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

• Published in: Proceedings of the National Academy of Sciences - PNAS 2014-12, Vol.111 (48), p.E5149-E5158
• Main Authors: Chavez, Lukas, Huang, Yun, Luong, Khai, Agarwal, Suneet, Iyer, Lakshminarayan M, Pastor, William A, Hench, Virginia K, Frazier-Bowers, Sylvia A, Korol, Evgenia, Liu, Shuo, Tahiliani, Mamta, Wang, Yinsheng, Clark, Tyson A, Korlach, Jonas, Pukkila, Patricia J, Aravind, L, Rao, Anjana
• Format: Article
• Language: English
• Subjects: 5-Methylcytosine - metabolism; Basidiomycetes; Basidiomycota - genetics; Basidiomycota - growth & development; Basidiomycota - metabolism; Biological Sciences; Chromosomes, Fungal - genetics; Deoxyribonucleic acid; Dioxygenases - genetics; Dioxygenases - metabolism; DNA; DNA Methylation; DNA Transposable Elements - genetics; Enzymes; Epigenetics; Fungal Proteins - genetics; Fungal Proteins - metabolism; Gene expression; Gene Expression Regulation, Developmental; Gene Expression Regulation, Fungal; Genome, Fungal - genetics; HEK293 Cells; Humans; Hyphae - genetics; Hyphae - growth & development; Hyphae - metabolism; Mammals; Oxidation-Reduction; PNAS Plus; Sequence Analysis - methods; Spores, Fungal - growth & development; Spores, Fungal - metabolism
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1419513111

Significance A prominent epigenetic mechanism for gene regulation is methylation of cytosine bases in DNA. TET enzymes facilitate DNA demethylation by converting 5-methylcytosine (5mC) to oxidized methylcytosines (oxi-mCs). We show that oxi-mCs are generated by conserved TET/JBP enzymes encoded in the genome of the model organism Coprinopsis cinerea and present a method for simultaneous mapping of the three different species of oxi-mCs at near–base-pair resolution. We observe that centromeres and transposable elements exhibit distinctive patterns of 5mC and oxi-mC, and show that gene body 5mC and oxi-mC mark silent paralogous multicopy genes. Our study describes a method to map three species of oxi-mC simultaneously and reveals the colocation of 5mC and oxi-mC at functional elements throughout the C. cinerea genome. 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.