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Series GSE56986 Query DataSets for GSE56986
Status Public on Sep 22, 2014
Title Tet proteins in DNA demethylation and cell fate restriction
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary DNA methylation at 5-position of cytosine (5mC) is one of the best studied epigenetic modifications that plays important roles in diverse biological processes. Iterative oxidation of 5mC by the Ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), which can be further processed by DNA repair proteins leading to DNA demethylation. Functional characterization of the Tet proteins has been complicated by the redundancy between the three Tet proteins. Using the CRISPR/Cas9 technology, we have generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (TKO). Whole genome bisulphite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs distal enhancers as well as promoters that significantly overlap with 5hmC, 5fC and 5caC. Characterization of the Tet TKO ESCs revealed a function for Tet proteins in cell fate restriction as Tet TKO ESCs tend to adopt both primed pluripotent stem cell-like state and 2-cell embryo-like state. In addition, Tet TKO ESCs exhibit elongated telomeres. Thus, our study reveals a role of Tet proteins not only in DNA demethylation, but also in cell fate restriction and telomere maintenance.
Overall design 2 samples for WGBS and 2 samples for RNA-seq
Contributor(s) Lu F, Liu Y, Jiang L, Yamaguchi S, Zhang Y
Citation(s) 25223896
Submission date Apr 23, 2014
Last update date May 15, 2019
Contact name Lan Jiang
Organization name Boston Children Hospital
Lab Yi Zhang
Street address 200 Longwood Ave
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (4)
GSM1372647 WT.E14.WGBS
GSM1372648 WT.E14.RNA-seq
GSM1372649 TetTKO.WGBS
BioProject PRJNA245171
SRA SRP041376

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
GSE56986_RAW.tar 144.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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