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. Thu, 09 Feb 2012 09:43:37 +0100 http://www.medworm.com/index.php?rid=5672433&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129460.111v3%3Frss%3D1 The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integration. Surprisingly, some insertions were found in mitochondrial DNA sequences, presumably reflecting insertion into mitochondrial DNA segments that had migrated to the nucleus. The overwhelming majority of insertions were associated with the 5' regions of Pol III transcribed genes; alignment of Ty1 insertion sites revealed a strong sequence motif centered on but extending beyond the target site duplication. A strong sequence-independent preference for nucleosomal integration... Genome Research journals http://www.medworm.com/rss/comments.php?id=5672433 Wed, 08 Feb 2012 05:00:00 +0100 5672433 http://www.medworm.com/index.php?rid=5672432&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131748.111v2%3Frss%3D1 We describe the use of the method to isolate nuclei from muscle of adult Caenorhabditis elegans and from mesoderm of Drosophila melanogaster embryos. As a case study, we determined expression and nucleosome occupancy profiles for affinity-purified nuclei from C. elegans muscle. We identified hundreds of genes that are specifically expressed in muscle tissues and found that these genes are depleted of nucleosomes at promoters and gene bodies in muscle relative to other tissues. This method should be universally applicable to all model systems that allow transgenesis and will make it possible to determine epigenetic and expression profiles of different tissues and cell types. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5672432 Wed, 08 Feb 2012 05:00:00 +0100 5672432 http://www.medworm.com/index.php?rid=5672431&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.132233.111v2%3Frss%3D1 Developmental genes are regulated by complex, distantly located cis-regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates and among insects. We have investigated GRBs associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million years of independent evolution, Iroquois genes are linked to ankyrin-repeat-containing Sowah genes in nearly all studied bilaterians. We show that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory constraints underlie the maintenance of the Iroquois–Sowah syntenic block. Surprisingly, tetrapod Sowah orthologs are intronless and not associated with Iroquois; however, teleost and elephant shark data demonstrate that this is a derived feature, and that many Iroquois... Genome Research journals http://www.medworm.com/rss/comments.php?id=5672431 Wed, 08 Feb 2012 05:00:00 +0100 5672431 http://www.medworm.com/index.php?rid=5672435&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131029.111v1%3Frss%3D1 Atopic dermatitis (AD) has long been associated with Staphylococcus aureus skin colonization or infection and is typically managed with regimens that include antimicrobial therapies. However, the role of microbial communities in the pathogenesis of AD is incompletely characterized. To assess the relationship between skin microbiota and disease progression, 16S ribosomal RNA bacterial gene sequencing was performed on DNA obtained directly from serial skin sampling of children with AD. The composition of bacterial communities was analyzed during AD disease states to identify characteristics associated with AD flares and improvement post-treatment. We found that microbial community structures at sites of disease predilection were dramatically different in AD patients compared with controls. M... Genome Research journals http://www.medworm.com/rss/comments.php?id=5672435 Mon, 06 Feb 2012 05:00:00 +0100 5672435 http://www.medworm.com/index.php?rid=5672434&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133025.111v1%3Frss%3D1 Adenosine deaminases that act on RNA bind double-stranded and structured RNAs and convert adenosines to inosines by hydrolytic deamination. Inosines are recognized as guanosines and hence, RNA editing alters the sequence information but also structure of RNAs. Editing by ADARs is widespread and essential for normal life and development. Precursors of miRNAs are abundantly edited by ADARs but neither the abundance nor the consequences of miRNA editing has been firmly established. Using transgenic mouse embryos that are deficient in the two enzymatically active editing enzymes ADAR1 and ADAR2 we compare relative frequencies but also sequence composition of miRNAs in these genetically modified backgrounds to wild-type mice by next gen sequencing. Deficiency of ADAR2 leads to a reproducible ch... Genome Research journals http://www.medworm.com/rss/comments.php?id=5672434 Mon, 06 Feb 2012 05:00:00 +0100 5672434 http://www.medworm.com/index.php?rid=5654647&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125864.111v2%3Frss%3D1 Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involvi... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654647 Thu, 02 Feb 2012 05:00:00 +0100 5654647 http://www.medworm.com/index.php?rid=5654646&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127324.111v1%3Frss%3D1 Over the course of ontogenesis, the human brain and human cognitive abilities develop in parallel, resulting in a phenotype strikingly distinct from that of other primates. Here, we used microarrays and RNA-sequencing to examine human-specific gene expression changes taking place during postnatal brain development in the prefrontal cortex and cerebellum of humans, chimpanzees, and rhesus macaques. We show that the most prominent human-specific expression change affects genes associated with synaptic functions and represents an extreme shift in the timing of synaptic development in the prefrontal cortex, but not the cerebellum. Consequently, peak expression of synaptic genes in the prefrontal cortex is shifted from <1 yr in chimpanzees and macaques to 5 yr in humans. This result was supp... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654646 Thu, 02 Feb 2012 05:00:00 +0100 5654646 http://www.medworm.com/index.php?rid=5654645&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129684.111v1%3Frss%3D1 Cancer is a disease driven by genetic variation and mutation. Exome sequencing can be utilized for discovering these variants and mutations across hundreds of tumors. Here we present an analysis tool, VarScan 2, for the detection of somatic mutations and copy number alterations (CNAs) in exome data from tumor–normal pairs. Unlike most current approaches, our algorithm reads data from both samples simultaneously; a heuristic and statistical algorithm detects sequence variants and classifies them by somatic status (germline, somatic, or LOH); while a comparison of normalized read depth delineates relative copy number changes. We apply these methods to the analysis of exome sequence data from 151 high-grade ovarian tumors characterized as part of the Cancer Genome Atlas (TCGA). We valid... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654645 Thu, 02 Feb 2012 05:00:00 +0100 5654645 http://www.medworm.com/index.php?rid=5654644&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131201.111v1%3Frss%3D1 A complex interplay between transcription factors (TFs) and the genome is essential for proper regulation of transcription. However, directly connecting variation in genomic DNA sequence with variation in TF binding and gene expression is challenging due to limited knowledge of where TFs bind and environmental differences between individuals and cell types. To address this problem, we measured genome-wide differential allelic occupancy of 24 sequence-specific TFs and EP300 in a human lymphoblastoid cell line (LCL), GM12878. Overall, 5% of human TF binding sites have an allelic imbalance in occupancy. At many sites, TFs were clustered together on the genome in TF-binding hubs, where they occupied the same homolog in regions of especially open chromatin. While genetic variation in core TF bi... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654644 Thu, 02 Feb 2012 05:00:00 +0100 5654644 http://www.medworm.com/index.php?rid=5654643&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133967.111v1%3Frss%3D1 Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1,265 CNV regions comprising ~55.6 Mbp sequence - 476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with aCGH, qPCR and FISH, achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable gene... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654643 Thu, 02 Feb 2012 05:00:00 +0100 5654643 http://www.medworm.com/index.php?rid=5654675&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F407%3Frss%3D1 Most of the studies characterizing DNA methylation patterns have been restricted to particular genomic loci in a limited number of human samples and pathological conditions. Herein, we present a compromise between an extremely comprehensive study of a human sample population with an intermediate level of resolution of CpGs at the genomic level. We obtained a DNA methylation fingerprint of 1628 human samples in which we interrogated 1505 CpG sites. The DNA methylation patterns revealed show this epigenetic mark to be critical in tissue-type definition and stemness, particularly around transcription start sites that are not within a CpG island. For disease, the generated DNA methylation fingerprints show that, during tumorigenesis, human cancer cells underwent a progressive gain of promoter ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654675 Wed, 01 Feb 2012 05:00:00 +0100 5654675 http://www.medworm.com/index.php?rid=5654674&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F398%3Frss%3D1 Although individual tumors of the same clinical type have surprisingly diverse genomic alterations, these events tend to occur in a limited number of pathways, and alterations that affect the same pathway tend to not co-occur in the same patient. While pathway analysis has been a powerful tool in cancer genomics, our knowledge of oncogenic pathway modules is incomplete. To systematically identify such modules, we have developed a novel method, Mutual Exclusivity Modules in cancer (MEMo). The method uses correlation analysis and statistical tests to identify network modules by three criteria: (1) Member genes are recurrently altered across a set of tumor samples; (2) member genes are known to or are likely to participate in the same biological process; and (3) alteration events within the m... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654674 Wed, 01 Feb 2012 05:00:00 +0100 5654674 http://www.medworm.com/index.php?rid=5654673&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F386%3Frss%3D1 Single variant or single gene analyses generally account for only a small proportion of the phenotypic variation in complex traits. Alternatively, gene set or pathway association analyses are playing an increasingly important role in uncovering genetic architectures of complex traits through the identification of systematic genetic interactions. Two dominant paradigms for gene set analyses are association analyses based on SNP genotypes and those based on gene expression profiles. However, gene–disease association can manifest in many ways, such as alterations of gene expression, genotype, and copy number; thus, an integrative approach combining multiple forms of evidence can more accurately and comprehensively capture pathway associations. We have developed a single statistical fram... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654673 Wed, 01 Feb 2012 05:00:00 +0100 5654673 http://www.medworm.com/index.php?rid=5654672&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F375%3Frss%3D1 Next-generation DNA sequencing technologies are enabling genome-wide measurements of somatic mutations in large numbers of cancer patients. A major challenge in the interpretation of these data is to distinguish functional "driver mutations" important for cancer development from random "passenger mutations." A common approach for identifying driver mutations is to find genes that are mutated at significant frequency in a large cohort of cancer genomes. This approach is confounded by the observation that driver mutations target multiple cellular signaling and regulatory pathways. Thus, each cancer patient may exhibit a different combination of mutations that are sufficient to perturb these pathways. This mutational heterogeneity presents a problem for predicting driver mutations solely from... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654672 Wed, 01 Feb 2012 05:00:00 +0100 5654672 http://www.medworm.com/index.php?rid=5654671&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F362%3Frss%3D1 During tumor initiation and progression, cancer cells acquire a selective advantage, allowing them to outcompete their normal counterparts. Identification of the genetic changes that underlie these tumor acquired traits can provide deeper insights into the biology of tumorigenesis. Regions of copy number alterations and germline DNA variants are some of the elements subject to selection during tumor evolution. Integrated examination of inherited variation and somatic alterations holds the potential to reveal specific nucleotide alleles that a tumor "prefers" to have amplified. Next-generation sequencing of tumor and matched normal tissues provides a high-resolution platform to identify and analyze such somatic amplicons. Within an amplicon, examination of informative (e.g., heterozygous) s... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654671 Wed, 01 Feb 2012 05:00:00 +0100 5654671 http://www.medworm.com/index.php?rid=5654670&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F346%3Frss%3D1 Cancer genomes are complex, carrying thousands of somatic mutations including base substitutions, insertions and deletions, rearrangements, and copy number changes that have been acquired over decades. Recently, technologies have been introduced that allow generation of high-resolution, comprehensive catalogs of somatic alterations in cancer genomes. However, analyses of these data sets generally do not indicate the order in which mutations have occurred, or the resulting karyotype. Here, we introduce a mathematical framework that begins to address this problem. By using samples with accurate data sets, we can reconstruct relatively complex temporal sequences of rearrangements and provide an assembly of genomic segments into digital karyotypes. For cancer genes mutated in rearranged region... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654670 Wed, 01 Feb 2012 05:00:00 +0100 5654670 http://www.medworm.com/index.php?rid=5654669&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F340%3Frss%3D1 Genetic testing for disease risk is an increasingly important component of medical care. However, testing can be expensive, which can lead to patients and physicians having limited access to the genetic information needed for medical decisions. To simplify DNA sample preparation and lower costs, we have developed a system in which any gene can be captured and sequenced directly from human genomic DNA without amplification, using no proteins or enzymes prior to sequencing. Extracted whole-genome DNA is acoustically sheared and loaded in a flow cell channel for single-molecule sequencing. Gene isolation, amplification, or ligation is not necessary. Accurate and low-cost detection of DNA sequence variants is demonstrated for the BRCA1 gene. Disease-causing mutations as well as common variants... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654669 Wed, 01 Feb 2012 05:00:00 +0100 5654669 http://www.medworm.com/index.php?rid=5654668&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F332%3Frss%3D1 Radiation exposure through environmental, medical, and occupational settings is increasingly common. While radiation has harmful effects, it has utility in many applications such as radiotherapy for cancer. To increase the efficacy of radiation treatment and minimize its risks, a better understanding of the individual differences in radiosensitivity and the molecular basis of radiation response is needed. Here, we integrated human genetic and functional genomic approaches to study the response of human cells to radiation. We measured radiation-induced changes in gene expression and cell death in B cells from normal individuals. We found extensive individual variation in gene expression and cellular responses. To understand the genetic basis of this variation, we mapped the DNA sequence var... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654668 Wed, 01 Feb 2012 05:00:00 +0100 5654668 http://www.medworm.com/index.php?rid=5654667&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F322%3Frss%3D1 Androgen receptor (AR) is a hormone-activated transcription factor that plays important roles in prostate development and function, as well as malignant transformation. The downstream pathways of AR, however, are incompletely understood. AR has been primarily known as a transcriptional activator inducing prostate-specific gene expression. Through integrative analysis of genome-wide AR occupancy and androgen-regulated gene expression, here we report AR as a globally acting transcriptional repressor. This repression is mediated by androgen-responsive elements (ARE) and dictated by Polycomb group protein EZH2 and repressive chromatin remodeling. In embryonic stem cells, AR-repressed genes are occupied by EZH2 and harbor bivalent H3K4me3 and H3K27me3 modifications that are characteristic of di... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654667 Wed, 01 Feb 2012 05:00:00 +0100 5654667 http://www.medworm.com/index.php?rid=5654666&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F307%3Frss%3D1 Histone H2A.Z (H2A.Z) is an evolutionarily conserved H2A variant implicated in the regulation of gene expression; however, its role in transcriptional deregulation in cancer remains poorly understood. Using genome-wide studies, we investigated the role of promoter-associated H2A.Z and acetylated H2A.Z (acH2A.Z) in gene deregulation and its relationship with DNA methylation and H3K27me3 in prostate cancer. Our results reconcile the conflicting reports of positive and negative roles for histone H2A.Z and gene expression states. We find that H2A.Z is enriched in a bimodal distribution at nucleosomes, surrounding the transcription start sites (TSSs) of both active and poised gene promoters. In addition, H2A.Z spreads across the entire promoter of inactive genes in a deacetylated state. In cont... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654666 Wed, 01 Feb 2012 05:00:00 +0100 5654666 http://www.medworm.com/index.php?rid=5654665&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F299%3Frss%3D1 An estimated 15% or more of the cancer burden worldwide is attributable to known infectious agents. We screened colorectal carcinoma and matched normal tissue specimens using RNA-seq followed by host sequence subtraction and found marked over-representation of Fusobacterium nucleatum sequences in tumors relative to control specimens. F. nucleatum is an invasive anaerobe that has been linked previously to periodontitis and appendicitis, but not to cancer. Fusobacteria are rare constituents of the fecal microbiota, but have been cultured previously from biopsies of inflamed gut mucosa. We obtained a Fusobacterium isolate from a frozen tumor specimen; this showed highest sequence similarity to a known gut mucosa isolate and was confirmed to be invasive. We verified overabundance of Fusobacter... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654665 Wed, 01 Feb 2012 05:00:00 +0100 5654665 http://www.medworm.com/index.php?rid=5654664&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F292%3Frss%3D1 The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbiota is the least well understood. We have characterized the composition of the microbiota in colorectal carcinoma using whole genome sequences from nine tumor/normal pairs. Fusobacterium sequences were enriched in carcinomas, confirmed by quantitative PCR and 16S rDNA sequence analysis of 95 carcinoma/normal DNA pairs, while the Bacteroidetes and Firmicutes phyla were depleted in tumors. Fusobacteria were also visualized within colorectal tumors using FISH. These findings reveal alterations in the colorectal cancer microbiota; ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654664 Wed, 01 Feb 2012 05:00:00 +0100 5654664 http://www.medworm.com/index.php?rid=5654663&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F283%3Frss%3D1 A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to b... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654663 Wed, 01 Feb 2012 05:00:00 +0100 5654663 http://www.medworm.com/index.php?rid=5654662&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F271%3Frss%3D1 Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. Here we performed comprehensive genome-scale DNA methylation profiling of 125 colorectal tumors and 29 adjacent normal tissues. We identified four DNA methylation–based subgroups of CRC using model-based cluster analyses. Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups. A CIMP-high (CIMP-H) subgroup, which exhibits an exceptionally high frequency of cancer-specific DNA hypermethylation, is strongly associated with MLH1 DNA hypermethylation and the BRAFV600E mutation. A CIMP-low (CIMP-L) subgroup is enriched for KRAS mutations and characterized by DNA hypermethylatio... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654662 Wed, 01 Feb 2012 05:00:00 +0100 5654662 http://www.medworm.com/index.php?rid=5654661&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F259%3Frss%3D1 Chromosomal translocations involving transcription factor genes have been identified in an increasingly wide range of cancers. Some translocations can create a protein "chimera" that is composed of parts from different proteins. How such chimeras cause cancer, and why they cause cancer in some cell types but not others, is not understood. One such chimera is EWS–FLI, the most frequently occurring translocation in Ewing Sarcoma, a malignant bone and soft tissue tumor of children and young adults. Using EWS–FLI and its parental transcription factor, FLI1, we created a unique experimental system to address questions regarding the genomic mechanisms by which chimeric transcription factors cause cancer. We found that in tumor cells, EWS–FLI targets regions of the genome distin... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654661 Wed, 01 Feb 2012 05:00:00 +0100 5654661 http://www.medworm.com/index.php?rid=5654660&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F246%3Frss%3D1 While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these re... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654660 Wed, 01 Feb 2012 05:00:00 +0100 5654660 http://www.medworm.com/index.php?rid=5654659&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F232%3Frss%3D1 DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood. Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage–fusion–bridge (BFB) cycle. Therefore, palindromes might be associated with gene amplicons in breast cancer. To address this possibility, we coupled high-resolution palindrome profiling by the Genome-wide Analysis of Palindrome Formation (GAPF) assay with genome-wide copy-number analyses on a set of breast cancer cell lines and primary tumors to spatially associate palindromes and c... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654659 Wed, 01 Feb 2012 05:00:00 +0100 5654659 http://www.medworm.com/index.php?rid=5654658&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F220%3Frss%3D1 Biomarkers in breast cancer to monitor minimal residual disease have remained elusive. We hypothesized that genomic analysis of circulating free DNA (cfDNA) isolated from plasma may form the basis for a means of detecting and monitoring breast cancer. We profiled 251 genomes using Affymetrix SNP 6.0 arrays to determine copy number variations (CNVs) and loss of heterozygosity (LOH), comparing 138 cfDNA samples with matched primary tumor and normal leukocyte DNA in 65 breast cancer patients and eight healthy female controls. Concordance of SNP genotype calls in paired cfDNA and leukocyte DNA samples distinguished between breast cancer patients and healthy female controls (P < 0.0001) and between preoperative patients and patients on follow-up who had surgery and treatment (P = 0.0016). Pr... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654658 Wed, 01 Feb 2012 05:00:00 +0100 5654658 http://www.medworm.com/index.php?rid=5654657&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F208%3Frss%3D1 This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they s... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654657 Wed, 01 Feb 2012 05:00:00 +0100 5654657 http://www.medworm.com/index.php?rid=5654656&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F196%3Frss%3D1 Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational rates in this acral melanoma sample pair were more comparable to the rates reported in cancer genomes not associated with mutagenic exposure than in the genome of a melanoma cell line or the transcriptome of melanoma short-term cultures. Despite the perception that acral skin is sun-protected, the dominant mutational signature in these samples is compatible with damage due to ultraviolet light exposure. A nonsense mutation in ERCC5 discovered in both the primary and metastatic tumors could also h... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654656 Wed, 01 Feb 2012 05:00:00 +0100 5654656 http://www.medworm.com/index.php?rid=5654655&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F188%3Frss%3D1 The genomics era has yielded great advances in the understanding of cancer biology. At the same time, the immense complexity of the cancer genome has been revealed, as well as a striking heterogeneity at the whole-genome (or omics) level that exists between even histologically similar tumors. The vast accrual and public availability of multi-omics databases with associated clinical annotation including tumor histology, patient response, and outcome are a rich resource that has the potential to lead to rapid translation of high-throughput omics to improved overall survival. We focus on the unique advantages of a multidimensional approach to genomic analysis in this new high-throughput omics age and discuss the implications of the changing cancer demographic to translational omics research. ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654655 Wed, 01 Feb 2012 05:00:00 +0100 5654655 http://www.medworm.com/index.php?rid=5654654&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F183%3Frss%3D1 Early detection and definitive treatment of cancer have been shown to decrease death and suffering in epidemiologic and intervention studies. Application of genomic approaches to many malignancies has produced thousands of candidate biomarkers for detection and prognostication, yet very few have become established in clinical practice. Fundamental issues related to tumor heterogeneity, cancer progression, natural history, and biomarker performance have provided challenges to biomarker development. Technical issues in biomarker assay detection limits, specificity, clinical deployment, and regulation have also slowed progress. The recent emergence of biomarkers and molecular imaging strategies for treatment selection and monitoring demonstrates the promise of cancer biomarkers. Organized eff... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654654 Wed, 01 Feb 2012 05:00:00 +0100 5654654 http://www.medworm.com/index.php?rid=5654653&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F2%2F177%3Frss%3D1 (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5654653 Wed, 01 Feb 2012 05:00:00 +0100 5654653 http://www.medworm.com/index.php?rid=5654649&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125187.111v1%3Frss%3D1 DNA methylation (DNAm) plays diverse roles in human biology, but this dynamic epigenetic mark remains far from fully characterized. Although earlier studies uncovered loci that undergo age-associated DNAm changes in adults, little is known about such changes during childhood. Despite profound DNAm plasticity during embryogenesis, monozygotic twins show indistinguishable childhood methylation, suggesting DNAm is highly coordinated throughout early development. Here we examine the methylation of 27,578 CpG dinucleotides in peripheral blood DNA from a cross-sectional study of 398 boys, aged 3 to 17 years, and find significant age-associated changes in DNAm at 2,078 loci. These findings correspond well with pyrosequencing data and replicate in a second pediatric population (N=78). Moreover, we... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654649 Wed, 01 Feb 2012 05:00:00 +0100 5654649 http://www.medworm.com/index.php?rid=5654648&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133850.111v1%3Frss%3D1 In the process of clone-based genome sequencing, initial assemblies frequently contain cloning gaps that can be resolved using cloning-independent methods, but the reason for their occurrence is largely unknown. By analyzing 9,328,693 sequencing clones from 393 microbial genomes we systematically mapped more than 15,000 genes residing in cloning gaps and experimentally showed that their expression products are toxic to the Escherichia coli host. A subset of these toxic sequences was further evaluated through a series of functional assays exploring the mechanisms of their toxicity. Among these genes our assays revealed novel toxins and restriction enzymes, and new classes of small non-coding toxic RNAs that reproducibly inhibit E. coli growth. Further analyses also revealed abundant, short ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654648 Wed, 01 Feb 2012 05:00:00 +0100 5654648 http://www.medworm.com/index.php?rid=5654652&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.128678.111v1%3Frss%3D1 Extensively drug resistant tuberculosis (XDR TB), which is resistant to both first- and second-line antibiotics, is an escalating problem, particularly in the Russian Federation. Molecular fingerprinting of 2,348 Mycobacterium tuberculosis isolates collected in Samara Oblast, Russia revealed that 72% belonged to the Beijing lineage, a genotype associated with enhanced acquisition of drug resistance and increased virulence. Whole genome sequencing of 34 Samaran isolates, plus 25 isolates representing global M. tuberculosis complex diversity, revealed that Beijing isolates originating in Eastern Europe formed a monophyletic group. Homoplasic polymorphisms within this clade were almost invariably associated with antibiotic resistance, indicating that evolution of this population is primarily ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654652 Tue, 31 Jan 2012 05:00:00 +0100 5654652 http://www.medworm.com/index.php?rid=5654651&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129585.111v2%3Frss%3D1 Ty1, the most abundant retrotransposon in Saccharomyces cerevisiae, integrates preferentially upstream of genes transcribed by RNA polymerase III (Pol III). Targeting is likely due to interactions between the Ty1 integration complex and a feature of chromatin characteristic of sites of Pol III transcription. To better understand Ty1 targeting determinants, >150,000 Ty1 insertions were mapped onto the S. cerevisiae genome sequence. Logistic regression was used to assess relationships between patterns of Ty1 integration and various genomic features, including genome-wide data sets of histone modifications and transcription-factor binding sites. Nucleosomes were positively associated with Ty1 insertions, and fine-scale mapping of insertions upstream of genes transcribed by Pol III indicate... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654651 Tue, 31 Jan 2012 05:00:00 +0100 5654651 http://www.medworm.com/index.php?rid=5654650&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.130468.111v3%3Frss%3D1 In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes who... Genome Research journals http://www.medworm.com/rss/comments.php?id=5654650 Tue, 31 Jan 2012 05:00:00 +0100 5654650 http://www.medworm.com/index.php?rid=5642405&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.130286.111v1%3Frss%3D1 The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ~40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III ge... Genome Research journals http://www.medworm.com/rss/comments.php?id=5642405 Fri, 27 Jan 2012 05:00:00 +0100 5642405 http://www.medworm.com/index.php?rid=5642404&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131219.111v1%3Frss%3D1 Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. In order to determine the extent to which other Pol III-transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III-transcribed types of gen... Genome Research journals http://www.medworm.com/rss/comments.php?id=5642404 Fri, 27 Jan 2012 05:00:00 +0100 5642404 http://www.medworm.com/index.php?rid=5642403&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.132647.111v1%3Frss%3D1 Evolutionary rate covariation (ERC) is a phylogenetic signature that reflects the covariation of a pair of proteins over evolutionary time. ERC is typically elevated between interacting proteins, and so is a promising signature to characterize molecular and functional interactions across the genome. ERC is often assumed to result from compensatory changes at interaction interfaces (i.e. intermolecular coevolution); however, its origin is still unclear and is likely to be complex. Here, we determine the biological factors responsible for ERC in a proteome-wide dataset of 4,459 proteins in 18 budding yeast species. We show that direct physical interaction is not required to produce ERC, because we observe strong correlations between non-interacting but co-functional enzymes. We also demonstr... Genome Research journals http://www.medworm.com/rss/comments.php?id=5642403 Fri, 27 Jan 2012 05:00:00 +0100 5642403 http://www.medworm.com/index.php?rid=5633753&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.128652.111v2%3Frss%3D1 Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of the pigment gene OCA2, and the region surrounding rs12913832 is highly conserved among animal species. However, the exact functional role of HERC2 rs12913832 in human pigmentation is unknown. Here we demonstrate that the HERC2 rs12913832 region functions as an enhancer regulating OCA2 transcription. In darkly pigmented human melanocytes carrying the rs12913832 T-allele, we detected binding of the transcription factors HLTF, LEF1, and MITF to the HERC2 rs12913832 enhancer, and... Genome Research journals http://www.medworm.com/rss/comments.php?id=5633753 Thu, 26 Jan 2012 05:00:00 +0100 5633753 http://www.medworm.com/index.php?rid=5633752&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.128819.111v2%3Frss%3D1 In this study, we analyzed the evolutionary trajectories of 583 literature-derived and 50,000 computationally predicted human TK circuits in 19 representative eukaryotic species and assigned their evolutionary origins. We found that human TK circuits for intracellular pTyr signaling originated largely from primitive organisms, whereas the inter- or extracellular signaling circuits experienced significant expansion in the bilaterian lineage through the "back-wiring" of newly evolved kinases to primitive substrates and SH2/PTB domains. Conversely, the TK circuits that are involved in tissue-specific signaling evolved mainly in vertebrates by the back-wiring of vertebrate substrates to primitive kinases and SH2/PTB domains. Importantly, we found that cancer signaling preferentially employs th... Genome Research journals http://www.medworm.com/rss/comments.php?id=5633752 Thu, 26 Jan 2012 05:00:00 +0100 5633752 http://www.medworm.com/index.php?rid=5633751&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129213.111v1%3Frss%3D1 A combinatorial genetic perturbation strategy was applied to interrogate the yeast kinome on a genome-wide scale. We assessed the global effects of gene overexpression or gene deletion to map an integrated genetic interaction network of Synthetic Dosage Lethal (SDL) and loss-of-function genetic interactions (GIs) for 92 kinases, producing a meta-network of 8,700 GIs enriched for pathways known to be regulated by cognate kinases. Kinases most sensitive to dosage perturbations had constitutive cell cycle or cell polarity functions under standard growth conditions. Condition-specific screens confirmed that the spectrum of kinase dosage interactions can be expanded substantially in activating conditions. An integrated network composed of systematic SDL, negative and positive loss-of-function G... Genome Research journals http://www.medworm.com/rss/comments.php?id=5633751 Thu, 26 Jan 2012 05:00:00 +0100 5633751 http://www.medworm.com/index.php?rid=5633754&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126201.111v2%3Frss%3D1 Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by about 1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. nanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel noncoding RNAs including antisense transcripts. We identified candidate transcription fact... Genome Research journals http://www.medworm.com/rss/comments.php?id=5633754 Tue, 24 Jan 2012 05:00:00 +0100 5633754 http://www.medworm.com/index.php?rid=5623720&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.123901.111v1%3Frss%3D1 Gene phylogenies provide a rich source of information about the way evolution shapes genomes, populations, and phenotypes. In addition to substitutions, evolutionary events such as gene duplication and loss (as well as horizontal transfer) play a major role in gene evolution, and many phylogenetic models have been developed in order to reconstruct and study these events. However, these models typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. While this assumption may have been reasonable in some settings, it has become increasingly problematic as increased genome sequencing has led to denser phylogenies, where effects such as ILS are more prominent. To address this challenge, we present a new probabilistic mod... Genome Research journals http://www.medworm.com/rss/comments.php?id=5623720 Mon, 23 Jan 2012 05:00:00 +0100 5623720 http://www.medworm.com/index.php?rid=5623719&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126953.111v2%3Frss%3D1 We describe algorithms to error-correct, assemble, and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95% of the reference genome (excluding contigs <200 bp in length). Because of the low memory requirements and parallelization without requiring inter-process communication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome on a low-end computing cluster. (Source: Genom... Genome Research journals http://www.medworm.com/rss/comments.php?id=5623719 Mon, 23 Jan 2012 05:00:00 +0100 5623719 http://www.medworm.com/index.php?rid=5623718&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133645.111v2%3Frss%3D1 The identification of the molecular events that drive cancer transformation is essential to the development of targeted agents that improve the clinical outcome of lung cancer. Many studies have reported genomic driver mutations in non-small-cell lung cancers (NSCLCs) over the past decade; however, the molecular pathogenesis of >40% of NSCLCs is still unknown. To identify new molecular targets in NSCLCs, we performed the combined analysis of massively parallel whole-genome and transcriptome sequencing for cancer and paired normal tissue of a 33-yr-old lung adenocarcinoma patient, who is a never-smoker and has no familial cancer history. The cancer showed no known driver mutation in EGFR or KRAS and no EML4-ALK fusion. Here we report a novel fusion gene between KIF5B and the RET proto-on... Genome Research journals http://www.medworm.com/rss/comments.php?id=5623718 Mon, 23 Jan 2012 05:00:00 +0100 5623718 http://www.medworm.com/index.php?rid=5615581&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.128124.111v1%3Frss%3D1 We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at cost of about $15 per sample. These libraries are effective not only for low-pass whole genome sequencing, but also for simultaneously enriching them in pools of approximately hundred individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2,000 samples from a prostate cancer study. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5615581 Fri, 20 Jan 2012 05:00:00 +0100 5615581 http://www.medworm.com/index.php?rid=5615580&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133926.111v1%3Frss%3D1 Hepatitis B virus (HBV) infection is a leading risk factor for hepatocellular carcinoma (HCC). HBV integration into the host genome has been reported but its scale, impact and contribution to HCC development is not clear. Here, we sequenced the tumor and non-tumor genomes (>80X coverage) and transcriptomes of four HCC patients and identified 255 HBV integration sites. Increased sequencing to 240X coverage revealed a proportionally higher number of integration sites. Clonal expansion of HBV-integrated hepatocytes was found specifically in tumor samples. We observe a diverse collection of genomic perturbations near viral integration sites, including direct gene disruption, viral promoter-driven human transcription, viral-human transcript fusion and DNA copy number alteration. Thus, we rep... Genome Research journals http://www.medworm.com/rss/comments.php?id=5615580 Fri, 20 Jan 2012 05:00:00 +0100 5615580 http://www.medworm.com/index.php?rid=5590832&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.130682.111v1%3Frss%3D1 Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. Analyzing chromatin immunoprecipitation datasets from 21 sequence-specific transcription factors active in the Drosophila embryo, we found that binding of all factors exhibits a dose-dependent relationship with "TAGteam" sequence motifs bound by the zinc-finger protein Vielfaltig, also known as Zelda, a recently discovered activator of the zygotic genome. TAGteam motifs are present and well-conserved in highly bound regions, and are associated with transcription factor binding even in the absence of canonical recognition motifs for these factors. Furthermore, levels of bindin... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590832 Fri, 13 Jan 2012 05:00:00 +0100 5590832 http://www.medworm.com/index.php?rid=5590833&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131383.111v3%3Frss%3D1 In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely and is not well correlated with statistics on contiguity. To enable others to replicate our results... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590833 Thu, 12 Jan 2012 05:00:00 +0100 5590833 http://www.medworm.com/index.php?rid=5590835&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.128652.111v1%3Frss%3D1 Pigmentation of skin, eye and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified, and the SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the non-pigment gene HERC2, 21 kb upstream of the pigment gene OCA2, and the region surrounding rs12913832 is highly conserved among animal species. However, the exact functional role of HERC2 rs12913832 in human pigmentation is unknown. Here we demonstrate that the HERC2 rs12913832 region functions as an enhancer regulating OCA2 transcription. In darkly pigmented human melanocytes carrying the rs12913832 T-allele, we detected binding of the transcription factors HLTF, LEF1 and MITF to the HERC2 rs12913832 enhancer, ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590835 Tue, 10 Jan 2012 05:00:00 +0100 5590835 http://www.medworm.com/index.php?rid=5590834&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.132233.111v1%3Frss%3D1 Developmental genes are regulated by complex, distantly located, cis-regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates and among insects. We have investigated GRBs associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million years of independent evolution, Iroquois genes are linked to ankyrin-repeat containing Sowah genes in nearly all studied bilaterians. We show that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory constraints underlie the maintenance of the Iroquois-Sowah syntenic block. Surprisingly, tetrapod Sowah orthologs are intronless and not associated with Iroquois, however, teleost and elephant shark data demonstrate that this is a derived feature and that many Iroquois-CRMs ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590834 Tue, 10 Jan 2012 05:00:00 +0100 5590834 http://www.medworm.com/index.php?rid=5590839&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.121897.111v2%3Frss%3D1 Insertions and deletions (indels), together with nucleotide substitutions, are major drivers of sequence evolution. An excess of deletions over insertions in genomic sequences—the so-called deletional bias—has been reported in a wide range of species, including mammals. However, this bias has not been found in the coding sequences of some mammalian species, such as human and mouse. To determine the strength of the deletional bias in mammals, and the influence of mutation and selection, we have quantified indels in both neutrally evolving noncoding sequences and protein-coding sequences, in six mammalian branches: human, macaque, ancestral primate, mouse, rat, and ancestral rodent. The results obtained with an improved algorithm for the placement of insertions in multiple alignm... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590839 Mon, 09 Jan 2012 05:00:00 +0100 5590839 http://www.medworm.com/index.php?rid=5590838&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127845.111v2%3Frss%3D1 There is an emerging consensus that when investigators obtain genomic data from research participants, they may incur an ethical responsibility to inform at-risk individuals about clinically significant variants discovered during the course of their research. With whole-exome sequencing becoming commonplace and the falling costs of full-genome sequencing, there will be an increasingly large number of variants identified in research participants that may be of sufficient clinical relevance to share. An explicit approach to triaging and communicating these results has yet to be developed, and even the magnitude of the task is uncertain. To develop an estimate of the number of variants that might qualify for disclosure, we apply recently published recommendations for the return of results to ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590838 Mon, 09 Jan 2012 05:00:00 +0100 5590838 http://www.medworm.com/index.php?rid=5590837&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129460.111v2%3Frss%3D1 The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions lying upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integration. Surprisingly, some insertions were found in mitochondrial DNA sequences, presumably reflecting insertion into mitochondrial DNA segments that had migrated to the nucleus. The overwhelming majority of insertions were associated with the 5' regions of Pol III transcribed genes; alignment of Ty1 insertion sites revealed a strong sequence motif centered on but extending beyond the target site duplication. A strong sequence-independent preference for nucleosomal integ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590837 Mon, 09 Jan 2012 05:00:00 +0100 5590837 http://www.medworm.com/index.php?rid=5590836&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133009.111v2%3Frss%3D1 Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time-series of RNA-seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1133 noncoding multi-exonic transcripts expressed duri... Genome Research journals http://www.medworm.com/rss/comments.php?id=5590836 Mon, 09 Jan 2012 05:00:00 +0100 5590836 http://www.medworm.com/index.php?rid=5575505&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131383.111v2%3Frss%3D1 In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic affect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely, and is not well correlated with statistics on contiguity. In order to enable others to replicate o... Genome Research journals http://www.medworm.com/rss/comments.php?id=5575505 Fri, 06 Jan 2012 05:00:00 +0100 5575505 http://www.medworm.com/index.php?rid=5567063&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129460.111v1%3Frss%3D1 The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions lying upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integration. Surprisingly, some insertions were found in mitochondrial DNA sequences, presumably reflecting insertion into mitochondrial DNA segments that had migrated to the nucleus. The overwhelming majority of insertions were associated with the 5' regions of Pol III transcribed genes; alignment of Ty1 insertion sites revealed a strong sequence motif centered on but extending beyond the target site duplication. A strong sequence-independent preference for nucleosomal integ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567063 Wed, 04 Jan 2012 05:00:00 +0100 5567063 http://www.medworm.com/index.php?rid=5567062&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129585.111v1%3Frss%3D1 Ty1, the most abundant retrotransposon in Saccharomyces cerevisiae, integrates preferentially upstream of genes transcribed by RNA polymerase III (Pol III). Targeting is likely due to interactions between the Ty1 integration complex and a feature of chromatin characteristic of sites of Pol III transcription. To better understand Ty1 targeting determinants, >150,000 Ty1 insertions were mapped onto the S. cerevisiae genome sequence. Logistic regression was used to assess relationships between patterns of Ty1 integration and various genomic features, including genome-wide datasets of histone modifications and transcription factor binding sites. Nucleosomes were positively associated with Ty1 insertions, and fine-scale mapping of insertions upstream of genes transcribed by Pol III indicate... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567062 Wed, 04 Jan 2012 05:00:00 +0100 5567062 http://www.medworm.com/index.php?rid=5567061&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131748.111v1%3Frss%3D1 We describe the use of the method to isolate nuclei from muscle of adult Caenorhabditis elegans and from mesoderm of Drosophila melanogaster embryos. As a case study, we determined expression and nucleosome occupancy profiles for affinity-purified nuclei from C. elegans muscle. We identified hundreds of genes that are specifically expressed in muscle tissues and found that these genes are depleted of nucleosomes at promoters and gene bodies in muscle relative to other tissues. This method should be universally applicable to all model systems that allow transgenesis and will make it possible to determine epigenetic and expression profiles of different tissues and cell-types. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5567061 Wed, 04 Jan 2012 05:00:00 +0100 5567061 http://www.medworm.com/index.php?rid=5567080&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F163%3Frss%3D1 We present small RNA data sets comprising more than 200 million aligned Illumina sequence reads covering all major cell types of the root as well as four distinct developmental zones. MicroRNAs (miRNAs) constitute a class of small ncRNAs that are particularly important for development. Of the 243 known miRNAs, 133 were found to be expressed in the root, and most showed tissue- or zone-specific expression patterns. We identified 66 new high-confidence miRNAs using a computational pipeline, PIPmiR, specifically developed for the identification of plant miRNAs. PIPmiR uses a probabilistic model that combines RNA structure and expression information to identify miRNAs with high precision. Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming th... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567080 Tue, 03 Jan 2012 05:00:00 +0100 5567080 http://www.medworm.com/index.php?rid=5567079&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F151%3Frss%3D1 Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in the callus than in the seedling. For DH sites detected in both the seedling and callus, 31% displayed significantly different levels of DNase I sensitivity... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567079 Tue, 03 Jan 2012 05:00:00 +0100 5567079 http://www.medworm.com/index.php?rid=5567078&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F142%3Frss%3D1 RNA editing enhances the diversity of gene products at the post-transcriptional level. Approaches for genome-wide identification of RNA editing face two main challenges: separating true editing sites from false discoveries and accurate estimation of editing levels. We developed an approach to analyze transcriptome sequencing data (RNA-seq) for global identification of RNA editing in cells for which whole-genome sequencing data are available. We applied the method to analyze RNA-seq data of a human glioblastoma cell line, U87MG. Around 10,000 DNA–RNA differences were identified, the majority being putative A-to-I editing sites. These predicted A-to-I events were associated with a low false-discovery rate (~5%). Moreover, the estimated editing levels from RNA-seq correlated well with t... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567078 Tue, 03 Jan 2012 05:00:00 +0100 5567078 http://www.medworm.com/index.php?rid=5567077&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F134%3Frss%3D1 RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA (~1 ng of total RNA) with this approach. We also present a strand-specific RNA-seq library construction protocol that combines transposon-based library construction with uracil DNA glycosylase and endonuclease VIII to specifically degrade the second strand constructed during cDNA synthesis. The dire... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567077 Tue, 03 Jan 2012 05:00:00 +0100 5567077 http://www.medworm.com/index.php?rid=5567076&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F125%3Frss%3D1 We describe how sequencing libraries can be reproducibly created from 20 pg of input DNA using a modified transpososome-mediated fragmentation technique. Resulting libraries incorporate in-line bar-coding, which facilitates sample multiplexes that can be sequenced using Illumina platforms with the manufacturer's sequencing primer. We demonstrate this technique by providing deep coverage sequence of the Escherichia coli K-12 genome that shows equivalent target coverage to a 1-μg input library prepared using standard Illumina methods. Reducing template quantity does, however, increase the proportion of duplicate reads and enriches coverage in low-GC regions. This finding was confirmed with exhaustive resequencing of a mouse library constructed from 20 pg of gDNA input (about seven haploid... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567076 Tue, 03 Jan 2012 05:00:00 +0100 5567076 http://www.medworm.com/index.php?rid=5567075&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F115%3Frss%3D1 Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in dairy environments, and it is proposed that dairy strains originate from the plant niche. Here we investigate the adaptation of a L. lactis strain isolated from a plant to a dairy niche by propagating it for 1000 generations in milk. Two out of three independently evolved strains displayed significantly increased acidification rates and biomass yields in milk. Genome resequencing, revealed six, seven, and 28 mutations in the three strains, including point mutations in loci related to amino aci... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567075 Tue, 03 Jan 2012 05:00:00 +0100 5567075 http://www.medworm.com/index.php?rid=5567074&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F106%3Frss%3D1 In this study, two strains of the endosymbiont Regiella insecticola (R. insecticola 5.15 and R. insecticola LSR1) were found to differ in ability to protect pea aphids attacked by the parasitoid Aphidius ervi. Parasitism trials reveal that R. insecticola 5.15, but not R. insecticola LSR1, significantly reduced parasitoid success and increased aphid survivorship. To address the potential genetic basis of protection conferred by R. insecticola 5.15 we sequenced the genome of this symbiont strain, and then compared its gene repertoire with that of the already sequenced nonprotective strain R. insecticola LSR1. We identified striking differences in gene sets related to eukaryote pathogenicity. The protective strain R. insecticola 5.15 encoded five categories of pathogenicity factors that were ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567074 Tue, 03 Jan 2012 05:00:00 +0100 5567074 http://www.medworm.com/index.php?rid=5567073&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F95%3Frss%3D1 Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional c... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567073 Tue, 03 Jan 2012 05:00:00 +0100 5567073 http://www.medworm.com/index.php?rid=5567072&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F84%3Frss%3D1 Nucleosomes play an important role in gene regulation. Molecular studies observed that nucleosome binding in promoters tends to be repressive. In contrast, genomic studies have delivered conflicting results: An analysis of yeast grown on diverse carbon sources reported that nucleosome occupancies remain largely unchanged between conditions, whereas a study of the heat-shock response suggested that nucleosomes get evicted at promoters of genes with increased expression. Consequently, there are few general principles that capture the relationship between chromatin organization and transcriptional regulation. Here, we present a qualitative model for nucleosome positioning in Saccharomyces cerevisiae that helps explain important properties of gene expression. By integrating publicly available ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567072 Tue, 03 Jan 2012 05:00:00 +0100 5567072 http://www.medworm.com/index.php?rid=5567071&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F76%3Frss%3D1 In this study we report on a novel pair of cis-regulatory motifs in promoter sequences of the nematode Caenorhabditis elegans. The motif pair exhibits extraordinary genomic traits: The order and the orientation of the two motifs are highly specific, and the distance between them is almost always one of two frequent distances. In contrast, the sequence between the motifs is variable across occurrences. Thus, the motif pair constitutes a nearly combinatorial sequence configuration. We further show that this module is conserved among, and unique to, the entire Caenorhabditis genus. By analyzing several gene expression data sets, our data suggest that this motif pair may function in germline development, oogenesis, and early embryogenesis. Finally, we verify that the motifs are indeed function... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567071 Tue, 03 Jan 2012 05:00:00 +0100 5567071 http://www.medworm.com/index.php?rid=5567070&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F64%3Frss%3D1 Precise DNA replication is crucial for genome maintenance, yet this process has been inherently difficult to study on a genome-wide level in untransformed differentiated metazoan cells. To determine how metazoan DNA replication can be repressed, we examined regions selectively under-replicated in Drosophila polytene salivary glands, and found they are transcriptionally silent and enriched for the repressive H3K27me3 mark. In the first genome-wide analysis of binding of the origin recognition complex (ORC) in a differentiated metazoan tissue, we find that ORC binding is dramatically reduced within these large domains, suggesting reduced initiation as one mechanism leading to under-replication. Inhibition of replication fork progression by the chromatin protein SUUR is an additional repressi... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567070 Tue, 03 Jan 2012 05:00:00 +0100 5567070 http://www.medworm.com/index.php?rid=5567069&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F51%3Frss%3D1 Analysis of diverse eukaryotes has revealed that recombination events cluster in discrete genomic locations known as hotspots. In humans, a zinc-finger protein, PRDM9, is believed to initiate recombination in >40% of hotspots by binding to a specific DNA sequence motif. However, the PRDM9 coding sequence is disrupted in the dog genome assembly, raising questions regarding the nature and control of recombination in dogs. By analyzing the sequences of PRDM9 orthologs in a number of dog breeds and several carnivores, we show here that this gene was inactivated early in canid evolution. We next use patterns of linkage disequilibrium using more than 170,000 SNP markers typed in almost 500 dogs to estimate the recombination rates in the dog genome using a coalescent-based approach. Broad-scal... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567069 Tue, 03 Jan 2012 05:00:00 +0100 5567069 http://www.medworm.com/index.php?rid=5567068&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F35%3Frss%3D1 Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3' and 5' splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567068 Tue, 03 Jan 2012 05:00:00 +0100 5567068 http://www.medworm.com/index.php?rid=5567067&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F25%3Frss%3D1 Non-allelic homologous recombination (NAHR), non-homologous end joining (NHEJ), and microhomology-mediated replication-dependent recombination (MMRDR) have all been put forward as mechanisms to explain DNA rearrangements associated with genomic disorders. However, many nonrecurrent rearrangements in humans remain unexplained. To further investigate the mutation mechanisms of these copy number variations (CNVs), we performed breakpoint mapping analysis for 62 clinical cases with intragenic deletions in the human DMD gene (50 cases) and other known disease-causing genes (one PCCB, one IVD, one DBT, three PAH, one STK11, one HEXB, three DBT, one HRPT1, and one EMD cases). While repetitive elements were found in only four individual cases, three involving DMD and one HEXB gene, microhomologies... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567067 Tue, 03 Jan 2012 05:00:00 +0100 5567067 http://www.medworm.com/index.php?rid=5567066&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F9%3Frss%3D1 Cell-type diversity is governed in part by differential gene expression programs mediated by transcription factor (TF) binding. However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. In the ENCODE Project, we have identified the genomic binding locations across 11 different human cell types of CTCF, RNA Pol II (RNAPII), and MYC, three TFs with diverse roles. Our data and analysis revealed how these factors bind in relation to genomic features and shape gene expression and cell-type specificity. CTCF bound predominantly in intergenic regions while RNAPII and MYC preferentially bound to core promoter regions. CTCF sites were relatively invariant across diverse cell types, w... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567066 Tue, 03 Jan 2012 05:00:00 +0100 5567066 http://www.medworm.com/index.php?rid=5567065&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F22%2F1%2F1%3Frss%3D1 Methotrexate is used to treat autoimmune diseases and malignancies, including acute lymphoblastic leukemia (ALL). Inter-individual variation in clearance of methotrexate results in heterogeneous systemic exposure, clinical efficacy, and toxicity. In a genome-wide association study of children with ALL, we identified SLCO1B1 as harboring multiple common polymorphisms associated with methotrexate clearance. The extent of influence of rare versus common variants on pharmacogenomic phenotypes remains largely unexplored. We tested the hypothesis that rare variants in SLCO1B1 could affect methotrexate clearance and compared the influence of common versus rare variants in addition to clinical covariates on clearance. From deep resequencing of SLCO1B1 exons in 699 children, we identified 93 SNPs, ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567065 Tue, 03 Jan 2012 05:00:00 +0100 5567065 http://www.medworm.com/index.php?rid=5567064&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.130468.111v2%3Frss%3D1 In this study, we have taken the first steps towards addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 non-human primates. Of the non-human primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5,721 genes per species, and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose r... Genome Research journals http://www.medworm.com/rss/comments.php?id=5567064 Tue, 03 Jan 2012 05:00:00 +0100 5567064 http://www.medworm.com/index.php?rid=5556112&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125864.111v1%3Frss%3D1 Phylogenomics offers the potential to fully resolve the Tree of Life, but increasing genomic coverage also reveals conflicting evolutionary histories among genes, demanding new analytical strategies for elucidating a single history of life. Here, we outline a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA. Using species-tree analysis that accounts for discord among hundreds of independent loci, we show that this class of marker is useful for recovering deep-level phylogeny in placental mammals. In broad outline, our phylogeny agrees with recent phylogenomic studies of mammals, including several formerly controversial relationships. Our results also inform two outstanding questions in placental mammal phylogeny involvi... Genome Research journals http://www.medworm.com/rss/comments.php?id=5556112 Thu, 29 Dec 2011 05:00:00 +0100 5556112 http://www.medworm.com/index.php?rid=5556111&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.130468.111v1%3Frss%3D1 In this study, we have taken the first steps towards addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 non-human primates. Of the non-human primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5,721 genes per species, and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose r... Genome Research journals http://www.medworm.com/rss/comments.php?id=5556111 Thu, 29 Dec 2011 05:00:00 +0100 5556111 http://www.medworm.com/index.php?rid=5548712&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.120790.111v2%3Frss%3D1 We report here the isolation and sequencing of 10 Y-specific tammar wallaby (Macropus eugenii) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All have partners on the tammar X, along with homologs on the human X. Nonsynonymous and synonymous substitution ratios for nine of the tammar XY gene pairs indicate that they are each under purifying selection. All 10 were also identified as being on the Y in Tasmanian devil (Sarcophilus harrisii; a distantly related Australian marsupial); however, seven have been lost from the human Y. Maximum likelihood phylogenetic analyses of the wallaby YX gene... Genome Research journals http://www.medworm.com/rss/comments.php?id=5548712 Wed, 28 Dec 2011 05:00:00 +0100 5548712 http://www.medworm.com/index.php?rid=5548711&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124784.111v2%3Frss%3D1 In this study, we examined 491,526 autosomal single nucleotide polymorphisms (SNPs) genotyped in 5210 individuals and conducted a genome-wide search for selection signals in 1890 AfA. Several genomic regions showing an excess of African or European ancestry, which were considered the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre- and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA-specific high-risk diseases such as prostate ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5548711 Wed, 28 Dec 2011 05:00:00 +0100 5548711 http://www.medworm.com/index.php?rid=5548714&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.121947.111v2%3Frss%3D1 DNA arrays have been widely used to perform transcriptome-wide analysis of gene expression, and many methods have been developed to measure gene expression variability and to compare gene expression between conditions. Because RNA-seq is also becoming increasingly popular for transcriptome characterization, the possibility exists for further quantification of individual alternative transcript isoforms, and therefore for estimating the relative ratios of alternative splice forms within a given gene. Changes in splicing ratios, even without changes in overall gene expression, may have important phenotypic effects. Here we have developed statistical methodology to measure variability in splicing ratios within conditions, to compare it between conditions, and to identify genes with condition-s... Genome Research journals http://www.medworm.com/rss/comments.php?id=5548714 Tue, 27 Dec 2011 05:00:00 +0100 5548714 http://www.medworm.com/index.php?rid=5548713&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127522.111v2%3Frss%3D1 Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs, and small indels. A total of 443 genes have at least 10 nonsynonymous substitutions in protein-coding regions, with enric... Genome Research journals http://www.medworm.com/rss/comments.php?id=5548713 Tue, 27 Dec 2011 05:00:00 +0100 5548713 http://www.medworm.com/index.php?rid=5541596&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126201.111v1%3Frss%3D1 Odorous chemicals are detected by the mouse main olfactory epithelium (MOE) by ~1100 types of olfactory receptors (OR) expressed by olfactory sensory neurons (OSNs). Each mature OSN is thought to express only one allele of a single OR gene. Major impediments to understand the transcriptional control of OR gene expression are the lack of a proper characterization of OR transcription start sites (TSSs) and promoters, and of regulatory transcripts at OR loci. We have applied the nanoCAGE technology to profile the transcriptome and the active promoters in the MOE. NanoCAGE analysis revealed the map and architecture of promoters for 87.5% of the mouse OR genes, as well as the expression of many novel non-coding RNAs including antisense transcripts. We identified candidate transcription factors ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5541596 Thu, 22 Dec 2011 05:00:00 +0100 5541596 http://www.medworm.com/index.php?rid=5541595&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.128819.111v1%3Frss%3D1 In this study, we analyzed the evolutionary trajectories of 583 literature-derived and 50,000 computationally predicted human TK circuits in 19 representative eukaryotic species and assigned their evolutionary origins. We found that human TK circuits for intracellular pTyr signaling originated largely from primitive organisms, whereas the inter- or extra-cellular signaling circuits experienced significant expansion in the bilaterian lineage through the "back-wiring" of newly evolved kinases to primitive substrates and SH2/PTB domains. Conversely, the TK circuits that are involved in tissue-specific signaling evolved mainly in vertebrates by the back-wiring of vertebrate substrates to primitive kinases and SH2/PTB domains. Importantly, we found that cancer signaling preferentially employs t... Genome Research journals http://www.medworm.com/rss/comments.php?id=5541595 Thu, 22 Dec 2011 05:00:00 +0100 5541595 http://www.medworm.com/index.php?rid=5541594&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133645.111v1%3Frss%3D1 Identification of the molecular events which drive cancer transformation is essential to the development of targeted agents which improve the clinical outcome of lung cancer. Many studies have reported genomic driver mutations in non-small cell lung cancers (NSCLC) over the past decade, however, the molecular pathogenesis of more than 40% of NSCLC is still unknown. To identify new molecular targets in NSCLC, we performed the combined analysis of massively parallel whole-genome and transcriptome sequencing for cancer and paired normal tissue of a 33-year-old lung adenocarcinoma patient, who is a never-smoker and has no familial cancer history. The cancer showed no known driver mutation in EGFR or KRAS and no EML4-ALK fusion. Here we report a novel fusion gene between KIF5B and RET proto-onc... Genome Research journals http://www.medworm.com/rss/comments.php?id=5541594 Thu, 22 Dec 2011 05:00:00 +0100 5541594 http://www.medworm.com/index.php?rid=5531264&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125591.111v1%3Frss%3D1 Next generation sequencing has enabled systematic discovery of mutational spectra in cancer samples. Here, we used whole genome sequencing to characterize somatic mutations and structural variation in a primary acral melanoma and its lymph node metastasis. Our data show that the somatic mutational rates in this acral melanoma sample pair were more comparable to the rates reported in cancer genomes not associated with mutagenic exposure than in the genome of a melanoma cell line or the transcriptome of melanoma short-term cultures. Despite the perception that acral skin is sun-protected, the dominant mutational signature in these samples is compatible with damage due to ultraviolet light exposure. A nonsense mutation in ERCC5 discovered in both the primary and metastatic tumors could also h... Genome Research journals http://www.medworm.com/rss/comments.php?id=5531264 Mon, 19 Dec 2011 05:00:00 +0100 5531264 http://www.medworm.com/index.php?rid=5531263&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126417.111v2%3Frss%3D1 The discovery of substantial amounts of 5-hydroxymethylcytosine (5hmC), formed by the oxidation of 5-methylcytosine (5mC), in various mouse tissues and human embryonic stem (ES) cells has necessitated a reevaluation of our knowledge of 5mC/5hmC patterns and functions in mammalian cells. Here, we investigate the tissue specificity of both the global levels and locus-specific distribution of 5hmC in several human tissues and cell lines. We find that global 5hmC content of normal human tissues is highly variable, does not correlate with global 5mC content, and decreases rapidly as cells from normal tissue adapt to cell culture. Using tiling microarrays to map 5hmC levels in DNA from normal human tissues, we find that 5hmC patterns are tissue specific; unsupervised hierarchical clustering base... Genome Research journals http://www.medworm.com/rss/comments.php?id=5531263 Mon, 19 Dec 2011 05:00:00 +0100 5531263 http://www.medworm.com/index.php?rid=5531262&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126540.111v1%3Frss%3D1 The degree to which the level of genetic variation for gene expression is shared across multiple tissues has important implications for research investigating the role of expression on the etiology of complex human traits and diseases. In the last few years, several studies have been published reporting the extent of overlap in expression quantitative trait loci (eQTL) identified in multiple tissues or cell types. Although these studies provide important information on the regulatory control of genes across tissues, their limited power means that they can typically only explain a small proportion of genetic variation for gene expression. Here, using expression data from monozygotic twins (MZ), we investigate the genetic control of gene expression in lymphoblastoid cell lines (LCL) and whol... Genome Research journals http://www.medworm.com/rss/comments.php?id=5531262 Mon, 19 Dec 2011 05:00:00 +0100 5531262 http://www.medworm.com/index.php?rid=5531261&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129635.111v1%3Frss%3D1 Despite the recent discoveries of and interest in numerous structural variations (SVs)—which include duplications and inversions—in the human and other higher eukaryotic genomes, little is known about the etiology and biology of these SVs, partly due to the lack of molecular tools with which to create individual SVs in cultured cells and model organisms. Here, we present a novel method of inducing duplications and inversions in a targeted manner without pre-manipulation of the genome. We found that zinc finger nucleases (ZFNs) designed to target two different sites in a human chromosome could introduce two concurrent double-strand breaks, whose repair via non-homologous end-joining (NHEJ) gives rise to targeted duplications and inversions of the genomic segments of up to a mega... Genome Research journals http://www.medworm.com/rss/comments.php?id=5531261 Mon, 19 Dec 2011 05:00:00 +0100 5531261 http://www.medworm.com/index.php?rid=5519544&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131508.111v1%3Frss%3D1 Androgen receptor (AR) is a hormone-activated transcription factor that plays important roles in prostate development and function, as well as malignant transformation. The downstream pathways of AR, however, are incompletely understood. AR has been primarily known as a transcriptional activator inducing prostate-specific gene expression. Through integrative analysis of genome-wide AR occupancy and androgen-regulated gene expression, here we report AR as a globally acting transcriptional repressor. This repression is mediated by androgen-responsive elements (ARE) and dictated by Polycomb group protein EZH2 and repressive chromatin remodeling. In embryonic stem cells, AR-repressed genes are occupied by EZH2 and harbor bivalent H3K4me3 and H3K27me3 modifications that are characteristic of di... Genome Research journals http://www.medworm.com/rss/comments.php?id=5519544 Fri, 16 Dec 2011 05:00:00 +0100 5519544 http://www.medworm.com/index.php?rid=5510649&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127738.111v2%3Frss%3D1 Establishing the molecular basis of DNA mutations that cause inherited disease is of fundamental importance to understanding the origin, nature, and clinical sequelae of genetic disorders in humans. The majority of disease-associated mutations constitute single-base substitutions and short deletions and/or insertions resulting from DNA replication errors and the repair of damaged bases. However, pathological mutations can also be introduced by nonreciprocal recombination events between paralogous sequences, a phenomenon known as interlocus gene conversion (IGC). IGC events have thus far been linked to pathology in more than 20 human genes. However, the large number of duplicated gene sequences in the human genome implies that many more disease-associated mutations could originate via IGC. ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5510649 Tue, 13 Dec 2011 05:00:00 +0100 5510649 http://www.medworm.com/index.php?rid=5491455&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.122564.111v2%3Frss%3D1 During tumor initiation and progression, cancer cells acquire a selective advantage, allowing them to outcompete their normal counterparts. Identification of the genetic changes that underlie these tumor acquired traits can provide deeper insights into the biology of tumorigenesis. Regions of copy number alterations and germline DNA variants are some of the elements subject to selection during tumor evolution. Integrated examination of inherited variation and somatic alterations holds the potential to reveal specific nucleotide alleles that a tumor "prefers" to have amplified. Next-generation sequencing of tumor and matched normal tissues provides a high-resolution platform to identify and analyze such somatic amplicons. Within an amplicon, examination of informative (e.g., heterozygous) s... Genome Research journals http://www.medworm.com/rss/comments.php?id=5491455 Fri, 09 Dec 2011 05:00:00 +0100 5491455 http://www.medworm.com/index.php?rid=5481644&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.123109.111v1%3Frss%3D1 This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they s... Genome Research journals http://www.medworm.com/rss/comments.php?id=5481644 Wed, 07 Dec 2011 05:00:00 +0100 5481644 http://www.medworm.com/index.php?rid=5481643&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125872.111v1%3Frss%3D1 While genetic mutation is a hallmark of cancer, many cancers also acquire epigenetic alterations during tumorigenesis including aberrant DNA hypermethylation of tumor suppressors, as well as changes in chromatin modifications as caused by genetic mutations of the chromatin-modifying machinery. However, the extent of epigenetic alterations in cancer cells has not been fully characterized. Here, we describe complete methylome maps at single nucleotide resolution of a low-passage breast cancer cell line and primary human mammary epithelial cells. We find widespread DNA hypomethylation in the cancer cell, primarily at partially methylated domains (PMDs) in normal breast cells. Unexpectedly, genes within these regions are largely silenced in cancer cells. The loss of DNA methylation in these re... Genome Research journals http://www.medworm.com/rss/comments.php?id=5481643 Wed, 07 Dec 2011 05:00:00 +0100 5481643 http://www.medworm.com/index.php?rid=5481642&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126953.111v1%3Frss%3D1 We describe algorithms to error correct, assemble and scaffold large sets of sequence data. SGA uses the overlap-based string graph model of assembly, unlike most de novo assemblers that rely on de Bruijn graphs, and is simply parallelizable. We demonstrate the error correction and assembly performance of SGA on 1.2 billion sequence reads from a human genome, which we are able to assemble using 54 GB of memory. The resulting contigs are highly accurate and contiguous, while covering 95% of the reference genome (excluding contigs less than 200bp in length). Because of the low memory requirements and parallelization without requiring inter-process communication, SGA provides the first practical assembler to our knowledge for a mammalian-sized genome on a low-end computing cluster. (Source: G... Genome Research journals http://www.medworm.com/rss/comments.php?id=5481642 Wed, 07 Dec 2011 05:00:00 +0100 5481642 http://www.medworm.com/index.php?rid=5481647&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127845.111v1%3Frss%3D1 There is an emerging consensus that when investigators obtain genomic data from research participants, they may incur an ethical responsibility to inform at-risk individuals about clinically significant variants discovered during the course of their research. With whole exome sequencing becoming commonplace and the falling costs of full genome sequencing, there will be an increasingly large number of variants identified in research participants that may be of sufficient clinical relevance to share. An explicit approach to triaging and communicating these results has yet to be developed, and even the magnitude of the task is uncertain. To develop an estimate of the number of variants that might qualify for disclosure, we apply recently published recommendations for return of results to a de... Genome Research journals http://www.medworm.com/rss/comments.php?id=5481647 Tue, 06 Dec 2011 05:00:00 +0100 5481647 http://www.medworm.com/index.php?rid=5481646&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.129668.111v1%3Frss%3D1 Methotrexate is used to treat autoimmune diseases and malignancies, including acute lymphoblastic leukemia (ALL). Inter-individual variation in clearance of methotrexate results in heterogeneous systemic exposure, clinical efficacy, and toxicity. In a genome-wide association study of children with ALL, we identified SLCO1B1 as harboring multiple common polymorphisms associated with methotrexate clearance. The extent of influence of rare versus common variants on pharmacogenomic phenotypes remains largely unexplored. We tested the hypothesis that rare variants in SLCO1B1 could affect methotrexate clearance and compared the influence of common versus rare variants in addition to clinical covariates on clearance. From deep resequencing of SLCO1B1 exons in 699 children, we identified 93 SNPs, ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5481646 Tue, 06 Dec 2011 05:00:00 +0100 5481646 http://www.medworm.com/index.php?rid=5481645&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131383.111v1%3Frss%3D1 In this study, we evaluated several of the leading de novo assembly algorithms on four different short-read data sets, all generated by Illumina sequencers. Our results describe the relative performance of the different assemblers as well as other significant differences in assembly difficulty that appear to be inherent in the genomes themselves. Three overarching conclusions are apparent: first, that data quality, rather than the assembler itself, has a dramatic affect on the quality of an assembled genome; second, that the degree of contiguity of an assembly varies enormously among different assemblers and different genomes; and third, that the correctness of an assembly also varies widely, and is not well correlated with statistics on contiguity. In order to enable others to replicate o... Genome Research journals http://www.medworm.com/rss/comments.php?id=5481645 Tue, 06 Dec 2011 05:00:00 +0100 5481645 http://www.medworm.com/index.php?rid=5463681&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2249%3Frss%3D1 (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5463681 Thu, 01 Dec 2011 05:00:00 +0100 5463681 http://www.medworm.com/index.php?rid=5463680&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2242%3Frss%3D1 (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5463680 Thu, 01 Dec 2011 05:00:00 +0100 5463680 http://www.medworm.com/index.php?rid=5463679&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2224%3Frss%3D1 We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assem... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463679 Thu, 01 Dec 2011 05:00:00 +0100 5463679 http://www.medworm.com/index.php?rid=5463678&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2213%3Frss%3D1 Next-generation sequencing (NGS) technologies are revolutionizing genome research, and in particular, their application to transcriptomics (RNA-seq) is increasingly being used for gene expression profiling as a replacement for microarrays. However, the properties of RNA-seq data have not been yet fully established, and additional research is needed for understanding how these data respond to differential expression analysis. In this work, we set out to gain insights into the characteristics of RNA-seq data analysis by studying an important parameter of this technology: the sequencing depth. We have analyzed how sequencing depth affects the detection of transcripts and their identification as differentially expressed, looking at aspects such as transcript biotype, length, expression level, ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463678 Thu, 01 Dec 2011 05:00:00 +0100 5463678 http://www.medworm.com/index.php?rid=5463677&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2203%3Frss%3D1 In this study we propose to move away from this two-step approach to a novel one in which all genomes are compared with the reference genome simultaneously for obtaining much higher accuracy in structural variation detection. For this purpose, we introduce the maximum parsimony–based simultaneous structural variation discovery problem for a set of high-throughput sequenced genomes and provide efficient algorithms to solve it. We compare the proposed framework with the conventional framework, on the genomes of the Yoruban mother–father–child trio, as well as the CEU trio of European ancestry (both sequenced by Illumina platforms). We observed that the conventional framework predicts an unexpectedly high number of de novo variations in the child in comparison to the parents... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463677 Thu, 01 Dec 2011 05:00:00 +0100 5463677 http://www.medworm.com/index.php?rid=5463676&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2190%3Frss%3D1 Fragile X syndrome (FXS) is the first cause of inherited intellectual disability, due to the silencing of the X-linked Fragile X Mental Retardation 1 gene encoding the RNA-binding protein FMRP. While extensive studies have focused on the cellular and molecular basis of FXS, neither human Fragile X patients nor the mouse model of FXS—the Fmr1-null mouse—have been profiled systematically at the metabolic and neurochemical level to provide a complementary perspective on the current, yet scattered, knowledge of FXS. Using proton high-resolution magic angle spinning nuclear magnetic resonance (1H HR-MAS NMR)-based metabolic profiling, we have identified a metabolic signature and biomarkers associated with FXS in various brain regions of Fmr1-deficient mice. Our study highlights for ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463676 Thu, 01 Dec 2011 05:00:00 +0100 5463676 http://www.medworm.com/index.php?rid=5463675&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2181%3Frss%3D1 Retroviral and transposon-based insertional mutagenesis (IM) screens are widely used for cancer gene discovery in mice. Exploiting the full potential of IM screens requires methods for high-throughput sequencing and mapping of transposon and retroviral insertion sites. Current protocols are based on ligation-mediated PCR amplification of junction fragments from restriction endonuclease-digested genomic DNA, resulting in amplification biases due to uneven genomic distribution of restriction enzyme recognition sites. Consequently, sequence coverage cannot be used to assess the clonality of individual insertions. We have developed a novel method, called shear-splink, for the semiquantitative high-throughput analysis of insertional mutations. Shear-splink employs random fragmentation of genomi... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463675 Thu, 01 Dec 2011 05:00:00 +0100 5463675 http://www.medworm.com/index.php?rid=5463674&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2167%3Frss%3D1 Accurately predicting regulatory sequences and enhancers in entire genomes is an important but difficult problem, especially in large vertebrate genomes. With the advent of ChIP-seq technology, experimental detection of genome-wide EP300/CREBBP bound regions provides a powerful platform to develop predictive tools for regulatory sequences and to study their sequence properties. Here, we develop a support vector machine (SVM) framework which can accurately identify EP300-bound enhancers using only genomic sequence and an unbiased set of general sequence features. Moreover, we find that the predictive sequence features identified by the SVM classifier reveal biologically relevant sequence elements enriched in the enhancers, but we also identify other features that are significantly depleted ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463674 Thu, 01 Dec 2011 05:00:00 +0100 5463674 http://www.medworm.com/index.php?rid=5463673&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2157%3Frss%3D1 The fungus Mycosphaerella graminicola emerged as a new pathogen of cultivated wheat during its domestication ~11,000 yr ago. We assembled 12 high-quality full genome sequences to investigate the genetic footprints of selection in this wheat pathogen and closely related sister species that infect wild grasses. We demonstrate a strong effect of natural selection in shaping the pathogen genomes with only ~3% of nonsynonymous mutations being effectively neutral. Forty percent of all fixed nonsynonymous substitutions, on the other hand, are driven by positive selection. Adaptive evolution has affected M. graminicola to the highest extent, consistent with recent host specialization. Positive selection has prominently altered genes encoding secreted proteins and putative pathogen effectors suppor... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463673 Thu, 01 Dec 2011 05:00:00 +0100 5463673 http://www.medworm.com/index.php?rid=5463672&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2143%3Frss%3D1 This study provides a basis for more powerful molecular profiling of visceral leishmaniasis, providing additional power to track the drug resistance and epidemiology of an important human pathogen. (Source: Genome Research) Genome Research journals http://www.medworm.com/rss/comments.php?id=5463672 Thu, 01 Dec 2011 05:00:00 +0100 5463672 http://www.medworm.com/index.php?rid=5463671&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2129%3Frss%3D1 Leishmania parasites cause a spectrum of clinical pathology in humans ranging from disfiguring cutaneous lesions to fatal visceral leishmaniasis. We have generated a reference genome for Leishmania mexicana and refined the reference genomes for Leishmania major, Leishmania infantum, and Leishmania braziliensis. This has allowed the identification of a remarkably low number of genes or paralog groups (2, 14, 19, and 67, respectively) unique to one species. These were found to be conserved in additional isolates of the same species. We have predicted allelic variation and find that in these isolates, L. major and L. infantum have a surprisingly low number of predicted heterozygous SNPs compared with L. braziliensis and L. mexicana. We used short read coverage to infer ploidy and gene copy nu... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463671 Thu, 01 Dec 2011 05:00:00 +0100 5463671 http://www.medworm.com/index.php?rid=5463670&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2114%3Frss%3D1 Coordinate regulation of ribosomal protein (RP) genes is key for controlling cell growth. In yeast, it is unclear how this regulation achieves the required equimolar amounts of the different RP components, given that some RP genes exist in duplicate copies, while others have only one copy. Here, we tested whether the solution to this challenge is partly encoded within the DNA sequence of the RP promoters, by fusing 110 different RP promoters to a fluorescent gene reporter, allowing us to robustly detect differences in their promoter activities that are as small as ~10%. We found that single-copy RP promoters have significantly higher activities, suggesting that proper RP stoichiometry is indeed partly encoded within the RP promoters. Notably, we also partially uncovered how this regulation... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463670 Thu, 01 Dec 2011 05:00:00 +0100 5463670 http://www.medworm.com/index.php?rid=5463669&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2096%3Frss%3D1 We report an expanded set of 283 readthrough candidates, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation. We report experimental evidence of translation using GFP tagging and mass spectrometry for several readthrough regions. We find that the set of readthrough candidates differs from other genes in length, composition, conservation, stop codon context, and in some cases, conserved stem–loops, providing clues about readthrough regulation and potential mechanisms. Lastly, we expand our studies beyond Drosophila and find evidence of abundant readthrough in several other insect species and one crustacean, and several readthrough candida... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463669 Thu, 01 Dec 2011 05:00:00 +0100 5463669 http://www.medworm.com/index.php?rid=5463668&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2087%3Frss%3D1 Gene duplication via retrotransposition has been shown to be an important mechanism in evolution, affecting gene dosage and allowing for the acquisition of new gene functions. Although fixed retrotransposed genes have been found in a variety of species, very little effort has been made to identify retrogene polymorphisms. Here, we examine 37 Illumina-sequenced North American Drosophila melanogaster inbred lines and present the first ever data set and analysis of polymorphic retrogenes in Drosophila. We show that this type of polymorphism is quite common, with any two gametes in the North American population differing in the presence or absence of six retrogenes, accounting for ~13% of gene copy-number heterozygosity. These retrogenes were identified by a straightforward method that can be ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463668 Thu, 01 Dec 2011 05:00:00 +0100 5463668 http://www.medworm.com/index.php?rid=5463667&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2082%3Frss%3D1 There has been extensive traffic of male-biased genes out of the mammalian and Drosophila X-chromosomes, and there are also reports of an under-representation of male-biased genes on the X. This may reflect an adaptive process driven by natural selection where an autosomal location of male-biased genes is favored since male genes are only exposed to selection one-third of the time when X-linked. However, there are several alternative explanations to "out-of-the-X" gene movement, including mutational bias and a means for X-linked genes to escape meiotic sex chromosome inactivation (MSCI) during spermatogenesis. As a critical test of the hypothesis that genomic relocation of sex-biased genes is an adaptive process, I examined the emergence, and loss, of genes on the chicken Z-chromosome, i.e... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463667 Thu, 01 Dec 2011 05:00:00 +0100 5463667 http://www.medworm.com/index.php?rid=5463666&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2067%3Frss%3D1 Drug development efforts against cancer are often hampered by the complex properties of signaling networks. Here we combined the results of an RNAi screen targeting the cellular signaling machinery, with graph theoretical analysis to extract the core modules that process both mitogenic and oncogenic signals to drive cell cycle progression. These modules encapsulated mechanisms for coordinating seamless transition of cells through the individual cell cycle stages and, importantly, were functionally conserved across different cancer cell types. Further analysis also enabled extraction of the core signaling axes that progressively guide commitment of cells to the division cycle. Importantly, pharmacological targeting of the least redundant nodes in these axes yielded a synergistic disruption ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463666 Thu, 01 Dec 2011 05:00:00 +0100 5463666 http://www.medworm.com/index.php?rid=5463665&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2058%3Frss%3D1 In mammals, germ cells undergo striking dynamic changes in DNA methylation during their development. However, the dynamics and mode of methylation are poorly understood for short interspersed elements (SINEs) dispersed throughout the genome. We investigated the DNA methylation status of mouse B1 SINEs in male germ cells at different developmental stages. B1 elements showed a large locus-to-locus variation in methylation; loci close to RNA polymerase II promoters were hypomethylated, while most others were hypermethylated. Interestingly, a mutation that eliminates Piwi-interacting RNAs (piRNAs), which are involved in methylation of long interspersed elements (LINEs), did not affect the level of B1 methylation, implying a piRNA-independent mechanism. Methylation at B1 loci in SINE-poor genom... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463665 Thu, 01 Dec 2011 05:00:00 +0100 5463665 http://www.medworm.com/index.php?rid=5463664&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2049%3Frss%3D1 We have determined methylation state differences in the epigenomes of uncultured cells purified from human, chimpanzee, and orangutan, using digestion with a methylation-sensitive enzyme, deep sequencing, and computational analysis of the sequence data. The methylomes show a high degree of conservation, but the methylation states of ~10% of CpG island-like regions differ significantly between human and chimp. The differences are not associated with changes in CG content and recapitulate the known phylogenetic relationship of the three species, indicating that they are stably maintained within each species. Inferences about the relationship between somatic and germline methylation states can be made by an analysis of CG decay, derived from methylation and sequence data. This indicates that ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463664 Thu, 01 Dec 2011 05:00:00 +0100 5463664 http://www.medworm.com/index.php?rid=5463663&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2038%3Frss%3D1 Microsatellites—tandem repeats of short DNA motifs—are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions,... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463663 Thu, 01 Dec 2011 05:00:00 +0100 5463663 http://www.medworm.com/index.php?rid=5463662&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2026%3Frss%3D1 Epigenetic mechanisms are important regulators of cell type–specific genes, including miRNAs. In order to identify cell type–specific miRNAs regulated by epigenetic mechanisms, we undertook a global analysis of miRNA expression and epigenetic states in three isogenic pairs of human mammary epithelial cells (HMEC) and human mammary fibroblasts (HMF), which represent two differentiated cell types typically present within a given organ, each with a distinct phenotype and a distinct epigenotype. While miRNA expression and epigenetic states showed strong interindividual concordance within a given cell type, almost 10% of the expressed miRNA showed a cell type–specific pattern of expression that was linked to the epigenetic state of their promoter. The tissue-specific miRNA gen... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463662 Thu, 01 Dec 2011 05:00:00 +0100 5463662 http://www.medworm.com/index.php?rid=5463661&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2014%3Frss%3D1 Recent RNA-sequencing studies have shown remarkable complexity in the mammalian transcriptome. The ultimate impact of this complexity on the predicted proteomic output is less well defined. We have undertaken strand-specific RNA sequencing of multiple cellular RNA fractions (>20 Gb) to uncover the transcriptional complexity of human embryonic stem cells (hESCs). We have shown that human embryonic stem (ES) cells display a high degree of transcriptional diversity, with more than half of active genes generating RNAs that differ from conventional gene models. We found evidence that more than 1000 genes express long 5' and/or extended 3'UTRs, which was confirmed by "virtual Northern" analysis. Exhaustive sequencing of the membrane-polysome and cytosolic/untranslated fractions of hESCs was u... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463661 Thu, 01 Dec 2011 05:00:00 +0100 5463661 http://www.medworm.com/index.php?rid=5463660&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F2004%3Frss%3D1 Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have evaluated the impact of CNVs, mapped at fine scale, on gene expression. Based on data from 129 individuals with ancestry from two populations, we identified CNVs associated with the expression of 110 genes, with 13% of the associations involving complex, multiallelic CNVs. Categorization of CNVs according to variant type, size, and gene overlap enabled us to examine the impact of different CNV classes on ex... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463660 Thu, 01 Dec 2011 05:00:00 +0100 5463660 http://www.medworm.com/index.php?rid=5463659&cid=s_33052_50_f&fid=33053&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Fcontent%2Ffull%2F21%2F12%2F1995%3Frss%3D1 The biological basis for the development of the cerebro-cerebellar structures required for posture and gait in humans is poorly understood. We investigated a large consanguineous family from Turkey exhibiting an extremely rare phenotype associated with quadrupedal locomotion, mental retardation, and cerebro-cerebellar hypoplasia, linked to a 7.1-Mb region of homozygosity on chromosome 17p13.1–13.3. Diffusion weighted imaging and fiber tractography of the patients' brains revealed morphological abnormalities in the cerebellum and corpus callosum, in particular atrophy of superior, middle, and inferior peduncles of the cerebellum. Structural magnetic resonance imaging showed additional morphometric abnormalities in several cortical areas, including the corpus callosum, precentral gyrus... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463659 Thu, 01 Dec 2011 05:00:00 +0100 5463659 http://www.medworm.com/index.php?rid=5463658&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.120790.111v1%3Frss%3D1 We report here the isolation and sequencing of ten Y-specific tammar wallaby (Macropus eugenii) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All have partners on the tammar X, along with homologues on the human X. Non-synonymous and synonymous substitution ratios for nine of the tammar XY gene pairs indicate that they are each under purifying selection. All ten were also identified as being on the Y in Tasmanian devil (Sarcophilus harrisii; a distantly related Australian marsupial); however, seven have been lost from the human Y. Maximum likelihood phylogenetic analyses of the wallaby YX... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463658 Tue, 29 Nov 2011 05:00:00 +0100 5463658 http://www.medworm.com/index.php?rid=5463657&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.121897.111v1%3Frss%3D1 Insertions and deletions (indels), together with nucleotide substitutions, are major drivers of sequence evolution. An excess of deletions over insertions in genomic sequences - the so-called deletional bias - has been reported in a wide range of species, including mammals. However, this bias has not been found in the coding sequences of some mammalian species, such as human and mouse. To determine the strength of the deletional bias in mammals and the influence of mutational and selective processes, we have quantified indels, in neutrally evolving non-coding sequences as well as in protein-coding sequences, in six mammalian branches - human, macaque, ancestral primate, mouse, rat and ancestral rodent. The results, obtained with an improved algorithm for the placement of insertions in mult... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463657 Tue, 29 Nov 2011 05:00:00 +0100 5463657 http://www.medworm.com/index.php?rid=5463656&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.123463.111v2%3Frss%3D1 Non-allelic homologous recombination (NAHR), non-homologous end joining (NHEJ), and microhomology-mediated replication-dependent recombination (MMRDR) have all been put forward as mechanisms to explain DNA rearrangements associated with genomic disorders. However, many nonrecurrent rearrangements in humans remain unexplained. To further investigate the mutation mechanisms of these copy number variations (CNVs), we performed breakpoint mapping analysis for 62 clinical cases with intragenic deletions in the human DMD gene (50 cases) and other known disease-causing genes (one PCCB, one IVD, one DBT, three PAH, one STK11, one HEXB, three DBT, one HRPT1, and one EMD cases). While repetitive elements were found in only four individual cases, three involving DMD and one HEXB gene, microhomologies... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463656 Tue, 29 Nov 2011 05:00:00 +0100 5463656 http://www.medworm.com/index.php?rid=5463655&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124016.111v2%3Frss%3D1 We describe how sequencing libraries can be reproducibly created from 20 pg of input DNA using a modified transpososome-mediated fragmentation technique. Resulting libraries incorporate in-line bar-coding, which facilitates sample multiplexes that can be sequenced using Illumina platforms with the manufacturer's sequencing primer. We demonstrate this technique by providing deep coverage sequence of the Escherichia coli K-12 genome that shows equivalent target coverage to a 1-μg input library prepared using standard Illumina methods. Reducing template quantity does, however, increase the proportion of duplicate reads and enriches coverage in low-GC regions. This finding was confirmed with exhaustive resequencing of a mouse library constructed from 20 pg of gDNA input (about seven haploid... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463655 Tue, 29 Nov 2011 05:00:00 +0100 5463655 http://www.medworm.com/index.php?rid=5463654&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124123.111v2%3Frss%3D1 Analysis of diverse eukaryotes has revealed that recombination events cluster in discrete genomic locations known as hotspots. In humans, a zinc-finger protein, PRDM9, is believed to initiate recombination in >40% of hotspots by binding to a specific DNA sequence motif. However, the PRDM9 coding sequence is disrupted in the dog genome assembly, raising questions regarding the nature and control of recombination in dogs. By analyzing the sequences of PRDM9 orthologs in a number of dog breeds and several carnivores, we show here that this gene was inactivated early in canid evolution. We next use patterns of linkage disequilibrium using more than 170,000 SNP markers typed in almost 500 dogs to estimate the recombination rates in the dog genome using a coalescent-based approach. Broad-scal... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463654 Tue, 29 Nov 2011 05:00:00 +0100 5463654 http://www.medworm.com/index.php?rid=5463653&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124370.111v2%3Frss%3D1 Single variant or single gene analyses generally account for only a small proportion of the phenotypic variation in complex traits. Alternatively, gene set or pathway association analyses are playing an increasingly important role in uncovering genetic architectures of complex traits through the identification of systematic genetic interactions. Two dominant paradigms for gene set analyses are association analyses based on SNP genotypes and those based on gene expression profiles. However, gene–disease association can manifest in many ways, such as alterations of gene expression, genotype, and copy number; thus, an integrative approach combining multiple forms of evidence can more accurately and comprehensively capture pathway associations. We have developed a single statistical fram... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463653 Tue, 29 Nov 2011 05:00:00 +0100 5463653 http://www.medworm.com/index.php?rid=5463652&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124784.111v1%3Frss%3D1 In this study, we examined 491,526 autosomal SNPs genotyped in 5,210 individuals and conducted a genome-wide search for selection signals in 1,890 AfA. Several genomic regions showing excess of African or European ancestry, which were thought as the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre-and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA specific high-risk diseases such as prostate cancer and hypertension, suggesting ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463652 Tue, 29 Nov 2011 05:00:00 +0100 5463652 http://www.medworm.com/index.php?rid=5463651&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125351.111v2%3Frss%3D1 In this study, two strains of the endosymbiont Regiella insecticola (R. insecticola 5.15 and R. insecticola LSR1) were found to differ in ability to protect pea aphids attacked by the parasitoid Aphidius ervi. Parasitism trials reveal that R. insecticola 5.15, but not R. insecticola LSR1, significantly reduced parasitoid success and increased aphid survivorship. To address the potential genetic basis of protection conferred by R. insecticola 5.15 we sequenced the genome of this symbiont strain, and then compared its gene repertoire with that of the already sequenced nonprotective strain R. insecticola LSR1. We identified striking differences in gene sets related to eukaryote pathogenicity. The protective strain R. insecticola 5.15 encoded five categories of pathogenicity factors that were ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463651 Tue, 29 Nov 2011 05:00:00 +0100 5463651 http://www.medworm.com/index.php?rid=5463650&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126003.111v2%3Frss%3D1 Precise DNA replication is crucial for genome maintenance, yet this process has been inherently difficult to study on a genome-wide level in untransformed differentiated metazoan cells. To determine how metazoan DNA replication can be repressed, we examined regions selectively under-replicated in Drosophila polytene salivary glands, and found they are transcriptionally silent and enriched for the repressive H3K27me3 mark. In the first genome-wide analysis of binding of the origin recognition complex (ORC) in a differentiated metazoan tissue, we find that ORC binding is dramatically reduced within these large domains, suggesting reduced initiation as one mechanism leading to under-replication. Inhibition of replication fork progression by the chromatin protein SUUR is an additional repressi... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463650 Tue, 29 Nov 2011 05:00:00 +0100 5463650 http://www.medworm.com/index.php?rid=5463649&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127373.111v1%3Frss%3D1 RNA-seq has been widely adopted as a gene-expression measurement tool due to the detail, resolution, and sensitivity of transcript characterization that the technique provides. Here we present two transposon-based methods that efficiently construct high-quality RNA-seq libraries. We first describe a method that creates RNA-seq libraries for Illumina sequencing from double-stranded cDNA with only two enzymatic reactions. We generated high-quality RNA-seq libraries from as little as 10 pg of mRNA (~1 ng of total RNA) with this approach. We also present a strand-specific RNA-seq library construction protocol that combines transposon-based library construction with uracil DNA glycosylase and endonuclease VIII to specifically degrade the second strand constructed during cDNA synthesis. The dire... Genome Research journals http://www.medworm.com/rss/comments.php?id=5463649 Tue, 29 Nov 2011 05:00:00 +0100 5463649 http://www.medworm.com/index.php?rid=5453081&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127597.111v2%3Frss%3D1 Cell-type diversity is governed in part by differential gene expression programs mediated by transcription factor (TF) binding. However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. In the ENCODE Project, we have identified the genomic binding locations across 11 different human cell types of CTCF, RNA Pol II (RNAPII), and MYC, three TFs with diverse roles. Our data and analysis revealed how these factors bind in relation to genomic features and shape gene expression and cell-type specificity. CTCF bound predominantly in intergenic regions while RNAPII and MYC preferentially bound to core promoter regions. CTCF sites were relatively invariant across diverse cell types, w... Genome Research journals http://www.medworm.com/rss/comments.php?id=5453081 Mon, 28 Nov 2011 05:00:00 +0100 5453081 http://www.medworm.com/index.php?rid=5446389&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.121947.111v1%3Frss%3D1 DNA arrays have been widely used to perform transcriptome wide analysis of gene expression and many methods have been developed to measure gene expression variability and to compare gene expression between conditions. As RNA-seq is also becoming increasingly popular for transcriptome characterization, the possibility exists for further quantification of individual alternative transcript isoforms, and therefore for estimating the relative ratios of alternative splice forms within a given gene. Changes in splicing ratios, even without changes in overall gene expression, may have important phenotypic effects. Here we have developed statistical methodology to measure variability in splicing ratios within conditions, to compare it between conditions and to identify genes with condition specific... Genome Research journals http://www.medworm.com/rss/comments.php?id=5446389 Wed, 23 Nov 2011 05:00:00 +0100 5446389 http://www.medworm.com/index.php?rid=5446388&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.125146.111v2%3Frss%3D1 Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional c... Genome Research journals http://www.medworm.com/rss/comments.php?id=5446388 Wed, 23 Nov 2011 05:00:00 +0100 5446388 http://www.medworm.com/index.php?rid=5446393&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.119834.110v2%3Frss%3D1 Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3' and 5' splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long... Genome Research journals http://www.medworm.com/rss/comments.php?id=5446393 Tue, 22 Nov 2011 05:00:00 +0100 5446393 http://www.medworm.com/index.php?rid=5446392&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124107.111v2%3Frss%3D1 RNA editing enhances the diversity of gene products at the post-transcriptional level. Approaches for genome-wide identification of RNA editing face two main challenges: separating true editing sites from false discoveries and accurate estimation of editing levels. We developed an approach to analyze transcriptome sequencing data (RNA-seq) for global identification of RNA editing in cells for which whole-genome sequencing data are available. We applied the method to analyze RNA-seq data of a human glioblastoma cell line, U87MG. Around 10,000 DNA–RNA differences were identified, the majority being putative A-to-I editing sites. These predicted A-to-I events were associated with a low false-discovery rate (~5%). Moreover, the estimated editing levels from RNA-seq correlated well with t... Genome Research journals http://www.medworm.com/rss/comments.php?id=5446392 Tue, 22 Nov 2011 05:00:00 +0100 5446392 http://www.medworm.com/index.php?rid=5446391&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.131342.111v1%3Frss%3D1 Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in the callus than in the seedling. For DH sites detected in both the seedling and callus, 31% displayed significantly different levels of DNase I sensitivity... Genome Research journals http://www.medworm.com/rss/comments.php?id=5446391 Tue, 22 Nov 2011 05:00:00 +0100 5446391 http://www.medworm.com/index.php?rid=5446390&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.133009.111v1%3Frss%3D1 Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts, while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1,133 non-coding multi-exonic transcripts expressed durin... Genome Research journals http://www.medworm.com/rss/comments.php?id=5446390 Tue, 22 Nov 2011 05:00:00 +0100 5446390 http://www.medworm.com/index.php?rid=5436137&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.123547.111v2%3Frss%3D1 We present small RNA data sets comprising more than 200 million aligned Illumina sequence reads covering all major cell types of the root as well as four distinct developmental zones. MicroRNAs (miRNAs) constitute a class of small ncRNAs that are particularly important for development. Of the 243 known miRNAs, 133 were found to be expressed in the root, and most showed tissue- or zone-specific expression patterns. We identified 66 new high-confidence miRNAs using a computational pipeline, PIPmiR, specifically developed for the identification of plant miRNAs. PIPmiR uses a probabilistic model that combines RNA structure and expression information to identify miRNAs with high precision. Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming th... Genome Research journals http://www.medworm.com/rss/comments.php?id=5436137 Mon, 21 Nov 2011 05:00:00 +0100 5436137 http://www.medworm.com/index.php?rid=5436136&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126417.111v1%3Frss%3D1 The discovery of substantial amounts of 5-hydroxymethylcytosine (5hmC), formed by the oxidation of 5-methylcytosine (5mC), in various mouse tissues and human ES cells has necessitated a re-evaluation of our knowledge of 5mC/5hmC patterns and functions in mammalian cells. Here, we investigate the tissue-specificity of both the global levels and locus-specific distribution of 5hmC in several human tissues and cell lines. We find that global 5hmC content of normal human tissues is highly variable, does not correlate with global 5mC content, and decreases rapidly as cells from normal tissue adapt to cell culture. Using tiling microarrays to map 5hmC levels in DNA from normal human tissues we find that 5hmC patterns are tissue-specific; unsupervised hierarchical clustering based solely on 5hmC ... Genome Research journals http://www.medworm.com/rss/comments.php?id=5436136 Mon, 21 Nov 2011 05:00:00 +0100 5436136 http://www.medworm.com/index.php?rid=5436135&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127522.111v1%3Frss%3D1 Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here we sequenced Arabidopsis Landsberg erecta (Ler) and two sets of all four meiotic products from a Columbia (Col)/Ler hybrid, to investigate genome-wide variation and meiotic recombination at nucleotide resolution. Comparing Ler and Col sequences uncovered 349,171 Single Nucleotide Polymorphisms (SNPs), 58,085 small and 2,315 large insertions/deletions (indels), with highly correlated genome-wide distributions of SNPs and small indels. 443 genes have at least 10 nonsynonymous substitutions in protein coding regions, with enrichment for d... Genome Research journals http://www.medworm.com/rss/comments.php?id=5436135 Mon, 21 Nov 2011 05:00:00 +0100 5436135 http://www.medworm.com/index.php?rid=5415564&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.122564.111v1%3Frss%3D1 During tumor initiation and progression, cancer cells acquire a selective advantage, allowing them to out-compete their normal counterparts. Identification of the genetic changes that underlie these tumor acquired traits can provide deeper insights into the biology of tumorigenesis. Regions of copy number alterations and germline DNA variants are some of the elements subject to selection during tumor evolution. Integrated examination of inherited variation and somatic alterations holds the potential to reveal specific nucleotide alleles that a tumor "prefers" to have amplified. Next-generation sequencing of tumor and matched normal tissues provides a high-resolution platform to identify and analyze such somatic amplicons. Within an amplicon, examination of informative (e.g. heterozygous) s... Genome Research journals http://www.medworm.com/rss/comments.php?id=5415564 Wed, 16 Nov 2011 05:00:00 +0100 5415564 http://www.medworm.com/index.php?rid=5415563&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.123463.111v1%3Frss%3D1 Non-allelic homologous recombination (NAHR), non-homologous end joining (NHEJ), fork stalling template switching (FoSTeS), and microhomology-mediated replication-dependent recombination (MMRDR) have all been put forward as mechanisms to explain DNA rearrangements associated with genomic disorders. However, many nonrecurrent rearrangements in humans remain unexplained. To further investigate the mutation mechanisms of these copy number variations (CNVs), we performed breakpoint mapping analysis for 62 clinical cases with intragenic deletions in the human DMD gene (DMD, 50 cases) and other known disease-causing genes (1 PCCB, 1 IVD, 1 DBT, 3 PAH, 1 STK11, 1 HEXB, 3 DBT, 1 HRPT1, and 1 EMD cases). While repetitive elements were found in only 4 individual cases, 3 involving DMD and 1 HEXB gene... Genome Research journals http://www.medworm.com/rss/comments.php?id=5415563 Wed, 16 Nov 2011 05:00:00 +0100 5415563 http://www.medworm.com/index.php?rid=5415562&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.124016.111v1%3Frss%3D1 We describe how sequencing libraries can be reproducibly created from 20pg input DNA using a modified transpososome-mediated fragmentation technique. Resulting libraries incorporate in-line barcoding which facilitates sample multiplexes that can be sequenced on the GAII platform using the manufacturer's sequencing primer. We demonstrate this technique by providing deep coverage sequence of the E. coli K-12 genome that shows equivalent target coverage to a 1μg input library prepared using standard Illumina methods. Reducing template quantity does, however, increase the proportion of duplicate reads and enriches coverage in low GC regions. This finding was confirmed with exhaustive re-sequencing of a mouse library constructed from 20pg gDNA input (approximately 7 haploid genomes) resultin... Genome Research journals http://www.medworm.com/rss/comments.php?id=5415562 Wed, 16 Nov 2011 05:00:00 +0100 5415562 http://www.medworm.com/index.php?rid=5415561&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.126003.111v1%3Frss%3D1 Precise DNA replication is crucial for genome maintenance, yet this process has been inherently difficult to study on a genome-wide level in untransformed differentiated metazoan cells. To determine how metazoan DNA replication can be repressed, we examined regions selectively under-replicated in Drosophila polytene salivary glands and found they are transcriptionally silent and enriched for the repressive H3K27me3 mark. In the first genome-wide analysis of binding of the Origin Recognition Complex (ORC) in a differentiated metazoan tissue, we find that ORC binding is dramatically reduced within these large domains, suggesting reduced initiation as one mechanism leading to under-replication. Inhibition of replication fork progression by the chromatin protein SUUR is an additional repressio... Genome Research journals http://www.medworm.com/rss/comments.php?id=5415561 Wed, 16 Nov 2011 05:00:00 +0100 5415561 http://www.medworm.com/index.php?rid=5415560&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127597.111v1%3Frss%3D1 Cell-type diversity is governed in part by differential gene expression programs mediated by transcription factor (TF) binding. However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. In the ENCODE Project, we have identified the genomic binding locations across 11 different human cell types of CTCF, RNA Pol II (RNAPII) and MYC, three TFs with diverse roles. Our data and analysis revealed how these factors bind in relation to genomic features and shape gene expression and cell-type specificity. CTCF bound predominantly in intergenic regions while RNAPII and MYC preferentially bound to core promoter regions. CTCF sites were relatively invariant across diverse cell types, wh... Genome Research journals http://www.medworm.com/rss/comments.php?id=5415560 Wed, 16 Nov 2011 05:00:00 +0100 5415560 http://www.medworm.com/index.php?rid=5415559&cid=s_33052_50_f&fid=33052&url=http%3A%2F%2Fgenome.cshlp.org%2Fcgi%2Freprint%2Fgr.127738.111v1%3Frss%3D1 Establishing the molecular basis of DNA mutations that cause inherited disease is of fundamental importance to understanding the origin, nature and clinical sequelae of genetic disorders in human. The majority of disease-associated mutations constitute single-base substitutions and short deletions and/or insertions resulting from DNA replication errors and the repair of damaged bases. Pathological mutations can however also be introduced by non-reciprocal recombination events between paralogous sequences, a phenomenon known as interlocus gene conversion (IGC). IGC events have been linked to pathology in more than 20 genes. However, the large number of duplicated gene sequences in the human genome implies that many more disease-associated mutations could originate via IGC. Here we have empl... Genome Research journals http://www.medworm.com/rss/comments.php?id=5415559 Wed, 16 Nov 2011 05:00:00 +0100 5415559