High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region.

PloS One
Satish SatiShantanu Sengupta

Abstract

DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play ...Continue Reading

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Citations

Jan 9, 2014·BMC Genomics·Jianmin SuYong Zhang
Oct 26, 2013·Molecular Biology and Evolution·Trees-Juen Chuang, Feng-Chi Chen
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Mar 20, 2020·Molecular and Cellular Biochemistry·Vinay Singh TanwarShantanu Sengupta
Jun 25, 2017·BMC Genomics·Stefano FrattiniPaola Crepaldi

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Methods Mentioned

BETA
chemical modifications
immunoprecipitation
MeDIP-Seq
PCR
ChIP-Seq
electrophoresis
MeDIP
Seq

Software Mentioned

R
MACS ( Model - based Analysis for ChIP - Seq )
UCSC Genome Browser
ENSEMBLE browser Bioinformatics
Seq
MeDIP
âmaqâ
GA pipeline
Proteome Discoverer
BiQ Analyzer

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