Abstract
Xist is indispensable for X chromosome inactivation. However, how Xist RNA directs chromosome-wide silencing and why some regions are more efficiently silenced than others remains unknown. Here, we explore the function of Xist by inducing ectopic Xist expression from multiple different X-linked and autosomal loci in mouse aneuploid and female diploid embryonic stem cells in which Xist-mediated silencing does not lead to lethal functional monosomy. We show that ectopic Xist expression faithfully recapitulates endogenous X chromosome inactivation from any location on the X chromosome, whereas long-range silencing of autosomal genes is less efficient. Long interspersed elements facilitate inactivation of genes located far away from the Xist transcription locus, and genes escaping X chromosome inactivation show enrichment of CTCF on X chromosomal but not autosomal loci. Our findings highlight important genomic and epigenetic features acquired during sex chromosome evolution to facilitate an efficient X chromosome inactivation process.
Highlights
Xist is indispensable for X chromosome inactivation
By inducing ectopic X chromosome inactivation (XCI) from several genomic regions in karyotypically normal and abnormal embryonic stem cell (ESC) lines, we discovered that: (I) Xist’s silencing efficiency is locus dependent, (II) specific Xlinked but not autosomal loci are intrinsically prone to become inactivated or to escape XCI, (III) long interspersed elements (LINE) facilitate gene silencing but are unlikely to work as X-specific way stations, and (IV) CTCF plays a X-specific role in directing XCI escape
To assess the efficiency of Xist-mediated silencing from several genomic contexts, we set up a doxycycline-responsive expression system in F1 2–1 ESC lines (129/Sv-Cast/Ei)
Summary
Xist is indispensable for X chromosome inactivation. how Xist RNA directs chromosome-wide silencing and why some regions are more efficiently silenced than others remains unknown. Escaping genes lack the epigenetic marks typical of inactivated genes and retain active marks[22, 23] They are located outside the Xist RNA domain[3, 24], have been suggested to be intrinsically competent to resist XCI25, and to be flanked by cis-acting elements that protect neighboring genes from escape[26]. By inducing ectopic XCI from several genomic regions in karyotypically normal and abnormal ESC lines, we discovered that: (I) Xist’s silencing efficiency is locus dependent, (II) specific Xlinked but not autosomal loci are intrinsically prone to become inactivated or to escape XCI, (III) LINEs facilitate gene silencing but are unlikely to work as X-specific way stations, and (IV) CTCF plays a X-specific role in directing XCI escape
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