PIRCh-seq

PIRCh-seq is a method to comprehensively survey and identify chromatin-associated RNAs in a manner specific to histone modifications. The method allows the identification of hundreds of chromatin-associated RNAs across various cell types with significantly reduced contamination from nascent transcripts. By analyzing the patterns of RNA association with specific histone modifications, non-coding RNAs enriched in chromatin can be classified into functional groups. The study also reveals that single-stranded RNA bases exhibit more chromatin association. Furthermore, PIRCh-seq enables the discovery of hundreds of allele-specific RNA-chromatin interactions. The results obtained from this method provide a unique resource for globally studying the functions of chromatin-associated long non-coding RNAs (lncRNAs) and elucidating the fundamental mechanisms underlying chromatin-RNA interactions.