A novel method to analyze 5-hydroxymethylcytosine in CpG sequences using maintenance DNA methyltransferase, DNMT1

Saori Takahashi; Isao Suetake; Jan Engelhardt; Shoji Tajima

doi:10.1016/j.fob.2015.09.003

A novel method to analyze 5-hydroxymethylcytosine in CpG sequences using maintenance DNA methyltransferase, DNMT1

FEBS Open Bio. 2015 Sep 8:5:741-7. doi: 10.1016/j.fob.2015.09.003. eCollection 2015.

Authors

Saori Takahashi¹, Isao Suetake², Jan Engelhardt³, Shoji Tajima¹

Affiliations

¹ Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
² Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan ; CREST, Japan Agency for Medical Research and Development (AMED), 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan.
³ Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany.

Abstract

Hydroxymethylcytosine has been shown to be involved in DNA demethylation and gene expression. Although methods to determine the position of hydroxymethylcytosine at single-base resolution have been reported, these methods involve some difficulties. Here, we report a simple method to analyze hydroxymethylcytosine in the CpG sequence utilizing the maintenance DNA methylation activity of DNMT1, which selectively methylates hemi-methylated but not hemi-hydroxymethylated CpG sequences. The method enables monitoring of the dynamics of the hydroxymethylation state of a specific genome site.

Keywords: 2i, two kinase inhibitors; 5hmC, hydroxymethylcytosine; 5mC, methylcytosine; Bisulfite sequencing; DNMT1; Dnmt, DNA methyltransferase; ES cells, embryonic stem cells; Hydroxymethylcytosine; SAM, S-adenosyl-l-methionine; Tet, ten eleven translocation.