PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Genome Biology 20(1):292- Dec 2019 

Fang, Jingwen; Ma, Qing; Chu, Ci; Huang, Beibei; Li, Lingjie; Cai, Pengfei; Batista, Pedro; Tolentino, Karen Erisse Martin; Xu, Jin; Li, Rui; Du, Pengcheng; Qu, Kun; Chang, Howard Y.


We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromatin and are classified into functional groups based on the patterns of their association with specific histone modifications. We find single-stranded RNA bases are more chromatin-associated, and we discover hundreds of allele-specific RNA-chromatin interactions. These results provide a unique resource to globally study the functions of chromatin-associated lncRNAs and elucidate the basic mechanisms of chromatin-RNA interactions.


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