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Series GSE129470 Query DataSets for GSE129470
Status Public on Apr 24, 2020
Title A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and Tet activity
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary DNA methylation is considered a stable epigenetic mark, yet methylation patterns can vary during differentiation and in diseases such as cancer. Local levels of DNA methylation result from opposing enzymatic activities, the rates of which remain largely unknown. Here we developed a theoretical and experimental framework enabling us to infer methylation and demethylation rates at 860,404 CpGs in the mouse genome. Surprisingly, enzymatic rates can vary as much as two orders of magnitude between CpGs with identical steady-state measurements. Unexpectedly, de novo and maintenance methylation activity is reduced at transcription factor binding sites, while methylation turnover is elevated in transcribed gene bodies. Furthermore, we show that TET activity contributes substantially more than passive demethylation to establishing low methylation levels at distal enhancers. Taken together, our work unveils the first genome-scale map of methylation kinetics, revealing highly variable and context specific activity for the DNA methylation machinery.
Overall design Analysis of DNA methylation dynamics in mouse embryonic stem cells
Contributor(s) Ginno P, Gaidatzis D, Feldmann A, Schübeler D
Citation(s) 32471981
Submission date Apr 08, 2019
Last update date Jun 16, 2020
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (102)
GSM3713369 WT_1_d0 (SureSelect)
GSM3713370 WT_2_d0 (SureSelect)
GSM3713371 WT_3_d0 (SureSelect)
BioProject PRJNA531453
SRA SRP191424

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

Supplementary file Size Download File type/resource
GSE129470_Supplemental_Table1.txt.gz 2.6 Kb (ftp)(http) TXT
GSE129470_Supplemental_Table2_AmpliconBS_WT_Timecourse.txt.gz 178.1 Kb (ftp)(http) TXT
GSE129470_Supplemental_Table3_AmpliconBS_TTKO_Timecourse.txt.gz 171.7 Kb (ftp)(http) TXT
GSE129470_Supplemental_Table4_SureSelectBS.txt.gz 107.5 Mb (ftp)(http) TXT
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