Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea.
Proc Natl Acad Sci U S A, 2014/12/02;111(48):E5149-58.
Chavez L[1], Huang Y[1], Luong K[2], Agarwal S[3], Iyer LM[4], Pastor WA[5], Hench VK[6], Frazier-Bowers SA[6], Korol E[7], Liu S[8], Tahiliani M[7], Wang Y[8], Clark TA[2], Korlach J[2], Pukkila PJ[6], Aravind L[4], Rao A[9]
Affiliations
PMID: 25406324DOI: 10.1073/pnas.1419513111
Impact factor: 12.779
Abstract
TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mCs) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a method based on diglucosylation of 5-hydroxymethylcytosine (5hmC) to simultaneously map 5hmC, 5-formylcytosine, and 5-carboxylcytosine at near-base-pair resolution. 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 previously unidentified class of DNA transposons. Like 5-methylcytosine 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-mCs simultaneously.
Keywords: 5caC; 5fC; 5mC; SMRT-seq; TET
MeSH terms
5-Methylcytosine; Basidiomycota; Chromosomes, Fungal; DNA Methylation; DNA Transposable Elements; Dioxygenases; Fungal Proteins; Gene Expression Regulation, Developmental; Gene Expression Regulation, Fungal; Genome, Fungal; HEK293 Cells; Humans; Hyphae; Oxidation-Reduction; Sequence Analysis; Spores, Fungal
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