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PMID: 22923516 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci.

Nucleic acids research ·Vol. 40 ·No. 20 ·2012-11-01 ·Pages 10018-31

Sati S, Ghosh S, Jain V, Scaria V, Sengupta S

Abstract

A major fraction of the transcriptome of higher organisms comprised an extensive repertoire of long non-coding RNA (lncRNA) which express in a cell type and development stage-specific manner. While lncRNAs are a proven component of epigenetic gene expression modulation, epigenetic regulation of lncRNA itself remains poorly understood. Here we have analysed pan-genomic DNA methylation and histone modification marks (H3K4me3, H3K9me3, H3K27me3 and H3K36me3) associated with transcription start site (TSS) of lncRNA in four different cell types and three different tissue types representing various cellular stages. We observe that histone marks associated with active transcription H3K4me3 and H3K36me3 along with the repressive histone mark H3K27me3 have similar distribution pattern around TSS irrespective of cell types. Also, the density of these marks correlates well with expression of protein-coding and lncRNA genes. In contrast, the lncRNA genes harbour higher methylation density around TSS than protein-coding genes regardless of their expression status. Furthermore, we found that DNA methylation along with the other repressive histone mark H3K9me3 does not seem to play a role in lncRNA expression. Thus, our observation suggests that epigenetic regulation of lncRNA shares common features with mRNA except the role of DNA methylation which is markedly dissimilar.

MeSH Terms
CpG Islands DNA Methylation Epigenesis, Genetic Genetic Loci Genome, Human Histones/metabolism Humans Proteins/genetics RNA, Long Noncoding/genetics Transcription Initiation Site
Chemicals
Histones Proteins RNA, Long Noncoding
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Sati Satish
Genomics and Molecular Medicine Unit and GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India.
Ghosh Sourav
Jain Vaibhav
Scaria Vinod
Sengupta Shantanu
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks776
Published
2012-11-01
Epub
2012-00-25
Pages
10018-31
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3488231
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gks776 PMC Full Text View journal details
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