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Series GSE42170 Query DataSets for GSE42170
Status Public on May 06, 2013
Title Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary Several organisms belonging to diverse animal groups have retained Dnmt2 as their only bona fide DNA methyltransferase gene. However, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which prompted us to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Using whole-genome bisulfite sequencing we show here that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in a Dnmt2-deficient fly strain. Furthermore, genetically modified mouse embryonic stem cells that had retained Dnmt2 as their only bona fide DNA methyltransferase gene, did not show any detectable DNA methylation patterns. Our results thus uncover fundamental differences among animal methylomes and suggest that Dnmt2-only organisms lack biologically relevant DNA methylation patterns.
Overall design Whole methylome analysis of Mus musculus. One sample was analyzed containing DNA from Dnmt1-/-, Dnmt3a-/- and Dnmt3b-/- mice.
Contributor(s) Lyko F, Reik W
Citation(s) 23641003
Submission date Nov 08, 2012
Last update date May 15, 2019
Contact name Guenter Raddatz
Organization name German Center for Cancer Research
Street address Im Neuenheimer Feld 580
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (1)
GSM1034004 TKO
BioProject PRJNA179289
SRA SRP017139

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Supplementary file Size Download File type/resource
GSE42170_RAW.tar 2.4 Gb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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