1. An oestrogen-receptor-α-bound human chromatin interactome
- Author
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Edwin Cheung, Andrea Ho, Peck Yean Tan, R. Krishna Murthy Karuturi, Shi Chi Leow, Roy Joseph, Kartiki V. Desai, Willem Welboren, Yijun Ruan, Hong Sain Ooi, Kar Sian Lim, Bing Zhao, Guillaume Bourque, Phillips Yao Hui Huang, Yuyuan Han, Pramila N. Ariyaratne, Chia-Lin Wei, Vinsensius B. Vega, Haixia Li, Yanquan Luo, You Fu Pan, Jane S. Thomsen, Han Xu, K. D. Senali Abayratna Wansa, Xiaoan Ruan, Elaine G.Y. Chew, Pei Ye Choy, Mei Hui Liu, Poh Huay Mei, Melissa J. Fullwood, Thoreau Herve, Valere Cacheux-Rataboul, Jun Liu, Edison T. Liu, Yuriy L. Orlov, Jit Sin Yow, Hendrik G. Stunnenberg, Yusoff Bin Mohamed, Yew Kok Lee, Wing-Kin Sung, and Stoyan Velkov
- Subjects
Transcriptional Activation ,Chromatin Immunoprecipitation ,Histone-modifying enzymes ,Transcription, Genetic ,Biology ,Article ,Chromatin remodeling ,Cell Line ,Chromosome conformation capture ,03 medical and health sciences ,0302 clinical medicine ,Formaldehyde ,Humans ,Promoter Regions, Genetic ,Scaffold/matrix attachment region ,ChIA-PET ,030304 developmental biology ,Genetics ,0303 health sciences ,Binding Sites ,Multidisciplinary ,Genome, Human ,Estrogen Receptor alpha ,Reproducibility of Results ,Sequence Analysis, DNA ,Chromatin ,ChIP-sequencing ,Cell biology ,Cross-Linking Reagents ,030220 oncology & carcinogenesis ,Protein Binding ,Bivalent chromatin - Abstract
Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes. © 2009 Macmillan Publishers Limited. All rights reserved.
- Published
- 2009
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