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Cell Rep. 2015 Feb 10;10(5):674-683. doi: 10.1016/j.celrep.2015.01.008. Epub 2015 Feb 5.

Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics.

Author information

1
Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy.
2
Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, via Fiorentina 1, 53100 Siena, Italy.
3
Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università di Torino, Via Pietro Giuria 5, 10125 Torino, Italy.
4
Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy. Electronic address: salvatore.oliviero@hugef-torino.org.

Abstract

Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-seq), that enables single-base resolution mapping of 5fC and 5caC and measures their abundance. Application of this method to mouse embryonic stem cells (ESCs) shows the occurrence of 5fC and 5caC residues on the hypomethylated promoters of highly expressed genes, which is increased upon Tdg silencing, revealing active DNA demethylation on these promoters. Genome-wide mapping of Tdg reveals extensive colocalization with Tet1 on active promoters. These regions were found to be methylated by Dnmt1 and Dnmt3a and demethylated by a Tet-dependent mechanism. Our work demonstrates the DNA methylation dynamics that occurs on the promoters of the expressed genes and provides a genomic reference map of 5fC and 5caC in ESCs.

PMID:
25660018
DOI:
10.1016/j.celrep.2015.01.008
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