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Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE50080 | GEO | 2013/09/09

SECONDARY ACCESSION(S): PRJNA215949

REPOSITORIES: GEO

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Deep sequencing reveals increased DNA methylation in chronic rat epilepsy.

Project description:Epilepsy is a frequent neurological disorder, although onset and progression of seizures remain difficult to predict in affected patients, irrespective of their epileptogenic condition. Previous studies in animal models as well as human epileptic brain tissue revealed a remarkably diverse pattern of gene expression implicating epigenetic changes to contribute to disease progression. Here we mapped for the first time global DNA methylation patterns in chronic epileptic rats and controls. Using methyl-CpG capture associated with massive parallel sequencing (Methyl-Seq) we report the genomic methylation signature of the chronic epileptic state. We observed a predominant increase, rather than loss of DNA methylation in chronic rat epilepsy. Aberrant methylation patterns were inversely correlated with gene expression changes using mRNA sequencing from same animals and tissue specimens. Administration of a ketogenic, high-fat, low-carbohydrate diet attenuated seizure progression and ameliorated DNA methylation mediated changes in gene expression. This is the first report of unsupervised clustering of an epigenetic mark being used in epilepsy research to separate epileptic from non-epileptic animals as well as from animals receiving anti-convulsive dietary treatment. We further discuss the potential impact of epigenetic changes as a pathogenic mechanism of epileptogenesis.

| S-EPMC3825532 | biostudies-literature

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy (MBD-seq)

Project description:Explore DNA methylation in chronic epilepsy and its relationship to gene expression.

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Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-09 | E-GEOD-50080 | biostudies-arrayexpress

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy (mRNA-seq)

Project description:Explore DNA methylation in chronic epilepsy and its relationship to gene expression.

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Deep sequencing reveals increased DNA methylation in chronic rat epilepsy (mRNA-seq)

Project description:Explore DNA methylation in chronic epilepsy and its relationship to gene expression. Examination of expression changes in pilocarpine-treated rats compared to controls and pilocarpine-treated rats on a ketogenic diet.

2013-09-09 | E-GEOD-50079 | biostudies-arrayexpress

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy (MBD-seq)

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2013-09-09 | E-GEOD-50077 | biostudies-arrayexpress

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Project description:Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

| PRJNA215949 | ENA

Etiology matters - Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy.

Project description:This study tested the hypothesis that acquired epileptogenesis is accompanied by DNA methylation changes independent of etiology. We investigated DNA methylation and gene expression in the hippocampal CA3/dentate gyrus fields at 3 months following epileptogenic injury in three experimental models of epilepsy: focal amygdala stimulation, systemic pilocarpine injection, or lateral fluid-percussion induced traumatic brain injury (TBI) in rats. In the models studies, DNA methylation and gene expression profiles distinguished controls from injured animals. We observed consistent increased methylation in gene bodies and hypomethylation at non-genic regions. We did not find a common methylation signature in all three different models and few regions common to any two models. Our data provide evidence that genome-wide alteration of DNA methylation signatures is a general pathomechanism associated with epileptogenesis and epilepsy in experimental animal models, but the broad pathophysiological differences between models (i.e. pilocarpine, amygdala stimulation, and post-TBI) are reflected in distinct etiology-dependent DNA methylation patterns.

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Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (TBI – MBD-seq)

Project description:Explore DNA methylation in traumatic brain injury model of epilepsy and its relationship to gene expression.

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Etiology matters - Comparing Genomic DNA Methylation Patterns in Three Rat Models of Acquired Epilepsy (Amygdala stimulation – MBD-seq)

Project description:Explore DNA methylation in focal amygdala stimulation model of epilepsy and its relationship to gene expression.

2016-09-06 | GSE75400 | GEO