|
| Status |
Public on Nov 02, 2014 |
| Title |
Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing |
| Organism |
Mus musculus |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
Active DNA demethylation in mammals involves TET-mediated iterative oxidation of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) and subsequent excision repair of highly oxidized cytosine bases 5-formylcytosine (5fC)/5-carboxylcytosine (5caC) by Thymine DNA glycosylase (TDG). However, quantitative and high-resolution analysis of active DNA demethylation activity remains challenging. Here we describe M.SssI methylase-assisted bisulfite sequencing (MAB-seq), a method that directly maps 5fC/5caC at single-base resolution. Genome-wide MAB-seq allows systematic identification of 5fC/5caC in Tdg-depleted embryonic stem cells, thereby generating a base-resolution map of active DNA demethylome. A comparison of 5fC/5caC and 5hmC distribution maps indicates that catalytic processivity of TET enzymes correlates with local chromatin accessibility. MAB-seq also reveals strong strand asymmetry of active demethylation within palindromic CpGs. Integrating MAB-seq with other base-resolution mapping methods enables quantitative measurement of cytosine modification states at key transitioning steps of active demethylation pathway, and reveals a regulatory role of 5fC/5caC excision repair in active DNA demethylation cascade.
|
| |
|
| Overall design |
Analysis of 5fC/5caC excision repair-dependent active DNA demethylome by MAB-seq in mouse embryonic stem cells.
|
| |
|
| Contributor(s) |
Wu H, Wu X, Zhang Y |
| Citation(s) |
25362244 |
| |
| Submission date |
Oct 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hao Wu |
| E-mail(s) |
[email protected]
|
| Phone |
617-713-8660
|
| Organization name |
Harvard Medical School/HHMI
|
| Department |
Genetics
|
| Lab |
Yi Zhang
|
| Street address |
149G Warren Alpert Building, 200 Longwood Avenue
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (16)
|
|
| Relations |
| BioProject |
PRJNA264577 |
| SRA |
SRP049191 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62631_NegCtrl_merged_H3K4me1.MABseq.txt.gz |
139.9 Mb |
(ftp)(http) |
TXT |
| GSE62631_RAW.tar |
435.2 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE62631_README.txt |
3.2 Kb |
(ftp)(http) |
TXT |
| GSE62631_mESC.5fC5caC.sites.mm9_pval0.00025_cov10.BEDGRAPH.gz |
5.2 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE62631_mESC.5fC5caC.sites.mm9_pval0.00025_cov5.BEDGRAPH.gz |
6.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE62631_mESC.MABseqRawSignal.mm9_cov5.BEDGRAPH.gz |
199.3 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE62631_mESC.coverage.mm9_cov5.BEDGRAPH.gz |
193.8 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE62631_shCtrl_noVc_Vc_merged_H3K4me1.MABseq.txt.gz |
147.6 Mb |
(ftp)(http) |
TXT |
| GSE62631_shTdg_Vc_merged_H3K27me3.MABseq.txt.gz |
31.6 Mb |
(ftp)(http) |
TXT |
| GSE62631_shTdg_Vc_merged_H3K4me1.MABseq.txt.gz |
134.6 Mb |
(ftp)(http) |
TXT |
| GSE62631_shTdg_Vc_merged_WG.MABseq.txt.gz |
247.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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