title: Site-specific silencing of regulatory elements as a mechanism of X inactivation.
abstract: The inactive X chromosome's (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequences is unknown. Therefore, we profiled Xi gene expression and chromatin states at high resolution via allele-specific sequencing in mouse trophoblast stem cells. Most notably, X-inactivated transcription start sites harbored distinct epigenetic signatures relative to surrounding Xi DNA. These sites displayed H3-lysine27-trimethylation enrichment and DNaseI hypersensitivity, similar to autosomal Polycomb targets, yet excluded Pol II and other transcriptional hallmarks, similar to nontranscribed genes. CTCF bound X-inactivated and escaping genes, irrespective of measured chromatin boundaries. Escape from X inactivation occurred within, and X inactivation was maintained exterior to, the area encompassed by Xist in cells subject to imprinted and random X inactivation. The data support a model whereby inactivation of specific regulatory elements, rather than a simple chromosome-wide separation from transcription machinery, governs gene silencing over the Xi.
authors.affiliation: Department of Genetics, the Carolina Center for Genome Sciences, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.
authors.forename: J Mauro
authors.initials: JM
authors.lastname: Calabrese
authors.forename: Wei
authors.initials: W
authors.lastname: Sun
authors.forename: Lingyun
authors.initials: L
authors.lastname: Song
authors.forename: Joshua W
authors.initials: JW
authors.lastname: Mugford
authors.forename: Lucy
authors.initials: L
authors.lastname: Williams
authors.forename: Della
authors.initials: D
authors.lastname: Yee
authors.forename: Joshua
authors.initials: J
authors.lastname: Starmer
authors.forename: Piotr
authors.initials: P
authors.lastname: Mieczkowski
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
authors.forename: Terry
authors.initials: T
authors.lastname: Magnuson
mesh_terms: D000818:Animals; D000076246:CCCTC-Binding Factor; D002843:Chromatin / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000378:metabolism; D020868:Gene Silencing; D042421:Histone Code; D020084:Long Interspersed Nucleotide Elements; D051379:Mice; D063146:Polycomb-Group Proteins / Q000378:metabolism; D012319:RNA Polymerase II / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D012097:Repressor Proteins / Q000378:metabolism; D013234:Stem Cells / Q000166:cytology / Q000378:metabolism; D014327:Trophoblasts / Q000166:cytology; D049951:X Chromosome Inactivation
chemical_list: D000076246:CCCTC-Binding Factor; D002843:Chromatin; C000619698:Ctcf protein, mouse; D063146:Polycomb-Group Proteins; D012097:Repressor Proteins; D012319:RNA Polymerase II; D003850:Deoxyribonuclease I