Denaturing purifications demonstrate that PRC2 and other widely-reported chromatin proteins do not appear to bind directly to RNA in vivo [ChIP-seq]
The Polycomb Repressive Complex 2 (PRC2) has been reported to bind to many RNAs and has become a central player in reports describing the mechanisms of how long non-coding RNAs (lncRNAs) regulate gene expression. Based largely on these observations of PRC2, many additional chromatin proteins have similarly been reported to bind RNA to enact their functions. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here we revisit the evidence supporting broad RNA binding by PRC2 and other chromatin proteins and show that many previously reported RNA-protein interactions do not represent in vivo interactions. We find that denaturing purification of in vivo crosslinked RNA-protein complexes leads to loss of detectable PRC2-RNA interactions. Similarly, we fail to detect in vivo RNA binding of other chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, WDR5, and others), despite accurately mapping bona fide RNA-protein binding sites across a range of proteins including several specific chromatin-associated proteins (SPEN, CHTOP, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms. Overall design: ChIP was used to map chromatin-associated proteins in HEK293T and mouse embryonic stem cells.