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Nucleic Acids Research 2006 34(4):1182-1188; doi:10.1093/nar/gkl002
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Published online 25 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Accuracy of DNA methylation pattern preservation by the Dnmt1 methyltransferase

Rachna Goyal1, Richard Reinhardt2 and Albert Jeltsch3,*

1Institut für Biochemie FB 08, Heinrich-Buff-Ring 58, Justus-Liebig-Universität Giessen, 35392 Giessen, Germany 2Max Planck Institute for Molecular Genetics Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany 3Biochemistry, International University Bremen, School of Engineering and Science Campus Ring 1, 28759 Bremen, Germany

*To whom correspondence should be addressed. Tel: +49 421 200 3247; Fax: +49 421 200 3249; Email: a.jeltsch{at}iu-bremen.de

Received December 22, 2005. Revised January 23, 2006. Accepted February 9, 2006.

DNA methyltransferase 1 (Dnmt1) has a central role in copying the pattern of DNA methylation after replication which is one manifestation of epigenetic inheritance. With oligonculeotide substrates we show that mouse Dnmt1 has a 30- to 40-fold preference for hemimethylated DNA that is almost lost after addition of fully methylated oligonucleotides. Using long hemimethylated DNA substrates that carry defined methylation patterns and bisulfite analysis of the methylation reaction products, we show a 15-fold preference for hemimethylated CG sites. Dnmt1 moves along the DNA in a random walk methylating hemimethylated substrates with high processivity (>50 sites are visited on average which corresponds to linear diffusion over 6000 bp). The frequency of skipping sites is very low (<0.3%) and there is no detectable flanking sequence preference. CGCTC sites tend to terminate the processive methylation of DNA by Dnmt1. Unmethylated DNA is modified non-processively with a preference for methylation at CCGG sites. We simulate the propagation of methylation patterns using a stochastic model with the specificity of Dnmt1 observed here and conclude that either methylation of several sites is required to propagate the methylation information over several cellular generations or additional epigenetic information must be used.


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