|
| Status |
Public on Oct 08, 2018 |
| Title |
Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
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 AID/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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| |
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| Overall design |
Whole-genome ACE-seq analysis of WT or Tet1-3 KO mouse embryonic stem cells as well as adult mouse cortical excitatory neurons
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| |
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| Contributor(s) |
Schutsky EK, Wu H, Kohli RM |
| Citation(s) |
30295673 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| DP2 HL142044 |
Charting oxygen-sensing gene regulatory network in cardiomyocytes through single-cell analysis and epigenome editing |
UNIVERSITY OF PENNSYLVANIA |
Hao Wu |
| R00 HG007982 |
Genomic and functional analysis of active DNA demethylation in mammalian cells |
UNIVERSITY OF PENNSYLVANIA |
Hao Wu |
|
| |
| Submission date |
Jun 19, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Hao Wu |
| E-mail(s) |
haowu2@pennmedicine.upenn.edu
|
| Phone |
215-573-9360
|
| Organization name |
University of Pennsylvania
|
| Department |
Genetics
|
| Lab |
Hao Wu
|
| Street address |
415 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA476795 |
| SRA |
SRP150875 |
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