Genome-wide map of regulatory interactions in the human genome.
Genome-wide map of regulatory interactions in the human genome.
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DOI：
10.1101/gr.176586.114
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发表时间：
2014-12
期刊：
影响因子：
7
通讯作者：
Snyder MP
中科院分区：
文献类型：
--
作者：
Heidari N;Phanstiel DH;He C;Grubert F;Jahanbani F;Kasowski M;Zhang MQ;Snyder MP
越来越多的证据表明，基因组调控元件之间的相互作用在调控基因表达中起着重要作用。我们使用染色质相互作用分析配对末端标签测序（ChIA-PET）实验，针对六个广泛分布的因子，在人类细胞（ENCODE 1级细胞，K562，GM 12878）中生成了调控元件的全基因组相互作用图谱。结合区域覆盖80%的DNase I超敏位点，包括99.7%的TSS和98%的增强子。将该图谱与ChIP-seq和RNA-seq数据集相关联，揭示了cohesin，CTCF和ZNF 143是三维染色质结构的关键组成部分，并揭示了远端染色质状态如何影响基因转录。细胞类型之间的相互作用的比较显示，增强子-启动子相互作用是高度细胞类型特异性的。远端和近端调控网络的构建和比较揭示了结构和生物学功能的明显差异。近端结合事件在具有管家功能的基因处富集，而远端结合事件与参与动态生物过程（包括对刺激的反应）的基因相互作用。这项研究揭示了新的机制和功能的见解调节区组织的核心。
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer–promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.
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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：
64.8
作者：
Jin, Fulai;Li, Yan;Dixon, Jesse R.;Selvaraj, Siddarth;Ye, Zhen;Lee, Ah Young;Yen, Chia-An;Schmitt, Anthony D.;Espinoza, Celso A.;Ren, Bing
通讯作者：
Ren, Bing
粘着素相关染色质相互作用的基因组景观。
影响因子：
7
作者：
DeMare LE;Leng J;Cotney J;Reilly SK;Yin J;Sarro R;Noonan JP
通讯作者：
Noonan JP
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
7
作者：
Dostie, Josee;Richmond, Todd A.;Dekker, Job
通讯作者：
Dekker, Job