HCFC1 and YY1 mediate recruitment of COMPASS and Integrator to initiate X chromosome inactivation

The evolution of mammalian sex chromosomes has driven the emergence of mechanisms that balance X-linked gene dosage between male (XY) and female (XX) cells. In females, dosage compensation is achieved through X chromosome inactivation (XCI), initiated by upregulation of the long non-coding RNA Xist, which spreads in cis, recruiting chromatin modifiers to silence gene expression on one X chromosome. Here, we conducted a forward genetic screen and identified X-encoded Host Cell Factor 1 (HCFC1), a member of the COMPASS H3K4 methyltransferase complex, as a dose-dependent XCI-activator. HCFC1 loss results in genome-wide reduction of H3K4me3 at specific regulatory elements and downregulation of nearby genes, including Xist. We show that HCFC1 and YY1 are co-recruited genome-wide to gene regulatory elements. Mass spectrometry analysis confirmed an interaction of HCFC1 and YY1 and uncovered the Integrator complex as another prominent YY1 partner. YY1 depletion results in genome-wide loss of Integrator recruitment at gene regulatory elements and reduced expression of nearby genes, including Xist cis-regulatory genes Jpx and Ftx. These results highlight a co-regulatory role for HCFC1 in COMPASS recruitment and Xist activation, alongside YY1-mediated recruitment of Integrator to Xist regulatory elements and genes to activate female-exclusive XCI.