An oestrogen-receptor-a-bound human chromatin interactome

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 re...

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Published in:Nature (London) 2009-11, Vol.462 (7269), p.58-64
Main Authors: FULLWOOD, Melissa J, MEI HUI LIU, CHEW, Elaine G. Y, HUANG, Phillips Yao Hui, WELBOREN, Willem-Jan, YUYUAN HAN, HONG SAIN OOI, ARIYARATNE, Pramila N, VEGA, Vinsensius B, YANQUAN LUO, PECK YEAN TAN, CHOY, Pei Ye, YOU FU PAN, SENALI ABAYRATNA WANSA, K. D, BING ZHAO, KAR SIAN LIM, SHI CHI LEOW, JIT SIN YOW, JOSEPH, Roy, HAIXIA LI, DESAI, Kartiki V, THOMSEN, Jane S, YEW KOK LEE, JUN LIU, KRISHNA MURTHY KARUTURI, R, HERVE, Thoreau, BOURQUE, Guillaume, STUNNENBERG, Hendrik G, XIAOAN RUAN, CACHEUX-RATABOUL, Valere, SUNG, Wing-Kin, LIU, Edison T, WEI, Chia-Lin, CHEUNG, Edwin, HAN XU, YIJUN RUAN, BIN MOHAMED, Yusoff, ORLOV, Yuriy L, VELKOV, Stoyan, HO, Andrea, MEI, Poh Huay
Format: Article
Language:English
Subjects:
Biological and medical sciences
Cell receptors
Cell structures and functions
Chromatin. Chromosome
Chromosomes
Data analysis
Deoxyribonucleic acid
DNA
Fluorescence in situ hybridization
Fundamental and applied biological sciences. Psychology
Libraries
Methods
Miscellaneous
Molecular and cellular biology
Molecular genetics
Proteins
RNA polymerase
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Description
Summary: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 a (ER-a) in the human genome. We found that most high-confidence remote ER-a-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-a 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.
ISSN:0028-0836
1476-4687
DOI:10.1038/nature08497