RADIP technology comprehensively identifies H3K27me3-associated RNA–chromatin interactions
Many RNAs associate with chromatin, either directly or indirectly. To investigate the function of these RNAs, many technologies for mapping regions where RNAs interact across the genome have been developed. Adding information on the proteins involved in these RNA–chromatin interactions is critical for further analysis. Here, we developed RADIP (RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation), a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA–chromatin interactions mediated by individual proteins. We applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells. We identified various RNAs, including protein-coding RNAs and non-coding RNAs, that were associated with chromatin via H3K27me3 mediation and that may facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome. Overall design: To Identify genome-wide H3K27me3-mediated RNA-chromatin interactions in mouse ESC.