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Genome Biology and Evolution Advance Access originally published online on September 9, 2009
Genome Biology and Evolution (2009) Vol. 2009:350; doi:10.1093/gbe/evp034 published on October 5, 2009
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© 2009 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Fragile Genomic Sites Are Associated with Origins of Replication

Sara C. Di Rienzi*, David Collingwood{dagger}, M. K. Raghuraman* and Bonita J. Brewer*

* Department of Genome Sciences, University of Washington
{dagger} Department of Mathematics, University of Washington

E-mail: bbrewer{at}gs.washington.edu.


  Abstract

Genome rearrangements are mediators of evolution and disease. Such rearrangements are frequently bounded by transfer RNAs (tRNAs), transposable elements, and other repeated elements, suggesting a functional role for these elements in creating or repairing breakpoints. Though not well explored, there is evidence that origins of replication also colocalize with breakpoints. To investigate a potential correlation between breakpoints and origins, we analyzed evolutionary breakpoints defined between Saccharomyces cerevisiae and Kluyveromyces waltii and S. cerevisiae and a hypothetical ancestor of both yeasts, as well as breakpoints reported in the experimental literature. We find that origins correlate strongly with both evolutionary breakpoints and those described in the literature. Specifically, we find that origins firing earlier in S phase are more strongly correlated with breakpoints than are later-firing origins. Despite origins being located in genomic regions also bearing tRNAs and Ty elements, the correlation we observe between origins and breakpoints appears to be independent of these genomic features. This study lays the groundwork for understanding the mechanisms by which origins of replication may impact genome architecture and disease.

Keywords: genomic rearrangements, tRNAs, transposable elements, S. cerevisiae, K. waltii, comparative genomics

Accepted August 28, 2009

Yoshihito Niimura, Associate Editor


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