Unknown,Transcriptomics,Genomics,Proteomics

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Functional DNA methylation is accompanied by chromatin accessibility [methylation]


ABSTRACT: Analysis of nucleosome positioning and chromatin state by using CpG methyltransferase M.SssI to methylate nuclei. Unmethylated regions that gain methylation (low to high beta value) are known to be accessible and nucleosome depleted. Method used to study changes after epigenetic drug treatments identified that majority of demethylation events are not accompanied by chromatin accessibility changes. Intact nuclei are harvested from cells and treated with M.SssI. DNA is then extracted, bisulfite converted and run on an Infinium methylation array, along with a no-enzyme control. Background subtracted beta values (listed below) are used to determine regions that have gained methylation on enzyme treatment compared to the control - and these are used to infer chromatin state

ORGANISM(S): Homo sapiens

SUBMITTER: Kurinji Pandiyan 

PROVIDER: E-GEOD-43851 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Functional DNA demethylation is accompanied by chromatin accessibility.

Pandiyan Kurinji K   You Jueng Soo JS   Yang Xiaojing X   Dai Chao C   Zhou Xianghong J XJ   Baylin Stephen B SB   Jones Peter A PA   Liang Gangning G  

Nucleic acids research 20130213 7


DNA methylation inhibitors such as 5-aza-2'-deoxycytidine (5-Aza-CdR) are currently used for the treatment of myelodysplastic syndrome. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression. We use the colorectal cancer cell line HCT116 as a model to address this question and determine that <2% of regions demethylated by 5-Aza-CdR treatment assume an open config  ...[more]

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