Site-Specific Silencing of Regulatory Elements as a Mechanism of X Inactivation

• Published in: Cell Vol. 151; no. 5; pp. 951 - 963
• Main Authors: Calabrese, J. Mauro, Sun, Wei, Song, Lingyun, Mugford, Joshua W., Williams, Lucy, Yee, Della, Starmer, Joshua, Mieczkowski, Piotr, Crawford, Gregory E., Magnuson, Terry
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.11.2012
• Subjects: Animals; CCCTC-Binding Factor; chromatin; Chromatin - metabolism; chromosomes; Deoxyribonuclease I - metabolism; DNA; epigenetics; gene expression; Gene Silencing; genes; Histone Code; hypersensitivity; Long Interspersed Nucleotide Elements; Mice; Polycomb-Group Proteins - metabolism; Regulatory Elements, Transcriptional; Repressor Proteins - metabolism; RNA Polymerase II - metabolism; stem cells; Stem Cells - cytology; Stem Cells - metabolism; transcription; transcription (genetics); trophoblast; Trophoblasts - cytology; X chromosome; X Chromosome Inactivation
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2012.10.037

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. [Display omitted] ► RNA-Seq analysis finds 13% of genes escape X inactivation in trophoblast stem cells ► Inactive X regulatory elements lack Pol II binding yet retain DNaseI hypersensitivity ► CTCF binds across the inactive X, mostly to locations shared with the active X ► X-inactivated genes near escapers are often separated from the measured Xist cloud The regulatory elements of silent genes on the inactive X chromosome bear a distinct epigenetic signature, consisting of both repressive and active chromatin characteristics. The site-specific inactivation of regulatory elements may control gene silencing on the inactive X to a greater extent than chromosome-wide alterations.