High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.
We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic analysis suggests 5hmCs in genic regions closely follow the 5mC distribution. 5hmC is generally depleted in CpG islands and only enriched in a small set of repetitive elements. A regularly spaced and oscillating 5hmC pattern was observed at the binding sites of CTCF. 5hmC is enriched at the poised enhancers with the monomethylated histone H3 lysine 4 (H3K4me1) marks, but not at the active enhancers with the acetylated histone H3 lysine 27 (H3K27Ac) marks. Non-CG hydroxymethylation appears to be prevalent in the mitochondrial genome. We propose that some amounts of transiently stable 5hmCs may indicate a poised epigenetic state or demethylation intermediate, whereas others may suggest a locally accessible chromosomal environment for the TET enzymatic apparatus.
New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA.
Zhiyi
Z
Sun
Jolyon
J
Terragni
Terragni
T
Jolyon
Janine G
JG
Borgaro
Yiwei
Y
Liu
Ling
L
Yu
Shengxi
S
Guan
Hua
H
Wang
Dapeng
D
Sun
Xiaodong
X
Cheng
Zhenyu
Z
Zhu
Sriharsa
S
Pradhan
Yu
Y
Zheng
D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D002460:Cell Line; D002874:Chromosome Mapping; D019295:Computational Biology; D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D023281:Genomics; D006657:Histones / Q000378:metabolism; D006900:Hydroxylation; D051379:Mice; D017422:Sequence Analysis, DNA
D006657:Histones; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004262:DNA Restriction Enzymes