Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
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DOI：
10.1126/science.1196914
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发表时间：
2010-12-24
期刊：
影响因子：
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通讯作者：
Waterston RH
中科院分区：
文献类型：
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作者：
Gerstein MB;Lu ZJ;Van Nostrand EL;Cheng C;Arshinoff BI;Liu T;Yip KY;Robilotto R;Rechtsteiner A;Ikegami K;Alves P;Chateigner A;Perry M;Morris M;Auerbach RK;Feng X;Leng J;Vielle A;Niu W;Rhrissorrakrai K;Agarwal A;Alexander RP;Barber G;Brdlik CM;Brennan J;Brouillet JJ;Carr A;Cheung MS;Clawson H;Contrino S;Dannenberg LO;Dernburg AF;Desai A;Dick L;Dosé AC;Du J;Egelhofer T;Ercan S;Euskirchen G;Ewing B;Feingold EA;Gassmann R;Good PJ;Green P;Gullier F;Gutwein M;Guyer MS;Habegger L;Han T;Henikoff JG;Henz SR;Hinrichs A;Holster H;Hyman T;Iniguez AL;Janette J;Jensen M;Kato M;Kent WJ;Kephart E;Khivansara V;Khurana E;Kim JK;Kolasinska-Zwierz P;Lai EC;Latorre I;Leahey A;Lewis S;Lloyd P;Lochovsky L;Lowdon RF;Lubling Y;Lyne R;MacCoss M;Mackowiak SD;Mangone M;McKay S;Mecenas D;Merrihew G;Miller DM 3rd;Muroyama A;Murray JI;Ooi SL;Pham H;Phippen T;Preston EA;Rajewsky N;Rätsch G;Rosenbaum H;Rozowsky J;Rutherford K;Ruzanov P;Sarov M;Sasidharan R;Sboner A;Scheid P;Segal E;Shin H;Shou C;Slack FJ;Slightam C;Smith R;Spencer WC;Stinson EO;Taing S;Takasaki T;Vafeados D;Voronina K;Wang G;Washington NL;Whittle CM;Wu B;Yan KK;Zeller G;Zha Z;Zhong M;Zhou X;modENCODE Consortium;Ahringer J;Strome S;Gunsalus KC;Micklem G;Liu XS;Reinke V;Kim SK;Hillier LW;Henikoff S;Piano F;Snyder M;Stein L;Lieb JD;Waterston RH
我们系统地生成了大规模的数据集，以改善线虫秀丽隐杆线虫，一个关键的模式生物的基因组注释。这些数据集包括整个发育时间过程中的转录组分析，转录因子结合位点的全基因组鉴定，以及染色质组织图。由此，我们创建了更完整和准确的基因模型，包括可变剪接形式和候选非编码RNA。我们构建了转录因子结合和microRNA相互作用的分层网络，并发现了由异常大量的转录因子结合的染色体位置。在染色体臂和中心之间揭示了不同的染色质组成和组蛋白修饰模式，在常染色体和X染色体之间具有类似的显著差异。整合数据类型，我们建立了染色质，转录因子结合和基因表达相关的统计模型。总的来说，我们的分析归因于大多数保守基因组的推定功能。
We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor–binding sites, and maps of chromatin organization. From this, we created more complete and accurate gene models, including alternative splice forms and candidate noncoding RNAs. We constructed hierarchical networks of transcription factor–binding and microRNA interactions and discovered chromosomal locations bound by an unusually large number of transcription factors. Different patterns of chromatin composition and histone modification were revealed between chromosome arms and centers, with similarly prominent differences between autosomes and the X chromosome. Integrating data types, we built statistical models relating chromatin, transcription factor binding, and gene expression. Overall, our analyses ascribed putative functions to most of the conserved genome.