High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region
IR@IGIB: CSIR-Institute of Genomics & Integrative Biology, New Delhi
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| Title |
High Resolution Methylome Map of Rat Indicates Role
of Intragenic DNA Methylation in Identification of
Coding Region
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| Creator |
Sati, Satish
Tanwar, Vinay Singh Kumar, K. Anand Patowary , Ashok Jain, Vaibhav Ghosh, Sourav Ahmed , Shadab Singh, Meghna Reddy, S. Umakar Chandak, Giriraj Raj Raghunath, Manchala Sivasubbu, Sridhar Chakraborty, Kaushik Scaria, Vinod Sangupta, Shantanu |
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| Subject |
G1 Genome informatics (General)
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| Description |
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 a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability.
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| Date |
2012-02-15
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| Type |
Article
PeerReviewed |
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| Format |
application/pdf
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| Identifier |
http://openaccess.igib.res.in/144/1/Satish2011_PloS%20One.pdf
Sati, Satish and Tanwar, Vinay Singh and Kumar, K. Anand and Patowary , Ashok and Jain, Vaibhav and Ghosh, Sourav and Ahmed , Shadab and Singh, Meghna and Reddy, S. Umakar and Chandak, Giriraj Raj and Raghunath, Manchala and Sivasubbu, Sridhar and Chakraborty, Kaushik and Scaria, Vinod and Sangupta, Shantanu (2012) High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region. First High Resolution Rat Methylome, 7 (2). pp. 1-11. |
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| Relation |
http://openaccess.igib.res.in/144/
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