An oestrogen-receptor-α-bound human chromatin interactome

Melissa J. Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L. Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei, Elaine G. Y. Chew, Phillips Yao Hui Huang, Willem-Jan Welboren, Yuyuan Han, Hong Sain Ooi, Pramila N. Ariyaratne, Vinsensius B. Vega, Yanquan Luo, Peck Yean Tan, Pei Ye Choy, K. D. Senali Abayratna Wansa, Bing Zhao, Kar Sian Lim, Shi Chi Leow, Jit Sin Yow, Roy Joseph, Haixia Li, Kartiki V. Desai, Jane S. Thomsen, Yew Kok Lee, R. Krishna Murthy Karuturi, Thoreau Herve, Guillaume Bourque, Hendrik G. Stunnenberg, Xiaoan Ruan, Valere Cacheux-Rataboul, Wing-Kin Sung, Edison T. Liu, Chia-Lin Wei, Edwin Cheung () and Yijun Ruan ()
Additional contact information
Melissa J. Fullwood: Genome Institute of Singapore, Agency for Science, Technology and Research
Mei Hui Liu: Genome Institute of Singapore, Agency for Science, Technology and Research
You Fu Pan: Genome Institute of Singapore, Agency for Science, Technology and Research
Jun Liu: Genome Institute of Singapore, Agency for Science, Technology and Research
Han Xu: Genome Institute of Singapore, Agency for Science, Technology and Research
Yusoff Bin Mohamed: Genome Institute of Singapore, Agency for Science, Technology and Research
Yuriy L. Orlov: Genome Institute of Singapore, Agency for Science, Technology and Research
Stoyan Velkov: Genome Institute of Singapore, Agency for Science, Technology and Research
Andrea Ho: Genome Institute of Singapore, Agency for Science, Technology and Research
Poh Huay Mei: Genome Institute of Singapore, Agency for Science, Technology and Research
Elaine G. Y. Chew: Genome Institute of Singapore, Agency for Science, Technology and Research
Phillips Yao Hui Huang: Genome Institute of Singapore, Agency for Science, Technology and Research
Willem-Jan Welboren: Nijmegen Centre for Molecular Life Sciences, Radboud University
Yuyuan Han: Genome Institute of Singapore, Agency for Science, Technology and Research
Hong Sain Ooi: Genome Institute of Singapore, Agency for Science, Technology and Research
Pramila N. Ariyaratne: Genome Institute of Singapore, Agency for Science, Technology and Research
Vinsensius B. Vega: Genome Institute of Singapore, Agency for Science, Technology and Research
Yanquan Luo: Genome Institute of Singapore, Agency for Science, Technology and Research
Peck Yean Tan: Genome Institute of Singapore, Agency for Science, Technology and Research
Pei Ye Choy: Genome Institute of Singapore, Agency for Science, Technology and Research
K. D. Senali Abayratna Wansa: Genome Institute of Singapore, Agency for Science, Technology and Research
Bing Zhao: Genome Institute of Singapore, Agency for Science, Technology and Research
Kar Sian Lim: Genome Institute of Singapore, Agency for Science, Technology and Research
Shi Chi Leow: Genome Institute of Singapore, Agency for Science, Technology and Research
Jit Sin Yow: Genome Institute of Singapore, Agency for Science, Technology and Research
Roy Joseph: Genome Institute of Singapore, Agency for Science, Technology and Research
Haixia Li: Genome Institute of Singapore, Agency for Science, Technology and Research
Kartiki V. Desai: Genome Institute of Singapore, Agency for Science, Technology and Research
Jane S. Thomsen: Genome Institute of Singapore, Agency for Science, Technology and Research
Yew Kok Lee: Genome Institute of Singapore, Agency for Science, Technology and Research
R. Krishna Murthy Karuturi: Genome Institute of Singapore, Agency for Science, Technology and Research
Thoreau Herve: Genome Institute of Singapore, Agency for Science, Technology and Research
Guillaume Bourque: Genome Institute of Singapore, Agency for Science, Technology and Research
Hendrik G. Stunnenberg: Nijmegen Centre for Molecular Life Sciences, Radboud University
Xiaoan Ruan: Genome Institute of Singapore, Agency for Science, Technology and Research
Valere Cacheux-Rataboul: Genome Institute of Singapore, Agency for Science, Technology and Research
Wing-Kin Sung: Genome Institute of Singapore, Agency for Science, Technology and Research
Edison T. Liu: Genome Institute of Singapore, Agency for Science, Technology and Research
Chia-Lin Wei: Genome Institute of Singapore, Agency for Science, Technology and Research
Edwin Cheung: Genome Institute of Singapore, Agency for Science, Technology and Research
Yijun Ruan: Genome Institute of Singapore, Agency for Science, Technology and Research

Nature, 2009, vol. 462, issue 7269, 58-64

Abstract: 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.

Date: 2009
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DOI: 10.1038/nature08497

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