Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs

The mechanisms and biological roles of Polycomb repressive complex (PRC) recruitment by lncRNAs remain unclear. To gain insight, we expressed two lncRNAs that recruit PRCs to multi-megabase domains, Airn and Xist, from an ectopic locus and compared effects. Unexpectedly, ectopic Airn recruited PRC1 and PRC2 to chromatin with a potency resembling Xist yet did not repress genes. Compared to PRC2, PRC1 was more proximal to Airn and Xist, where its enrichment over C-rich elements required the RNA-binding protein HNRNPK. Fusing Airn to Repeat A, the domain required for gene silencing by Xist, enabled gene silencing and altered local patterns but not relative levels of PRC-directed modifications. Our data suggest that endogenously, Airn recruits PRCs to maintain rather than initiate gene silencing; that PRC recruitment occurs independently of Xist Repeat A; and that protein-bridged interactions, not direct RNA contacts, underlie PRC recruitment by Airn, Xist, and other lncRNAs. Chromatin Immunoprecipitation DNA (ChIP-) and total RNA sequencing (RNA-Seq) in RMCE ESCs and TSCs. RNA immunoprecipitation-sequencing (RIP-Seq) in RMCE ESCs. Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) in RMCE ESCs. Total RNA sequencing (RNA-Seq) in RMCE ESCs and TSCs. Nuclear, chromatin, and Cytoplasm RNA-seq from Cellular fractionation of TSCs. RNA immunoprecipitation-sequencing (RIP-Seq) in TSCs.