title: An oestrogen-receptor-alpha-bound human chromatin interactome.
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 alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha 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.
authors.affiliation: Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Fullwood
authors.forename: Mei Hui
authors.initials: MH
authors.lastname: Liu
authors.forename: You Fu
authors.initials: YF
authors.lastname: Pan
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.forename: Yusoff Bin
authors.initials: YB
authors.lastname: Mohamed
authors.forename: Yuriy L
authors.initials: YL
authors.lastname: Orlov
authors.forename: Stoyan
authors.initials: S
authors.lastname: Velkov
authors.forename: Andrea
authors.initials: A
authors.lastname: Ho
authors.forename: Poh Huay
authors.initials: PH
authors.lastname: Mei
authors.forename: Elaine G Y
authors.initials: EG
authors.lastname: Chew
authors.forename: Phillips Yao Hui
authors.initials: PY
authors.lastname: Huang
authors.forename: Willem-Jan
authors.initials: WJ
authors.lastname: Welboren
authors.forename: Yuyuan
authors.initials: Y
authors.lastname: Han
authors.forename: Hong Sain
authors.initials: HS
authors.lastname: Ooi
authors.forename: Pramila N
authors.initials: PN
authors.lastname: Ariyaratne
authors.forename: Vinsensius B
authors.initials: VB
authors.lastname: Vega
authors.forename: Yanquan
authors.initials: Y
authors.lastname: Luo
authors.forename: Peck Yean
authors.initials: PY
authors.lastname: Tan
authors.forename: Pei Ye
authors.initials: PY
authors.lastname: Choy
authors.forename: K D Senali Abayratna
authors.initials: KD
authors.lastname: Wansa
authors.forename: Bing
authors.initials: B
authors.lastname: Zhao
authors.forename: Kar Sian
authors.initials: KS
authors.lastname: Lim
authors.forename: Shi Chi
authors.initials: SC
authors.lastname: Leow
authors.forename: Jit Sin
authors.initials: JS
authors.lastname: Yow
authors.forename: Roy
authors.initials: R
authors.lastname: Joseph
authors.forename: Haixia
authors.initials: H
authors.lastname: Li
authors.forename: Kartiki V
authors.initials: KV
authors.lastname: Desai
authors.forename: Jane S
authors.initials: JS
authors.lastname: Thomsen
authors.forename: Yew Kok
authors.initials: YK
authors.lastname: Lee
authors.forename: R Krishna Murthy
authors.initials: RK
authors.lastname: Karuturi
authors.forename: Thoreau
authors.initials: T
authors.lastname: Herve
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Hendrik G
authors.initials: HG
authors.lastname: Stunnenberg
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.forename: Valere
authors.initials: V
authors.lastname: Cacheux-Rataboul
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
authors.forename: Edison T
authors.initials: ET
authors.lastname: Liu
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Edwin
authors.initials: E
authors.lastname: Cheung
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
mesh_terms: D001665:Binding Sites; D002460:Cell Line; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D003432:Cross-Linking Reagents; D047628:Estrogen Receptor alpha / Q000378:metabolism*; D005557:Formaldehyde; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: D002843:Chromatin; D003432:Cross-Linking Reagents; D047628:Estrogen Receptor alpha; D005557:Formaldehyde