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

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

in Animal Genetics and Genomics / Animals / Bioinformatics / Biomedical and Life Sciences / Chromatin / Chromatin - metabolism / Chromosomes / Contamination / Deoxyribonucleic acid / DNA / Epigenetics / Evolutionary Biology / Fibroblasts / Gene loci / Genetic Techniques / genome / High-Throughput Nucleotide Sequencing / Histone Code / histones / Human Genetics / Humans / Immunoglobulins / Life Sciences / Method / Mice / Microbial Genetics and Genomics / Non-coding RNA / Plant Genetics and Genomics / Proteins / Ribonucleic acid / RNA / RNA, Untranslated - metabolism / Stem cells / surveys

2019

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

2019

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

2019

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Journal Article

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

Huang, Beibei,

Cai, Pengfei,

Tolentino, Karen Erisse Martin,

Ma, Qing,

Li, Lingjie,

Batista, Pedro J.,

Du, Pengcheng,

Chu, Ci,

Fang, Jingwen,

Li, Rui,

Qu, Kun,

Chang, Howard Y.,

Xu, Jin

2019

Overview

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.

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Animal Genetics and Genomics

/ Animals

/ Bioinformatics

/ Biomedical and Life Sciences

/ Chromatin

/ Chromatin - metabolism

/ Chromosomes