An oestrogen-receptor-a-bound human chromatin interactome

• Published in: Nature (London) Vol. 462; no. 7269; pp. 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: Journal Article
• Language: English
• Published: London Nature Publishing Group 05.11.2009
• Subjects: Biological and medical sciences; Cell receptors; Cell structures and functions; Chromatin. Chromosome; Chromosomes; Data analysis; Fluorescence in situ hybridization; Fundamental and applied biological sciences. Psychology; Libraries; Methods; Miscellaneous; Molecular and cellular biology; Molecular genetics; Proteins; RNA polymerase; Human; Estrogen receptor α; Chromosome; Chromatin; Interactome; Biological receptor
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature08497

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.