title: CTCF-mediated functional chromatin interactome in pluripotent cells.
abstract: Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.
authors.affiliation: Genome Institute of Singapore, Singapore.
authors.forename: Lusy
authors.initials: L
authors.lastname: Handoko
authors.forename: Han
authors.initials: H
authors.lastname: Xu
authors.forename: Guoliang
authors.initials: G
authors.lastname: Li
authors.forename: Chew Yee
authors.initials: CY
authors.lastname: Ngan
authors.forename: Elaine
authors.initials: E
authors.lastname: Chew
authors.forename: Marie
authors.initials: M
authors.lastname: Schnapp
authors.forename: Charlie Wah Heng
authors.initials: CW
authors.lastname: Lee
authors.forename: Chaopeng
authors.initials: C
authors.lastname: Ye
authors.forename: Joanne Lim Hui
authors.initials: JL
authors.lastname: Ping
authors.forename: Fabianus
authors.initials: F
authors.lastname: Mulawadi
authors.forename: Eleanor
authors.initials: E
authors.lastname: Wong
authors.forename: Jianpeng
authors.initials: J
authors.lastname: Sheng
authors.forename: Yubo
authors.initials: Y
authors.lastname: Zhang
authors.forename: Thompson
authors.initials: T
authors.lastname: Poh
authors.forename: Chee Seng
authors.initials: CS
authors.lastname: Chan
authors.forename: Galih
authors.initials: G
authors.lastname: Kunarso
authors.forename: Atif
authors.initials: A
authors.lastname: Shahab
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Valere
authors.initials: V
authors.lastname: Cacheux-Rataboul
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D002478:Cells, Cultured; D002843:Chromatin / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism*; D057890:Epigenomics; D005786:Gene Expression Regulation; D005809:Genes, Regulator; D017404:In Situ Hybridization, Fluorescence; D051379:Mice; D039904:Pluripotent Stem Cells / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D012097:Repressor Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D004268:DNA-Binding Proteins; D034741:RNA, Small Interfering; D012097:Repressor Proteins