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Nucleic Acids Research Advance Access originally published online on April 7, 2009
Nucleic Acids Research 2009 37(11):3531-3544; doi:10.1093/nar/gkp214
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Nucleic Acids Research, 2009, Vol. 37, No. 11 3531-3544
© 2009 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.

Genome Integrity, Repair and Replication

Cleavage of a model DNA replication fork by a Type I restriction endonuclease

Ken Ishikawa1,2, Naofumi Handa2 and Ichizo Kobayashi1,2,3,*

1Graduate Program in Biophysics and Biochemistry, Graduate School of Science, 2Department of Medical Genome Sciences, Graduate School of Frontier Science and 3Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan

*To whom correspondence should be addressed. Email: ikobaya{at}ims.u-tokyo.ac.jp

Received February 17, 2009. Revised March 11, 2009. Accepted March 16, 2009.

Cleavage of a DNA replication fork leads to fork restoration by recombination repair. In prokaryote cells carrying restriction–modification systems, fork passage reduces genome methylation by the modification enzyme and exposes the chromosome to attack by the restriction enzyme. Various observations have suggested a relationship between the fork and Type I restriction enzymes, which cleave DNA at a distance from a recognition sequence. Here, we demonstrate that a Type I restriction enzyme preparation cleaves a model replication fork at its branch. The enzyme probably tracks along the DNA from an unmethylated recognition site on the daughter DNA and cuts the fork upon encountering the branch point. Our finding suggests that these restriction–modification systems contribute to genome maintenance through cell death and indicates that DNA replication fork cleavage represents a critical point in genome maintenance to choose between the restoration pathway and the destruction pathway.


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