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PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications. Genome biology Fang, J. n., Ma, Q. n., Chu, C. n., Huang, B. n., Li, L. n., Cai, P. n., Batista, P. J., Tolentino, K. E., Xu, J. n., Li, R. n., Du, P. n., Qu, K. n., Chang, H. Y. 2019; 20 (1): 292

Abstract

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.

View details for DOI 10.1186/s13059-019-1880-3

View details for PubMedID 31862000