PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

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

doi:10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

Genome Biol. 2019 Dec 20;20(1):292. doi: 10.1186/s13059-019-1880-3.

Authors

Jingwen Fang¹, Qing Ma^{2

3}, Ci Chu², Beibei Huang¹, Lingjie Li², Pengfei Cai¹, Pedro J Batista^{2

4}, Karen Erisse Martin Tolentino², Jin Xu², Rui Li², Pengcheng Du¹, Kun Qu⁵, Howard Y Chang^{6

7}

Affiliations

¹ Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
² Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA.
³ Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
⁴ Present Address: Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
⁵ Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China. [email protected].
⁶ Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA. [email protected].
⁷ Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA. [email protected].

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.

Publication types

Evaluation Study
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Chromatin / metabolism*
Genetic Techniques*
High-Throughput Nucleotide Sequencing
Histone Code*
Humans
Mice
RNA, Untranslated / metabolism*

Substances

Chromatin
RNA, Untranslated

Abstract

Publication types

MeSH terms

Substances

Grants and funding