Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat

Scientific Reports
Aimin LiLei Wang

Abstract

Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads from 59 publications together with RefSeq and UniGene annotated RNAs, we report 39,154 lincRNA transcripts encoded by 19,162 lincRNA genes in the rat. We reveal sequence and expression similarities in lincRNAs of rat, mouse and human. DNA methylation level of lincRNAs is higher than that of protein-coding genes across the transcription start sites (TSSs). And, three lincRNA genes overlap with differential methylation regions (DMRs) which associate with spontaneously hypertensive disease. In addition, there are similar binding trends for three transcription factors (HNF4A, CEBPA and FOXA1) between lincRNA genes and protein-coding genes, indicating that they harbour similar transcription regulatory mechanisms. To date, this is the most comprehensive assessment of lincRNAs in the rat genome. We provide valuable data that will advance lincRNA research using rat as a model.

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Citations

Apr 5, 2018·Journal of Molecular Cell Biology·Giuseppe MilitelloShizuka Uchida

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Datasets Mentioned

BETA
SRP037986
28

Methods Mentioned

BETA
RNA-seq
immunoprecipitation
BS-Seq
MeDIP-seq
ChIP-seq
methylation

Software Mentioned

BLASTN
Ensembl Biomart
gplots
TopHat
DAVID Bioinformatics Tool
BLAST
RatTransc
Ensembl
Bismark
Bsseq bioconductor

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