GSE109395
Xist RNA antagonizes the chromatin remodeler, BRG1, from the inactive X chromosome
The noncoding Xist RNA recruits silencing factors to the inactive X (Xi) and facilitates re-organization of Xi structure. Here, we examine the epigenomic landscape of the Xi and assess how Xist alters chromatin accessibility. Interestingly, Xist deletion propels selective chromatin re-accessibility on the Xi, affecting various Xi regions differentially. Re-accessibility is regulated by BRG1, an ATPase subunit of SWI/SNF chromatin remodeling complex. In vitro, RNA binding inhibits the nucleosome remodeling and ATPase activities of BRG1. In vivo, Xist directly interacts with BRG1 and expels BRG1 from the Xi. Xist ablation leads to a selective return of BRG1 in cis, emanating from pre-existing BRG1 sites that are Xist-free. BRG1's return correlates with cohesin re-binding and restoration of topologically associated domains (TADs), and results in formation of de novo Xi "superloops." Thus, Xist RNA binding inhibits BRG1's nucleosome remodeling activity and results in expulsion of the SWI/SNF complex from the Xi. Overall design: The role of Xist RNA as a safeguard of the Xi chromsome during X-chromosome inactivation (XCI) was explored by performing DNA accessibility assay (ATAC-seq) in WT and Xist-KO fibroblast cells. Xist's role in repulsion of the catalytic subunit of SWI/SNF complex, BRG1, was determined by native chromatin immunoprecipitation (ChIP-seq) in these cells. Xist's role on gene regulation during XCI maintenance was investigated by genome-wide expression profiling (RNA-seq).