Nucleic Acids Research Advance Access originally published online on October 22, 2008
Nucleic Acids Research 2008 36(21):6656-6663; doi:10.1093/nar/gkn747
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Nucleic Acids Research, 2008, Vol. 36, No. 21 6656-6663
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Gene regulation, Chromatin and Epigenetics |
Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L
1Biochemistry Lab, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, 2Abt. Genetik, CINSaT, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, 3Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany, 4Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30033, USA and 5Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin-Dahlem, Germany
*To whom correspondence should be addressed. Tel: +49 421 200 3247; Fax: +49 421 200 3249; Email: a.jeltsch{at}jacobs-university.de
Received August 19, 2008. Revised September 29, 2008. Accepted October 3, 2008.
The C-terminal domains of Dnmt3a and Dnmt3L form elongated heterotetramers (3L-3a-3a-3L). Analytical ultracentrifugation confirmed the Dnmt3a-C/3L-C complex exists as a 2:2 heterotetramer in solution. The 3a–3a interface is the DNA-binding site, while both interfaces are essential for AdoMet binding and catalytic activity. Hairpin bisulfite analysis shows correlated methylation of two CG sites in a distance of 
8-10 bp in the opposite DNA strands, which corresponds to the geometry of the two active sites in one Dnmt3a-C/3L-C tetramer. Correlated methylation was also observed for two CG sites at similar distances in the same DNA strand, which can be attributed to the binding of two tetramers next to each other. DNA-binding experiments show that Dnmt3a-C/3L-C complexes multimerize on the DNA. Scanning force microscopy demonstrates filament formation rather than binding of single tetramers and shows that protein–DNA filament formation leads to a 1.5-fold shortening of the DNA length.
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