title: Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci.
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.
authors.affiliation: Genomics and Molecular Medicine Unit and GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India.
authors.forename: Satish
authors.initials: S
authors.lastname: Sati
authors.forename: Sourav
authors.initials: S
authors.lastname: Ghosh
authors.forename: Vaibhav
authors.initials: V
authors.lastname: Jain
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.forename: Shantanu
authors.initials: S
authors.lastname: Sengupta
mesh_terms: D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D056426:Genetic Loci; D015894:Genome, Human; D006657:Histones / Q000378:metabolism; D006801:Humans; D011506:Proteins / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; D011506:Proteins; D062085:RNA, Long Noncoding