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Series GSE56429 Query DataSets for GSE56429
Status Public on Jan 20, 2015
Title Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary 5-methylcytosine (5mC), the predominant epigenetic modification on DNA, plays critical roles in mammalian development and is dysregulated in various human pathologies. In mammals, the TET family of dioxygenases can oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a stepwise manner. 5fC and 5caC are selectively recognized and excised by mammalian thymine DNA glycosylase (TDG), and restored to normal cytosine through base excision repair (BER). Once 5mC/5hmC is converted to 5fC and/or 5caC, the modified cytosine is committed to demethylation through BER. Thus 5fC and 5caC most likely mark active demethylation in the mammalian genome. Here we introduce a genome-wide approach to obtain single-base resolution maps of 5fC and 5caC, respectively. We show that, in mouse embryonic stem cells (mESCs), 5fC and 5caC are preferentially generated at highly hypomethylated regions and more active enhancers. Moreover, 5caC-marked regions are characterized by the lowest methylation and highest enhancer activity among all modification sites associated with 5hmC, 5fC and 5caC, and are enriched adjacent to pluripotency transcription factor (TF)-binding motifs. These observations, together with the surprising lack of overlap between 5fC and 5caC sites, highlight a gradient of Tet-mediated 5mC oxidation activity at regulatory elements in tuning epigenetic dynamics11.
Overall design DNA immunoprecipitation coupled chemical-modification assisted bisulfite sequencing (DIP-CAB-Seq) for Tdg fl/fl and Tdg-/- mESCs
Contributor(s) Lu X, Han D, Zhao BS, He C
Citation(s) 25591929
Submission date Apr 01, 2014
Last update date May 15, 2019
Contact name Dali Han
Organization name University of Chicago
Department Department of Chemisty
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (8)
GSM1361263 TDG_KO_caC_DIP
GSM1361264 TDG_KO_caC_protect
GSM1361265 TDG_KO_fC_DIP
BioProject PRJNA243290
SRA SRP040775

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56429_5caC_TDG_KO_site.txt.gz 67.6 Kb (ftp)(http) TXT
GSE56429_5fC_TDG_KO_site.txt.gz 99.6 Kb (ftp)(http) TXT
GSE56429_RAW.tar 516.6 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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