Originally published as Genetics Published Articles Ahead of Print on September 12, 2005.

Genetics, Vol. 171, 1549-1559, December 2005, Copyright © 2005
doi:10.1534/genetics.105.047092

Analysis of Repeat-Mediated Deletions in the Mitochondrial Genome of Saccharomyces cerevisiae

Naina Phadnis^*, Rey A. Sia and Elaine A. Sia^*,1

^* Department of Biology, University of Rochester, Rochester, New York 14627 and Department of Biological Sciences, SUNY, Brockport, New York 14420

¹ Corresponding author: Department of Biology, RC Box 270211, University of Rochester, Rochester, NY 14627-0211.
E-mail: esia{at}mail.rochester.edu

Mitochondrial DNA deletions and point mutations accumulate in an age-dependent manner in mammals. The mitochondrial genome in aging humans often displays a 4977-bp deletion flanked by short direct repeats. Additionally, direct repeats flank two-thirds of the reported mitochondrial DNA deletions. The mechanism by which these deletions arise is unknown, but direct-repeat-mediated deletions involving polymerase slippage, homologous recombination, and nonhomologous end joining have been proposed. We have developed a genetic reporter to measure the rate at which direct-repeat-mediated deletions arise in the mitochondrial genome of Saccharomyces cerevisiae. Here we analyze the effect of repeat size and heterology between repeats on the rate of deletions. We find that the dependence on homology for repeat-mediated deletions is linear down to 33 bp. Heterology between repeats does not affect the deletion rate substantially. Analysis of recombination products suggests that the deletions are produced by at least two different pathways, one that generates only deletions and one that appears to generate both deletions and reciprocal products of recombination. We discuss how this reporter may be used to identify the proteins in yeast that have an impact on the generation of direct-repeat-mediated deletions.

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