A novel cis regulatory element regulates human XIST in CTCF-dependent manner

Abstract

The long non-coding RNA XIST is the master regulator for the process of X chromosome inactivation in mammalian females. Here we report the existence of a hitherto uncharacterized cis regulatory element within the first exon of human XIST, which by associating with the promoter region through chromatin looping defines the transcriptional status of XIST. This interaction is brought about by CTCF, which in turn assists towards the maintenance of YY1 binding at the promoter and governs XIST transcription. Strikingly, the cis element is competitively bound by pluripotency factors and CTCF, wherein the enrichment of the former disrupts its interaction with thepromoter, leading to downregulation of XIST. Based on sequence similarity of this element across species we propose that this mechanism is conserved between the human and mouse systems. Collectively, our study uncovers the