A novel method to analyze 5-hydroxymethylcytosine in CpG sequences using maintenance DNA methyltransferase, DNMT1.
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.
Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Saori
S
Takahashi
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.
Isao
I
Suetake
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, 04107 Leipzig, Germany.
Jan
J
Engelhardt
Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Shoji
S
Tajima
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