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Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):E5149-58. doi: 10.1073/pnas.1419513111. Epub 2014 Nov 18.

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

Author information

1
Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037;
2
Pacific Biosciences, Menlo Park, CA 94025;
3
Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115;
4
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;
5
Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;
6
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
7
Skirball Institute, NYU Langone Medical Center, New York University, New York, NY 10016;
8
Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, CA 92521; and.
9
Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093 arao@liai.org.

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

PMID:
25406324
PMCID:
PMC4260599
DOI:
10.1073/pnas.1419513111
[Indexed for MEDLINE]
Free PMC Article

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