Journal
NATURE BIOTECHNOLOGY
Volume 36, Issue 11, Pages 1083-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.4204
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Funding
- US National Institutes of Health [R21-HG009545]
- Penn Epigenetics Institute
- NSF
- NIH [T32-GM07229, F30-CA196097]
- [R00-HG007982]
- [DP2-HL142044]
- [R01-GM118501]
- NATIONAL CANCER INSTITUTE [F30CA196097] Funding Source: NIH RePORTER
- NATIONAL HEART, LUNG, AND BLOOD INSTITUTE [DP2HL142044] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R00HG007982, R21HG009545] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM118501, T32GM007229] Funding Source: NIH RePORTER
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Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that A ID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.
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