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Escape from X inactivation is directly modulated by Xist non-coding RNA [CUT&Run]

ABSTRACT: X-chromosome inactivation silences one copy of the X-chromosome in female cells, but a number of genes escapes this inactivation. We asked whether increased levels of Xist RNA, the molecular actor driving X-inactivation, impacts expression levels of escapees. To this end, we performed CUT&RUN profiling for two Xi-enriched histone marks, H2AK119Ub and H3K27me3 in a clonal neural progenitor cell line with transgenes that allow for the overexpression of Xist on the inactive X chromosome. We perform Xist overexpression experiments for up to three weeks and also test the reversibility of Xist overexpression using washout experiments.

ORGANISM(S): Mus

PROVIDER: GSE289899 | GEO | 2025/12/09

REPOSITORIES: GEO

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Escape from X inactivation is directly modulated by Xist non-coding RNA [methylation]

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Escape from X inactivation is directly modulated by Xist non-coding RNA [ATAC-seq]

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The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA.

Project description:3D-topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between transcriptional activity and spatial environment of a gene, we have used allele-specific 4C-technology to produce high-resolution topology maps of the active and inactive X-chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial re-folding of the inactive X into a conformation resembling the active X, without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X-chromosome independently of transcription. Five or six 4C viewpoints were applied on the mouse female wild type active X-chromosome, the wild type inactive X-chromosome, the conditional Xist X-chromosome and the Xist knock out X-chromosome

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