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Cell Rep. 2013 Feb 21;3(2):567-76. doi: 10.1016/j.celrep.2013.01.001. Epub 2013 Jan 24.

High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells.

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New England Biolabs Inc., 240 County Road, Ipswich, MA 01938, USA.

Erratum in

  • Cell Rep. 2013 Mar 28;3(3):968. Jolyon, Terragni [corrected to Terragni, Jolyon].


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.

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