Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Dnmt2-dependent methylomes lack biologically relevant DNA methylation patterns

ABSTRACT: 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. Whole methylome analysis of Mus musculus. One sample was analyzed containing DNA from Dnmt1-/-, Dnmt3a-/- and Dnmt3b-/- mice.

ORGANISM(S): Mus musculus

SUBMITTER: Guenter Raddatz 

PROVIDER: E-GEOD-42170 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dnmt2-dependent methylomes lack defined DNA methylation patterns.

Raddatz Günter G   Guzzardo Paloma M PM   Olova Nelly N   Fantappié Marcelo Rosado MR   Rampp Markus M   Schaefer Matthias M   Reik Wolf W   Hannon Gregory J GJ   Lyko Frank F  

Proceedings of the National Academy of Sciences of the United States of America 20130502 21

Several organisms have retained methyltransferase 2 (Dnmt2) as their only candidate DNA methyltransferase gene. However, information about Dnmt2-dependent methylation patterns has been limited to a few isolated loci and the results have been discussed controversially. In addition, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which raised the possibility that Dnmt2-only genomes might be unmethylated. We have now used whole-genome bisulfite sequencing to analyze the  ...[more]

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