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Functional classification of chromatin associated lncRNAs via histone modification specific PIRCh-seq analysis

ABSTRACT: 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.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE119006 | GEO | 2019/10/30

REPOSITORIES: GEO

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Functional classification of chromatin associated lncRNAs via histone modification specific PIRCh-seq analysis

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