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Author Notes:
Correspondence: zhuz@neb.com (Z.Z.), zhengy@neb.com (Y.Z.)
We thank Dr. Shannon Kinney for providing E14 genomic DNA, Drs. Rich Roberts and William Jack for helpful comments, and Drs. Peng Jin and Chuan He for providing us TAB-seq dataset of mouse E14 cells.
We thank Cynthia Hendrickson and HudsonAlpha Institute for Biotechnology for sequencing.
Subject:
Research Funding:
This work is supported by NIH SBIR grants (GM096723 to Z.Z. and GM095209 to Y.Z.) and New England Biolabs. Subjects of this paper may be potential future products of New England Biolabs.
Keywords:
- Science & Technology
- Life Sciences & Biomedicine
- Cell Biology
- BASE-RESOLUTION
- MAMMALIAN DNA
- 5-METHYLCYTOSINE
- METHYLATION
- 5-CARBOXYLCYTOSINE
- TRANSCRIPTION
- PLURIPOTENT
- ENHANCERS
- STATE
- TET1
High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells
Abstract:
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.
Copyright information:
© 2013 The Authors. Published by Elsevier Inc.
This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (http://creativecommons.org/licenses/by-nc-nd/4.0/).
