title: Spatial partitioning of the regulatory landscape of the X-inactivation centre.
abstract: In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the non-protein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C) and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist. We discover a series of discrete 200-kilobase to 1 Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains. TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre.
authors.affiliation: Institut Curie, 26 rue d'Ulm, Paris F-75248, France.
authors.forename: Elphège P
authors.initials: EP
authors.lastname: Nora
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Lajoie
authors.forename: Edda G
authors.initials: EG
authors.lastname: Schulz
authors.forename: Luca
authors.initials: L
authors.lastname: Giorgetti
authors.forename: Ikuhiro
authors.initials: I
authors.lastname: Okamoto
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.forename: Tristan
authors.initials: T
authors.lastname: Piolot
authors.forename: Nynke L
authors.initials: NL
authors.lastname: van Berkum
authors.forename: Johannes
authors.initials: J
authors.lastname: Meisig
authors.forename: John
authors.initials: J
authors.lastname: Sedat
authors.forename: Joost
authors.initials: J
authors.lastname: Gribnau
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
authors.forename: Nils
authors.initials: N
authors.lastname: Blüthgen
authors.forename: Job
authors.initials: J
authors.lastname: Dekker
authors.forename: Edith
authors.initials: E
authors.lastname: Heard
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D021901:DNA, Intergenic / Q000235:genetics; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D044127:Epigenesis, Genetic; D057890:Epigenomics; D005260:Female; D005347:Fibroblasts; D005786:Gene Expression Regulation; D006657:Histones / Q000378:metabolism; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D008745:Methylation; D051379:Mice; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated / Q000235:genetics*; D059467:Transcriptome; D014960:X Chromosome / Q000737:chemistry / Q000235:genetics*; D049951:X Chromosome Inactivation / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D006657:Histones; D062085:RNA, Long Noncoding; D022661:RNA, Untranslated; C465658:Tsix transcript, mouse; C077885:XIST non-coding RNA