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Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea

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

ORGANISM(S): Coprinopsis cinerea

PROVIDER: GSE46965 | GEO | 2014/12/02

SECONDARY ACCESSION(S): PRJNA203151

REPOSITORIES: GEO

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Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.

Project description: Not available

| S-EPMC4260599 | biostudies-literature

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [CMS-seq]

Project description:TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mC) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a novel diglucosylation-based method to simultaneously map 5hmC, 5fC and 5caC at near base-pair resolution, and verify the results using independent methods. We have used the method to map the distribution of oxi-mC across the genome of Coprinopsis cinerea, a basidiomycete that encodes 47 TET/JBP paralogs in a new class of DNA transposons. Like 5-methylcytosine (5mC) residues from which they are derived, oxi-mC modifications are enriched at centromeres, TET/JBP transposons, and multicopy paralogous genes that are not expressed, but rarely mark genes whose expression changes between two developmental stages. Our study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage, and describes a method to map all three different species of oxi-mC simultaneously.

2014-12-02 | GSE46963 | GEO