A cis-regulatory map of the Drosophila genome.
A cis-regulatory map of the Drosophila genome.
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DOI：
10.1038/nature09990
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发表时间：
2011-03-24
期刊：
影响因子：
64.8
通讯作者：
White, Kevin P.
中科院分区：
文献类型：
--
作者：
Negre, Nicolas;Brown, Christopher D.;Ma, Lijia;Bristow, Christopher Aaron;Miller, Steven W.;Wagner, Ulrich;Kheradpour, Pouya;Eaton, Matthew L.;Loriaux, Paul;Sealfon, Rachel;Li, Zirong;Ishii, Haruhiko;Spokony, Rebecca F.;Chen, Jia;Hwang, Lindsay;Cheng, Chao;Auburn, Richard P.;Davis, Melissa B.;Domanus, Marc;Shah, Parantu K.;Morrison, Carolyn A.;Zieba, Jennifer;Suchy, Sarah;Senderowicz, Lionel;Victorsen, Alec;Bild, Nicholas A.;Grundstad, A. Jason;Hanley, David;MacAlpine, David M.;Mannervik, Mattias;Venken, Koen;Bellen, Hugo;White, Robert;Gerstein, Mark;Russell, Steven;Grossman, Robert L.;Ren, Bing;Posakony, James W.;Kellis, Manolis;White, Kevin P.
基因调控元件的系统注释是基因组科学中的一个主要挑战。全基因组染色质修饰标记和转录因子结合位点的直接作图已经成功地识别了特定亚型的调控元件。在果蝇中，一些开创性的研究已经提供了多梳反应元件、染色质状态、转录因子结合位点(TFBS)、PolII调控和绝缘元件的全基因组鉴定；然而，调控基因组的全面注释仍然是一个重大挑战。在这里，我们描述了modENCODE顺式调控注释项目的结果。我们基于300多个染色质免疫沉淀(CHIP)数据集制作了一张果蝇黑腹果蝇调控基因组图，这些数据集涉及8种染色质特征、5种组蛋白脱乙酰酶(HDAC)和38种不同发育阶段的位点特异性转录因子(TF)。利用这些数据，我们推断了20,000多个候选调控元件，并验证了体内启动子、增强子和绝缘子的预测子集。我们还确定了近2000个与染色质活性和可及性相关的密集Tf结合的基因组区域。我们发现了数百种新的TF共结合关系，并定义了一个具有800多个潜在调控关系的TF网络。
Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements . In Drosophila several pioneering studies have provided genome-wide identification of Polycomb-Response Elements , chromatin states , transcription factor binding sites (TFBS) , PolII regulation , and insulator elements ; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome based on more than 300 chromatin immuno-precipitation (ChIP) datasets for eight chromatin features, five histone deacetylases (HDACs) and thirty-eight site-specific transcription factors (TFs) at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and we validated a subset of predictions for promoters, enhancers, and insulators in vivo. We also identified nearly 2,000 genomic regions of dense TF binding associated with chromatin activity and accessibility. We discovered hundreds of new TF co-binding relationships and defined a TF network with over 800 potential regulatory relationships.
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影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
影响因子：
4.5
作者：
Nègre N;Brown CD;Shah PK;Kheradpour P;Morrison CA;Henikoff JG;Feng X;Ahmad K;Russell S;White RA;Stein L;Henikoff S;Kellis M;White KP
通讯作者：
White KP
影响因子：
9.8
作者：
Li XY;MacArthur S;Bourgon R;Nix D;Pollard DA;Iyer VN;Hechmer A;Simirenko L;Stapleton M;Luengo Hendriks CL;Chu HC;Ogawa N;Inwood W;Sementchenko V;Beaton A;Weiszmann R;Celniker SE;Knowles DW;Gingeras T;Speed TP;Eisen MB;Biggin MD
通讯作者：
Biggin MD
DOI：
10.1002/neu.480210711
发表时间：
1990-10-01
期刊：
JOURNAL OF NEUROBIOLOGY
影响因子：
--
作者：
TRUMAN, JW
通讯作者：
TRUMAN, JW
影响因子：
4.5
作者：
Kwong, Camilla;Adryan, Boris;White, Robert
通讯作者：
White, Robert