共查询到20条相似文献,搜索用时 356 毫秒
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The accessible chromatin landscape of the human genome 总被引:2,自引:0,他引:2
RE Thurman E Rynes R Humbert J Vierstra MT Maurano E Haugen NC Sheffield AB Stergachis H Wang B Vernot K Garg S John R Sandstrom D Bates L Boatman TK Canfield M Diegel D Dunn AK Ebersol T Frum E Giste AK Johnson EM Johnson T Kutyavin B Lajoie BK Lee K Lee D London D Lotakis S Neph F Neri ED Nguyen H Qu AP Reynolds V Roach A Safi ME Sanchez A Sanyal A Shafer JM Simon L Song S Vong M Weaver Y Yan Z Zhang Z Zhang B Lenhard M Tewari MO Dorschner RS Hansen PA Navas G Stamatoyannopoulos VR Iyer 《Nature》2012,489(7414):75-82
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Nègre N Brown CD Ma L Bristow CA Miller SW Wagner U Kheradpour P Eaton ML Loriaux P Sealfon R Li Z Ishii H Spokony RF Chen J Hwang L Cheng C Auburn RP Davis MB Domanus M Shah PK Morrison CA Zieba J Suchy S Senderowicz L Victorsen A Bild NA Grundstad AJ Hanley D MacAlpine DM Mannervik M Venken K Bellen H White R Gerstein M Russell S Grossman RL Ren B Posakony JW Kellis M White KP 《Nature》2011,471(7339):527-531
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An integrated encyclopedia of DNA elements in the human genome 总被引:4,自引:0,他引:4
ENCODE Project Consortium BE Bernstein E Birney I Dunham ED Green C Gunter M Snyder 《Nature》2012,489(7414):57-74
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A high-resolution map of active promoters in the human genome 总被引:1,自引:0,他引:1
Kim TH Barrera LO Zheng M Qu C Singer MA Richmond TA Wu Y Green RD Ren B 《Nature》2005,436(7052):876-880
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The T-helper-cell 1 and 2 (T(H)1 and T(H)2) pathways, defined by cytokines interferon-gamma (IFN-gamma) and interleukin-4 (IL-4), respectively, comprise two alternative CD4+ T-cell fates, with functional consequences for the host immune system. These cytokine genes are encoded on different chromosomes. The recently described T(H)2 locus control region (LCR) coordinately regulates the T(H)2 cytokine genes by participating in a complex between the LCR and promoters of the cytokine genes Il4, Il5 and Il13. Although they are spread over 120 kilobases, these elements are closely juxtaposed in the nucleus in a poised chromatin conformation. In addition to these intrachromosomal interactions, we now describe interchromosomal interactions between the promoter region of the IFN-gamma gene on chromosome 10 and the regulatory regions of the T(H)2 cytokine locus on chromosome 11. DNase I hypersensitive sites that comprise the T(H)2 LCR developmentally regulate these interchromosomal interactions. Furthermore, there seems to be a cell-type-specific dynamic interaction between interacting chromatin partners whereby interchromosomal interactions are apparently lost in favour of intrachromosomal ones upon gene activation. Thus, we provide an example of eukaryotic genes located on separate chromosomes associating physically in the nucleus via interactions that may have a function in coordinating gene expression. 相似文献
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Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals 总被引:4,自引:0,他引:4
Xie X Lu J Kulbokas EJ Golub TR Mootha V Lindblad-Toh K Lander ES Kellis M 《Nature》2005,434(7031):338-345
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Transcriptional regulatory code of a eukaryotic genome 总被引:2,自引:0,他引:2
Harbison CT Gordon DB Lee TI Rinaldi NJ Macisaac KD Danford TW Hannett NM Tagne JB Reynolds DB Yoo J Jennings EG Zeitlinger J Pokholok DK Kellis M Rolfe PA Takusagawa KT Lander ES Gifford DK Fraenkel E Young RA 《Nature》2004,431(7004):99-104
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Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells. 相似文献
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Sequencing and comparison of yeast species to identify genes and regulatory elements 总被引:135,自引:0,他引:135
Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human. 相似文献
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project 总被引:2,自引:0,他引:2
ENCODE Project Consortium Birney E Stamatoyannopoulos JA Dutta A Guigó R Gingeras TR Margulies EH Weng Z Snyder M Dermitzakis ET Thurman RE Kuehn MS Taylor CM Neph S Koch CM Asthana S Malhotra A Adzhubei I Greenbaum JA Andrews RM Flicek P Boyle PJ Cao H Carter NP Clelland GK Davis S Day N Dhami P Dillon SC Dorschner MO Fiegler H Giresi PG Goldy J Hawrylycz M Haydock A Humbert R James KD Johnson BE Johnson EM Frum TT Rosenzweig ER Karnani N Lee K Lefebvre GC Navas PA Neri F Parker SC Sabo PJ 《Nature》2007,447(7146):799-816
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Ernst J Kheradpour P Mikkelsen TS Shoresh N Ward LD Epstein CB Zhang X Wang L Issner R Coyne M Ku M Durham T Kellis M Bernstein BE 《Nature》2011,473(7345):43-49
Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease. 相似文献
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