Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
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DOI：
10.1016/j.cell.2011.12.014
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发表时间：
2012-01-20
期刊：
影响因子：
64.5
通讯作者：
Ruan Y
中科院分区：
文献类型：
--
作者：
Li G;Ruan X;Auerbach RK;Sandhu KS;Zheng M;Wang P;Poh HM;Goh Y;Lim J;Zhang J;Sim HS;Peh SQ;Mulawadi FH;Ong CT;Orlov YL;Hong S;Zhang Z;Landt S;Raha D;Euskirchen G;Wei CL;Ge W;Wang H;Davis C;Fisher-Aylor KI;Mortazavi A;Gerstein M;Gingeras T;Wold B;Sun Y;Fullwood MJ;Cheung E;Liu E;Sung WK;Snyder M;Ruan Y
在真核生物中，对于转录调控的高阶染色体组织知之甚少。使用全基因组染色质相互作用分析与配对末端标签测序（ChIA-PET），我们绘制了人类细胞中与RNA聚合酶II相关的长距离染色质相互作用，并发现了广泛的以启动子为中心的基因内，基因外和基因间相互作用。这些相互作用进一步聚集成高阶簇，其中近端和远端基因通过启动子-启动子相互作用参与。大多数具有启动子-启动子相互作用的基因是活性的，并且协同转录，并且一些相互作用的启动子可以相互影响，这意味着转录控制的组合复杂性。不同细胞系的比较分析表明，细胞特异性的染色质相互作用可以提供细胞特异性转录的结构框架，并建议显着丰富的增强子-启动子相互作用的细胞特异性功能。此外，发现遗传鉴定的疾病相关非编码元件通过长程相互作用与相应基因在空间上接合。总体而言，我们的研究提供了深入了解人类细胞中管家基因和细胞特异性基因的三维染色质相互作用的转录调控。
Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intra-genic, extra-genic and inter-genic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated non-coding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into the transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.
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影响因子：
12.3
作者：
Li G;Fullwood MJ;Xu H;Mulawadi FH;Velkov S;Vega V;Ariyaratne PN;Mohamed YB;Ooi HS;Tennakoon C;Wei CL;Ruan Y;Sung WK
通讯作者：
Sung WK
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
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影响因子：
16.8
作者：
通讯作者：
--
影响因子：
12.3
作者：
Cope NF;Fraser P;Eskiw CH
通讯作者：
Eskiw CH
影响因子：
64.5
作者：
Hah N;Danko CG;Core L;Waterfall JJ;Siepel A;Lis JT;Kraus WL
通讯作者：
Kraus WL