ArticlePloS one2012
High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 88 citations in OpenAlex.
- Implementation of the Methyl-Seq platform to identify tissue- and sex-specific DNA methylation differences in the rat epigenome.Epigenetics · 2024Article
- Molecular and Structural Alterations of Skeletal Muscle Tissue Nuclei during Aging.International journal of molecular sciences · 2024Review
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- Comparative Analysis of Skeletal Muscle DNA Methylation and Transcriptome of the Chicken Embryo at Different Developmental Stages.Frontiers in physiology · 2021Article
- Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation.BMC genomics · 2020Article
- Maternal vitamin BMolecular and cellular biochemistry · 2020Article
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- Dynamic transcriptome and DNA methylome analyses on longissimus dorsi to identify genes underlying intramuscular fat content in pigs.BMC genomics · 2017Article
- Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus.BMC genomics · 2017Article
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- MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination.Epigenetics & chromatin · 2017Article
- Does skeletal muscle have an 'epi'-memory? The role of epigenetics in nutritional programming, metabolic disease, aging and exercise.Aging cell · 2016Review
- Epigenetics and cortical spreading depression: changes of DNA methylation level at retrotransposon sequences.Molecular biology reports · 2016Article
- Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds.Scientific reports · 2016Article
- DNA Methylation Signature of Post-injury Neointimal Cells During Vascular Remodeling in the Rat Balloon Injury Model.Molecular biology (Los Angeles, Calif.) · 2016Article
- Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.Scientific reports · 2016Article
- Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs.BMC genomics · 2016Article
- DNA Methylation in Skeletal Muscle Stem Cell Specification, Proliferation, and Differentiation.Stem cells international · 2016Review
- DNA methylation Landscape of body size variation in sheep.Scientific reports · 2015Article
Corrections and comments
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.