The role of XIST in X-inactivation maintenance in B cells (RNA-seq)

The long noncoding RNA (lncRNA) XIST establishes X chromosome inactivation (XCI) in female cells in early development and thereafter is thought to be largely dispensable. Here we show XIST is continually required in adult human B cells to silence a subset of X-linked immune genes such as TLR7. XIST-dependent genes lack promoter DNA methylation and require continual XIST-dependent histone deacetylation. XIST RNA-directed proteomics and CRISPRi screen reveal distinctive somatic cell-specific XIST complexes, and identify TRIM28 that mediates Pol II pausing at promoters of X-linked genes in B cells. XIST dysregylation, reflected by escape of XIST-dependent genes, occurs in CD11c+ atypical memory B cells across single-cell transcriptome data in patients with female-biased autoimmunity and COVID-19 infection. XIST inactivation with TLR7 agonism suffices to promote isotype-switched atypical B cells. These results suggest cell-type-specific diversification of lncRNA-protein complexes increase lncRNA functionalities, and expand roles for XIST in sex-differences in biology and medicine. Overall design: RNA-seq of dCas9-Krab+ GM B cells transduced with guide RNA and treated with DNMT and EZH2 epigenetic inhibitors (sgNT+DMSO, sgXIST+DMSO, sgNT+inhibitors, sgXIST+inhibitors), Trim28_KO GM B cells, Spen_deltaRRM GM B cells, sgNT and sgXIST cells that are overexpressed with anti-CRISPR protein ( sgNT+ACRIIA4, sgXIST+ACRIIA4), dCas9-Krab+ IMR90 cells transduced with guide RNA (IMR90_sgNT, IMR90_sgXIST) .