed proteins. This selection pressure is apparent in unicellular organisms, but is mitigated in higher eukaryotes. In human, this effect reveals a capacitance toward dosage imbalance. This capacitance is not expected in organisms with larger population size, where evolutionary forces are more efficient at promo... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043410 Tue, 01 Dec 2009 15:04:07 +0100 3043410 http://www.medworm.com/index.php?rid=3043409&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2172%3Frss%3D1 The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis-regulatory modules, co-occupancy with other transcription factors, and the effects of histone modifications, are poorly understood. We studied these problems genome-wide in a Gata1 knockout erythroblast cell line that undergoes GATA1-dependent terminal maturation, identifying 2616 GATA1-responsive genes and 15,360 GATA1-occupied DNA segments after restoration of GATA1. Virtually all occupied DNA segments have high levels of H3K4 monomethylation and low levels of H3K27me3 around the canonical GATA binding motif, regardless of whether the nearby gene is induced or repressed. ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043409 Tue, 01 Dec 2009 15:04:07 +0100 3043409 http://www.medworm.com/index.php?rid=3043408&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F12%2F2163%3Frss%3D1 The glucocorticoid steroid hormone cortisol is released by the adrenal glands in response to stress and serves as a messenger in circadian rhythms. Transcriptional responses to this hormonal signal are mediated by the glucocorticoid receptor (GR). We determined GR binding throughout the human genome by using chromatin immunoprecipitation followed by next-generation DNA sequencing, and measured related changes in gene expression with mRNA sequencing in response to the glucocorticoid dexamethasone (DEX). We identified 4392 genomic positions occupied by the GR and 234 genes with significant changes in expression in response to DEX. This genomic census revealed striking differences between gene activation and repression by the GR. While genes activated with DEX treatment have GR bound within a... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043408 Tue, 01 Dec 2009 15:04:07 +0100 3043408 http://www.medworm.com/index.php?rid=3043407&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.095406.109v1%3Frss%3D1 Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruitflies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruitflies, we provide evidence that piRNA can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) piRNAs can signif... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043407 Mon, 30 Nov 2009 19:50:53 +0100 3043407 http://www.medworm.com/index.php?rid=3043406&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096115.109v1%3Frss%3D1 This study describes a new approach for improving ancestral genome reconstruction, the ancestral coevolver (ACE), which utilizes coevolutionary information to improve the accuracy of such reconstructions over previous approaches. The principal idea is to reduce the potentially large solution space by choosing a single optimal (or near optimal) solution that is in accord with the coevolutionary relationships between protein families. Simulation experiments, both on artificial and real biological data, show that ACE yields a marked decrease in error rate compared with ML or MP. Applied to a large data set (95 organisms, 4873 protein families, and 10,000 coevolutionary relationships), some of the ancestral genomes reconstructed by ACE were remarkably different in their gene content from those... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043406 Mon, 30 Nov 2009 16:38:21 +0100 3043406 http://www.medworm.com/index.php?rid=3043405&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099622.109v2%3Frss%3D1 Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subp... Genome Research journals http://www.medworm.com/rss/comments.php?id=3043405 Mon, 30 Nov 2009 16:38:20 +0100 3043405 http://www.medworm.com/index.php?rid=3043404&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100073.109v2%3Frss%3D1 This study identifies an ERV-K-type family in rats that shows obvious signs of recent activity. Ongoing retrotranspositional activity may significantly add to genomic variability among inbred rat strains. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3043404 Mon, 30 Nov 2009 16:38:20 +0100 3043404 http://www.medworm.com/index.php?rid=3028974&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098509.109v2%3Frss%3D1 Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression, and has led to mechanistic hypotheses regarding the rules by which chromatin structure is established. High-throughput sequencing has recently become the technology of choice for chromatin mapping studies, yet analysis of these experiments is still in its infancy. Here, we introduce a pipeline for analyzing deep sequencing maps of chromatin structure and apply it to data from S. cerevisiae. We analyze a digestion series where nucleosomes are isolated from under- and overdigested chromatin. We find that certain classes of nucleosomes are unusually susceptible or resistant to overdigestion, with promoter nucleosomes easily digested and mid-coding re... Genome Research journals http://www.medworm.com/rss/comments.php?id=3028974 Wed, 25 Nov 2009 20:47:31 +0100 3028974 http://www.medworm.com/index.php?rid=3028975&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097857.109v2%3Frss%3D1 Methods for detecting nucleotide substitution rates that are faster or slower than expected under neutral drift are widely used to identify candidate functional elements in genomic sequences. However, most existing methods consider either reductions (conservation) or increases (acceleration) in rate but not both, or assume that selection acts uniformly across the branches of a phylogeny. Here we examine the more general problem of detecting departures from the neutral rate of substitution in either direction, possibly in a clade-specific manner. We consider four statistical, phylogenetic tests for addressing this problem: a likelihood ratio test, a score test, a test based on exact distributions of numbers of substitutions, and the genomic evolutionary rate profiling (GERP) test. All four ... Genome Research journals http://www.medworm.com/rss/comments.php?id=3028975 Wed, 25 Nov 2009 20:47:30 +0100 3028975 http://www.medworm.com/index.php?rid=3025514&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100396.109v2%3Frss%3D1 This study highlights transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation in Bacteria and Archaea. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=3025514 Tue, 24 Nov 2009 14:59:45 +0100 3025514 http://www.medworm.com/index.php?rid=3011261&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097121.109v2%3Frss%3D1 ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces. The "ProPhylER Interface" displays predictive analyses in sequence space; the "CrystalPainter" maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylE... Genome Research journals http://www.medworm.com/rss/comments.php?id=3011261 Thu, 19 Nov 2009 15:57:35 +0100 3011261 http://www.medworm.com/index.php?rid=3011262&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.092114.109v1%3Frss%3D1 Embryonic stem (ES) cells are under precise control of both intrinsic self-renewal gene regulatory network and extrinsic growth factor-triggered signaling cascades. How external signaling pathways connect to core self-renewal transcriptional circuits is largely unknown. To probe this, we chose BMP signaling, which is previously recognized as a master control for both self-renewal and lineage commitment of murine ES cells. Here, we mapped target gene promoter occupancy of SMAD1/5 and SMAD4 on a genome-wide scale and found that they associate with a large group of developmental regulators that are enriched for H3K27 trimethylation and H3K4 trimethylation bivalent marks and are repressed in the self-renewing state, whereas they are rapidly induced upon differentiation. Smad knockdown experime... Genome Research journals http://www.medworm.com/rss/comments.php?id=3011262 Thu, 19 Nov 2009 15:57:34 +0100 3011262 http://www.medworm.com/index.php?rid=3007042&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097212.109v1%3Frss%3D1 Acetaminophen-induced liver toxicity is the most frequent precipitating cause of acute liver failure and liver transplant, but contemporary medical practice has mainly focused on patient management after a liver injury has been induced. An integrative genetic, transcriptional, and two-dimensional NMR-based metabolomic analysis performed using multiple inbred mouse strains, along with knowledge-based filtering of these data, identified betaine-homocysteine methyltransferase 2 (Bhmt2) as a diet-dependent genetic factor that affected susceptibility to acetaminophen-induced liver toxicity in mice. Through an effect on methionine and glutathione biosynthesis, Bhmt2 could utilize its substrate (S-methylmethionine [SMM]) to confer protection against acetaminophen-induced injury in vivo. Since SMM... Genome Research journals http://www.medworm.com/rss/comments.php?id=3007042 Thu, 19 Nov 2009 00:32:52 +0100 3007042 http://www.medworm.com/index.php?rid=3007043&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.093302.109v2%3Frss%3D1 Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq). Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least ~42% of intron-containing genes in Arabidopsis are alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing. Random validation confirm... Genome Research journals http://www.medworm.com/rss/comments.php?id=3007043 Wed, 18 Nov 2009 16:15:52 +0100 3007043 http://www.medworm.com/index.php?rid=2980023&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.099622.109v1%3Frss%3D1 Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (I) monogenomic and (II) polygenomic. Monogenomic tumors appear to contain a single major clonal sub... Genome Research journals http://www.medworm.com/rss/comments.php?id=2980023 Tue, 10 Nov 2009 15:07:27 +0100 2980023 http://www.medworm.com/index.php?rid=2976495&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.091017.109v1%3Frss%3D1 Whereas most nontyphoidal Salmonella (NTS) are associated with gastroenteritis, there has been a dramatic increase in reports of NTS-associated invasive disease in sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multilocus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, which currently is rarely reported outside of Africa. Whole-genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene forma... Genome Research journals http://www.medworm.com/rss/comments.php?id=2976495 Mon, 09 Nov 2009 14:53:21 +0100 2976495 http://www.medworm.com/index.php?rid=2969534&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.094276.109v1%3Frss%3D1 Fuel ethanol is now a global energy commodity that is competitive with gasoline. Using microarray-based comparative genome hybridization (aCGH), we have determined gene copy number variations (CNVs) common to five industrially important fuel ethanol Saccharomyces cerevisiae strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. These strains have significant amplifications of the telomeric SNO and SNZ genes, which are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that increased copy number of these genes confers the ability to grow more efficiently under the repressing effects of thiamin, especially in medium lacking pyridoxine and with high sugar concentrations. These genetic changes have likely been adap... Genome Research journals http://www.medworm.com/rss/comments.php?id=2969534 Fri, 06 Nov 2009 09:01:29 +0100 2969534 http://www.medworm.com/index.php?rid=2966096&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.094060.109v2%3Frss%3D1 The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replicatio... Genome Research journals http://www.medworm.com/rss/comments.php?id=2966096 Thu, 05 Nov 2009 17:32:37 +0100 2966096 http://www.medworm.com/index.php?rid=2957837&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100073.109v1%3Frss%3D1 This study identifies an ERV-K-type family in rats that shows obvious signs of recent activity. Ongoing retrotranspositional activity may significantly add to genomic variability among inbred rat strains. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=2957837 Tue, 03 Nov 2009 22:39:24 +0100 2957837 http://www.medworm.com/index.php?rid=2957840&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096685.109v1%3Frss%3D1 DNA methylation is an important epigenetic mechanism, affecting normal development and playing a key role in reprogramming epigenomes during stem cell derivation. Here we report on DNA methylation patterns in native monkey embryonic stem cells (ESCs), fibroblasts, and ESCs generated through somatic cell nuclear transfer (SCNT), identifying and comparing epigenome programming and reprogramming. We characterize hundreds of regions that are hyper- or hypomethylated in fibroblasts compared to native ESCs and show that these are conserved in human cells and tissues. Remarkably, the vast majority of these regions are reprogrammed in SCNT ESCs, leading to almost perfect correlation between the epigenomic profiles of the native and reprogrammed lines. At least 58% of these changes are correlated i... Genome Research journals http://www.medworm.com/rss/comments.php?id=2957840 Tue, 03 Nov 2009 15:18:40 +0100 2957840 http://www.medworm.com/index.php?rid=2957839&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.097022.109v2%3Frss%3D1 The glucocorticoid steroid hormone cortisol is released by the adrenal glands in response to stress and serves as a messenger in circadian rhythms. Transcriptional responses to this hormonal signal are mediated by the glucocorticoid receptor (GR). We determined GR binding throughout the human genome by using chromatin immunoprecipitation followed by next-generation DNA sequencing, and measured related changes in gene expression with mRNA sequencing in response to the glucocorticoid dexamethasone (DEX). We identified 4392 genomic positions occupied by the GR and 234 genes with significant changes in expression in response to DEX. This genomic census revealed striking differences between gene activation and repression by the GR. While genes activated with DEX treatment have GR bound within a... Genome Research journals http://www.medworm.com/rss/comments.php?id=2957839 Tue, 03 Nov 2009 15:18:40 +0100 2957839 http://www.medworm.com/index.php?rid=2957838&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098921.109v1%3Frss%3D1 The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis-regulatory modules, co-occupancy with other transcription factors, and the effects of histone modifications, are poorly understood. We studied these problems genome-wide in a Gata1 knockout erythroblast cell line that undergoes GATA1-dependent terminal maturation, identifying 2616 GATA1-responsive genes and 15,360 GATA1-occupied DNA segments after restoration of GATA1. Virtually all occupied DNA segments have high levels of H3K4 monomethylation and low levels of H3K27me3 around the canonical GATA binding motif, regardless of whether the nearby gene is induced or repressed. ... Genome Research journals http://www.medworm.com/rss/comments.php?id=2957838 Tue, 03 Nov 2009 15:18:40 +0100 2957838 http://www.medworm.com/index.php?rid=2953619&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096297.109v2%3Frss%3D1 During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the transition from mitosis to meiosis in the budding yeast Saccharomyces cerevisiae. We found that meiosis-induced opening of chromatin is associated with meiotic DSB hotpots. The positive association between open chromatin and DSB hotspots is most prominent 3 h into meiosis, when the early meiotic genes DMC1 and HOP1 exhibit maximum transcription and the early recombination genes SPO11 and RAD51 are strongly up-regulated. While the degree of chromatin openness is positively assoc... Genome Research journals http://www.medworm.com/rss/comments.php?id=2953619 Mon, 02 Nov 2009 18:30:39 +0100 2953619 http://www.medworm.com/index.php?rid=2953618&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.096651.109v2%3Frss%3D1 The Human Microbiome Project (HMP), funded as an initiative of the NIH Roadmap for Biomedical Research (http://nihroadmap.nih.gov), is a multi-component community resource. The goals of the HMP are: (1) to take advantage of new, high-throughput technologies to characterize the human microbiome more fully by studying samples from multiple body sites from each of at least 250 "normal" volunteers; (2) to determine whether there are associations between changes in the microbiome and health/disease by studying several different medical conditions; and (3) to provide both a standardized data resource and new technological approaches to enable such studies to be undertaken broadly in the scientific community. The ethical, legal, and social implications of such research are being systematically st... Genome Research journals http://www.medworm.com/rss/comments.php?id=2953618 Mon, 02 Nov 2009 18:30:38 +0100 2953618 http://www.medworm.com/index.php?rid=2953617&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.098640.109v2%3Frss%3D1 Although a highly accurate sequence of the Caenorhabditis elegans genome has been available for 10 years, the exact transcript structures of many of its protein-coding genes remain unsettled. Approximately two-thirds of the ORFeome has been verified reactively by amplifying and cloning computationally predicted transcript models; still a full third of the ORFeome remains experimentally unverified. To fully identify the protein-coding potential of the worm genome including transcripts that may not satisfy existing heuristics for gene prediction, we developed a computational and experimental platform adapting rapid amplification of cDNA ends (RACE) for large-scale structural transcript annotation. We interrogated 2000 unverified protein-coding genes using this platform. We obtained RACE data... Genome Research journals http://www.medworm.com/rss/comments.php?id=2953617 Mon, 02 Nov 2009 18:30:38 +0100 2953617 http://www.medworm.com/index.php?rid=2953616&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2Fgr.100396.109v1%3Frss%3D1 This study highlights transcriptome sequencing as a key tool for understanding the mechanisms and extent of RNA-based regulation for bacteria and archaea. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=2953616 Mon, 02 Nov 2009 18:25:16 +0100 2953616 http://www.medworm.com/index.php?rid=2950018&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F11%2F2154%3Frss%3D1 The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed a... Genome Research journals http://www.medworm.com/rss/comments.php?id=2950018 Mon, 02 Nov 2009 15:03:32 +0100 2950018 http://www.medworm.com/index.php?rid=2950017&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F11%2F2144%3Frss%3D1 In this study, we use organic matter collected by a moving vehicle to design and test a comprehensive pipeline for phylogenetic profiling of metagenomic samples that includes all steps from processing and quality control of data generated by next-generation sequencing technologies to statistical analyses and data visualization. To the best of our knowledge, this is also the first publication that features a live online supplement providing access to exact analyses and workflows used in the article. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=2950017 Mon, 02 Nov 2009 15:03:32 +0100 2950017 http://www.medworm.com/index.php?rid=2950016&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F11%2F2133%3Frss%3D1 We present a highly accurate gene-prediction system for eukaryotic genomes, called mGene. It combines in an unprecedented manner the flexibility of generalized hidden Markov models (gHMMs) with the predictive power of modern machine learning methods, such as Support Vector Machines (SVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. Considering the average of sensitivity and specificity, the developmental version of mGene exhibited the best prediction performance on nucleotide, exon, and transcript level for ab initio and multiple-genome gene-prediction tasks. The fully developed version shows superior performance in 10 out of 12 evaluation criteria compared with the other participating gene finders, including... Genome Research journals http://www.medworm.com/rss/comments.php?id=2950016 Mon, 02 Nov 2009 15:03:32 +0100 2950016 http://www.medworm.com/index.php?rid=2950015&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F11%2F2125%3Frss%3D1 Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an overview of a genomic region to fine details such as heterogeneity within the sample. A specific problem, particularly if the sample is heterogeneous, is how to depict information about structural variation. LookSeq provides a simple graphical representation of paired sequence reads that is more revealin... Genome Research journals http://www.medworm.com/rss/comments.php?id=2950015 Mon, 02 Nov 2009 15:03:32 +0100 2950015 http://www.medworm.com/index.php?rid=2950014&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Fshort%2F19%2F11%2F2113%3Frss%3D1 Live-cell imaging allows detailed dynamic cellular phenotyping for cell biology and, in combination with small molecule or drug libraries, for high-content screening. Fully automated analysis of live cell movies has been hampered by the lack of computational approaches that allow tracking and recognition of individual cell fates over time in a precise manner. Here, we present a fully automated approach to analyze time-lapse movies of dividing cells. Our method dynamically categorizes cells into seven phases of the cell cycle and five aberrant morphological phenotypes over time. It reliably tracks cells and their progeny and can thus measure the length of mitotic phases and detect cause and effect if mitosis goes awry. We applied our computational scheme to annotate mitotic phenotypes induc... Genome Research journals http://www.medworm.com/rss/comments.php?id=2950014 Mon, 02 Nov 2009 15:03:32 +0100 2950014