High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation

Abstract

During mammalian X-chromosome inactivation, the Xist long noncoding RNA coats the future inactive X chromosome and recruits polycomb repressive complex 2 to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear; here high-resolution maps of Xist binding sites across the X chromosome are generated and show that Xist does not spread across the inactive X chromosome uniformly but in two steps, initially targeting gene-rich islands before later spreading to intervening gene-poor domains. During mammalian X-chromosome inactivation (XCI), the Xist long noncoding RNA coats the future inactive X (Xi) and recruits polycomb repressive complex 2 (PRC2) to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear. Here, Jeannie Lee and colleagues generate high-resolution maps of Xist binding sites across the X chromosome using a technique termed CHART-seq. By following four early developmental stages in female mouse cells undergoing XCI, they show that Xist does not spread across the Xi uniformly but in two steps — initially targeting gene-rich islands and later spreading to intervening gene-poor domains. The Xist long noncoding RNA (lncRNA) is essential for X-chromosome inactivation (XCI), the process by which mammals compensate for unequal numbers of sex chromosomes1,2,3. During XCI, Xist coats the future inactive X chromosome (Xi)4 and recruits Polycomb repressive complex 2 (PRC2) to the X-inactivation centre (Xic)5. How Xist spreads silencing on a 150-megabases scale is unclear. Here we generate high-resolution maps of Xist binding on the X chromosome across a developmental time course using CHART-seq. In female cells undergoing XCI de novo, Xist follows a two-step mechanism, initially targeting gene-rich islands before spreading to intervening gene-poor domains. Xist is depleted from genes that escape XCI but may concentrate near escapee boundaries. Xist binding is linearly proportional to PRC2 density and H3 lysine 27 trimethylation (H3K27me3), indicating co-migration of Xist and PRC2. Interestingly, when Xist is acutely stripped off from the Xi in post-XCI cells, Xist recovers quickly within both gene-rich and gene-poor domains on a timescale of hours instead of days, indicating a previously primed Xi chromatin state. We conclude that Xist spreading takes distinct stage-specific forms. During initial establishment, Xist follows a two-step mechanism, but during maintenance, Xist spreads rapidly to both gene-rich and gene-poor regions.