GSE119006
Functional classification of chromatin associated lncRNAs via histone modification specific PIRCh-seq analysis
Many long noncoding RNAs (lncRNAs) regulate gene transcription through binding to histone modifying complexes, therefore a comprehensive study of chromatin associated RNA in a histone modification specific manner is critical to understand their regulatory mechanisms. In this study, we developed a new method named Profiling Interacting RNAs on Chromatin followed by deep sequencing (PIRCh-seq), and profiled chromatin associated transcriptome on 3 cell types, mouse v6.5 embryonic stem cells (mESC), mouse embryonic fibroblasts (MEF) and mouse neuronal precursor cells (NPC), with antibodies attached to histone H3 and 6 active and repressive histone modifications. Compared with existing methods, PIRCh-seq identifies chromatin associated RNAs with significant lower nascent transcription, and classifies chromatin enriched lncRNAs into 6 functional groups based on the patterns of their attachment to nucleosome with specific chemical modifications. Further analysis showed that lncRNAs were also enriched with different modified chromatin in different cell types, suggesting lncRNAs' regulation may also be cell type specific. By integrating profiles of RNA secondary structure from icSHAPE and RNA m(6)A modification, we noticed that RNA bases attached with chromatin tend to be more single stranded. These results provide a unique resource to globally study the functions of chromatin associated lncRNAs and elucidates the basic mechanisms of chromatin-RNA association. Overall design: In this study, we developed a new method named Profiling Interacting RNAs on Chromatin followed by deep sequencing (PIRCh-seq), which enriches chromatin associated RNAs at a histone modification specific manner and classifies functional lncRNAs based on the patterns of their attachment to nucleosome with specific chemical modifications. Compare to existing chromatin-RNA association detection techniques, PIRCh-seq efficiently reduces the influence of nascent transcripts with significantly lower number of intronic reads. Through performing PIRCh-seq with histone H3 and a number of different histone modification specific antibodies on different cell-types, we identify cell type specific relationship between lncRNAs and epigenetics. We found chromatin associated lncRNAs can be classified into 6 functional groups, based on their association with chromatin under histone modifications, and is partly conserved among several cell types. We also discovered lncRNAs were associated with different chromatin modifications in different cell types, indicating lncRNAs' regulation may also be cell type specific. In addition, we found that bases on lncRNAs attached with chromatin tends to be more single stranded. In total, the PIRCh-seq data provides insights into global functional and mechanistic study of chromatin associated lncRNAs.