Genomics

Dataset Information

240

Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells


ABSTRACT: In this study, we analyzed the DNA methylation levels of 4799 IAP LTRs in three murine cell types: AB2.2 ES cells, somatic cells and a neuroblastoma cell line Neuro2A. According to the results, half of the IAP LTR retrotransposons show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all of this group are hypomethylated in Neuro2A cells. Interestingly, the observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study alterations in DNA methylation at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression. HT-TREBS has been used with the Ion Torrent PGM platform to analyze the DNA methylation of 4799 IAP LTRs in a locus-specific manner in 3 cell types: somatic cells (previously submitted under GEO Accession GSE49222), AB2.2 ES cells and Neuro2A cells

ORGANISM(S): Mus musculus  

SUBMITTER: Joomyeong Kim   Arundhati Bakshi 

PROVIDER: E-GEOD-60007 | ArrayExpress | 2015-06-15

SECONDARY ACCESSION(S): GSE60007SRP045175PRJNA257271

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing.

Bakshi Arundhati A   Ekram Muhammad B MB   Kim Joomyeong J  

Genomics data 20150301


DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a new protocol termed High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS) (Ekram and Kim, 2014 [1]). We have used this technique to characterize the locus-specific patterns of DNA methylation of 4799 members of the mouse IAP LTR (Intra  ...[more]

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