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Series GSE28533 Query DataSets for GSE28533
Status Public on Apr 21, 2011
Title Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells (bisulfite sequencing data)
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation of C5-cytosine (5mC) in the mammalian genome is a key epigenetic event that is critical for various cellular processes. However, how the genome-wide 5mC pattern is dynamically regulated remains a fundamental question in epigenetic biology. The TET family of 5mC hydroxylases, which convert 5mC to 5-hydroxymethylcytosine (5hmC), have provided a new potential mechanism for the dynamic regulation of DNA methylation. The extent to which individual Tet family members contribute to the genome-wide 5mC and 5hmC patterns and associated gene network remains largely unknown. Here we report genome-wide mapping of Tet1 and 5hmC in mESCs and reveal a mechanism of action by which Tet1 controls 5hmC and 5mC levels in mESCs. In combination with microarray and mRNA-seq expression profiling, we identify a comprehensive yet intricate gene network influenced by Tet1. We propose a model whereby Tet1 controls DNA methylation both by binding to CpG-rich regions to prevent unwanted DNA methyltransferase activity, and by converting the existing 5mC to 5hmC through its enzymatic activity. This Tet1-mediated antagonism of CpG methylation imparts differential maintenance of DNA methylation status at Tet1 target loci, thereby providing a new regulatory mechanism for establishing the epigenetic landscape of mESCs, which ultimately contributes to mESC differentiation and the onset of embryonic development.
Overall design To determine the genome-wide DNA methylation changes caused by Tet1 depletion in mouse ES cells. Tet1 protein was depleted by specific siRNA treatment. The DNA methylation levels in control and Tet1 siRNA-transfected ES cells were determined by targeted bisulfite sequencing.
Contributor(s) Xu Y, Shi Y
Citation(s) 21514197
Submission date Apr 11, 2011
Last update date May 15, 2019
Contact name Feizhen Wu
Phone 86-21-54237821
Organization name Fudan Univ, Shanghai, China
Department Institutes of Biomedical Sciences
Lab Epigenetics lab
Street address Dongan Road 131, Rm 511 Mingdao Building
City Shanghai
State/province Shanghai
ZIP/Postal code 200032
Country China
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM706683 Control_CH_Methylation_bisulfite_sequencing
GSM706684 TET1_CH_Methylation_bisulfite_sequencing
GSM706685 Control_CpG_Methylation_bisulfite_sequencing
This SubSeries is part of SuperSeries:
GSE28500 Genome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells
SRA SRP006419
BioProject PRJNA143029

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28533_RAW.tar 6.9 Mb (http)(custom) TAR (of BED)
GSE28533_readme.txt 493 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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