TY - JOUR AU - Fang, Jingwen AU - Ma, Qing AU - Chu, Ci AU - Huang, Beibei AU - Li, Lingjie AU - Cai, Pengfei AU - Batista, Pedro J. AU - Tolentino, Karen Erisse Martin AU - Xu, Jin AU - Li, Rui AU - Du, Pengcheng AU - Qu, Kun AU - Chang, Howard Y. PY - 2019 DA - 2019/12/20 TI - PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications JO - Genome Biology SP - 292 VL - 20 IS - 1 AB - 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. SN - 1474-760X UR - https://doi.org/10.1186/s13059-019-1880-3 DO - 10.1186/s13059-019-1880-3 ID - Fang2019 ER -