Dataset Information

Active chromatin marks are retained on X chromosomes lacking gene or repeat silencing despite XIST/Xist expression in somatic cell hybrids.

ABSTRACT:

Background

X-chromosome inactivation occurs early in mammalian development and results in the inactive X chromosome acquiring numerous hallmarks of heterochromatin. While XIST is a key player in the inactivation process, the method of action of this ncRNA is yet to be determined.

Methodology/principal findings

To assess which features of heterochromatin may be directly recruited by the expression and localization of the XIST RNA we have analyzed a mouse/human somatic cell hybrid in which expression of human and mouse XIST/Xist has been induced from the active X by demethylation. Such hybrids had previously been demonstrated to disconnect XIST/Xist expression from gene silencing and we confirm maintenance of X-linked gene expression, even close to the Xist locus, despite the localized expression of mouse Xist.

Conclusions/significance

Loss of the active chromatin marks H3 acetylation and H3 lysine 4 methylation was not observed upon XIST/Xist expression, nor was there a gain of DNA methylation; thus these marks of facultative heterochromatin are not solely dependent upon Xist expression. Cot-1 holes, regions of depleted RNA hybridization with a Cot-1 probe, were observed upon Xist expression; however, these were at reduced frequency and intensity in these somatic cells. Domains of human Cot-1 transcription were observed corresponding to the human chromosomes in the somatic cell hybrids. The Cot-1 domain of the X was not reduced with the expression of XIST, which fails to localize to the human X chromosome in a mouse somatic cell background. The human inactive X in a mouse/human hybrid cell also shows delocalized XIST expression and an ongoing Cot-1 domain, despite X-linked gene silencing. These results are consistent with recent reports separating Cot-1 silencing from genic silencing, but also demonstrate repetitive element expression from an otherwise silent X chromosome in these hybrid cells.

SUBMITTER: Thorogood NP

PROVIDER: S-EPMC2875404 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature

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Publications

Active chromatin marks are retained on X chromosomes lacking gene or repeat silencing despite XIST/Xist expression in somatic cell hybrids.

Thorogood Nancy P NP Brown Carolyn J CJ

PloS one 20100524 5

<h4>Background</h4>X-chromosome inactivation occurs early in mammalian development and results in the inactive X chromosome acquiring numerous hallmarks of heterochromatin. While XIST is a key player in the inactivation process, the method of action of this ncRNA is yet to be determined.<h4>Methodology/principal findings</h4>To assess which features of heterochromatin may be directly recruited by the expression and localization of the XIST RNA we have analyzed a mouse/human somatic cell hybrid i ...[more]

PMID: 20520737

Similar Datasets

Project description:The long non-coding RNA XIST is critical during early female development for establishing X-chromosome inactivation. XIST continues to be expressed from the inactive X throughout life, and can establish silenced heterochromatin when ectopically expressed; yet silencing of most genes on the inactive X has been shown to continue in the absence of XIST in somatic cells. As changes in XIST expression are observed in cancers and aging we sought to re-examine the impact of complete or partial XIST loss on gene expression and chromatin structure in the hTERT RPE-1 cell line. Loss of the A repeat region resulted in complete loss of XIST expression. While loss of an adjacent enhancer region spanning the small F repeat region impacted expression and loss of the repeat E region impacted localization, both deletions maintained partial silencing. Upon XIST loss there was reactivation of a subset of X-linked genes, with escape genes showing an average 20% increase in expression; consistent with other studies. Comparison with other studies of XIST loss in human somatic cells revealed some common XIST-dependent escapees, while autosomal genes demonstrated no consistent XIST-dependencies. Loss of XIST in hTERT RPE-1 resulted in loss of H3K27me3 and H2AK119ub; however, inhibition of each of these pathways failed to upregulate candidate escapees on the inactive X. In contrast, reduction of H3K9me3 caused partial reactivation of USP9X but not MED14. XIST regulatory elements lie within the gene, with ongoing expression dependent on the A repeat region, as well as enhancer function from the adjacent F-containing region. Unlike the E region, the F region is not involved in XIST localization. Our work, in agreement with previous studies, reveals that in somatic cells XIST expression and localization suppresses the expression of escape genes, likely through loss of XIST-dependent chromatin modifications. No single chromatin modification was responsible for the XIST-dependency, varying across both genes and studied cell lines, thus implicating combinatorial action of silencing pathways on the inactive X. While disruption of autosomal gene expression is observed, there are no consistent autosomal XIST-dependencies to implicate a direct action of XIST on autosomes across cell types.

Dataset Information

Active chromatin marks are retained on X chromosomes lacking gene or repeat silencing despite XIST/Xist expression in somatic cell hybrids.

Background

Methodology/principal findings

Conclusions/significance

Publications

Active chromatin marks are retained on X chromosomes lacking gene or repeat silencing despite XIST/Xist expression in somatic cell hybrids.

Similar Datasets

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