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Series GSE44038 Query DataSets for GSE44038
Status Public on Jun 04, 2014
Title TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells [DREAM]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary We report that full length TET1 (TET1-FL) overexpression fails to induce global DNA demethylation in HEK293T cells. The preferential binding of TET1-FL to hypomethylated CpG islands (CGIs) through its CXXC domain leads to its inhibited 5-hydroxymethylcytosine (5hmC) production as methylation level increases. TET1-FL-induced 5hmC accumulates at CGI edges, while TET1 knockdown induces methylation spreading from methylated edges into hypomethylated CGIs. However, TET1 can regulate gene transcription independent of its dioxygenase catalytic function. Thus, our results identify TET1 as a maintenance DNA demethylase that does not purposely decrease methylation levels, but specifically maintains the DNA hypomethylation state of CGIs in adult cells.
 
Overall design Digital restriction enzyme analysis of methylation (DREAM) was performed to determine the DNA methylation profiles of HEK293T cells overexpressing mTET1-CD, TET1-CD, mTET1-FL, or TET1-FL. In this approach, genomic DNA is sequentially cut at CCCGGG sites with the methylation sensitive enzyme SmaI (blunt ends) and its methylation-tolerant neoschizomer XmaI (5’CCGG overhangs), creating different end sequences that represent methylation status of the CCCGGG sites. These end sequences are analyzed by next generation sequencing, and thereafter the methylation status at individual CCCGGG sites across the genome can be determined.
 
Contributor(s) Jin C, Lu Y, Jelinek J, Liang S, Estecio MR, Barton M, Issa JJ
Citation(s) 24875481
Submission date Feb 04, 2013
Last update date May 15, 2019
Contact name CHUNLEI JIN
E-mail(s) jincl1980@gmail.com
Organization name The University of Texas MD Anderson Cancer Center
Street address 1515 Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (4)
GSM1077162 mTET1-CD_DREAM
GSM1077163 mTET1-FL_DREAM
GSM1077164 TET1-CD_DREAM
This SubSeries is part of SuperSeries:
GSE44039 TET1 is a maintenance DNA demethylase that prevents methylation spreading in adult cells
Relations
BioProject PRJNA188410
SRA SRP018556
SRA SRP018481

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
GSE44038_RAW.tar 11.7 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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