Marker structure and recombination substrate environment influence conversion preference of broken and unbroken alleles
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O R I GI N A L P A P E R
Y-s. Weng á S. L. Barton á J. W. Cho á J. A. Nickolo
Marker structure and recombination substrate environment in¯uence conversion preference of broken and unbroken alleles in Saccharomyces cerevisiae Received: 8 June 2000 / Accepted: 2 November 2000 / Published online: 21 February 2001 Ó Springer-Verlag 2001
Abstract Double-strand break (DSB)-induced gene conversion was investigated using plasmid ´ chromosome (P ´ C) and chromosomal direct-repeat recombination substrates with markers arranged such that functional (selected) products could not arise by longpatch mismatch repair initiated from the DSB. As seen previously with analogous substrates, these substrates yield products with discontinuous conversion tracts, albeit at low frequency. Most conversion tracts were of minimum length, suggesting that heteroduplex DNA (hDNA) is limiting, or that co-repair imposes selective pressure against products with more extensive hDNA. When functional products can arise by long-patch mismatch repair, the broken allele is converted in nearly all products. In contrast, in the absence of long-patch mismatch repair, unbroken alleles are frequently converted, and we show that such conversion depends on both marker structure (i.e., long palindromic vs. nonpalindromic insertions) and the chromosomal environment of the recombination substrate. We propose that conversion of unbroken alleles is largely a consequence of the segregation of unrepaired markers, and that dierences in mismatch repair eciency underlie the observed eects of marker structure and chromosome environment on allele conversion preference. Key words Yeast á Mismatch repair á Homologous recombination á Double-strand break repair Communicated by H. Ikeda Y-s. Weng á J. W. Cho á J. A. Nickolo (&) Department of Cancer Biology, Harvard University School of Public Health, Boston, MA 02115, USA E-mail: jnickolo@salud.unm.edu Tel.: +1-505-2726960 Fax: +1-505-2726029 S. L. Barton á J. A. Nickolo Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131
Introduction Double-strand breaks (DSBs) are strong initiators of mitotic recombination in Saccharomyces cerevisiae, including reciprocal exchange (Ray et al. 1988), nonconservative exchange (Fishman-Lobell et al. 1992), and gene conversion events (Nickolo et al. 1986, 1989; Ray et al. 1988). Recombination between homologous DNA sequences is a major pathway for the repair of DSBs (reviewed by Paques and Haber 1999). Naturally occurring DSBs initiate meiotic recombination (Sun et al. 1989) and mating-type switching (Strathern et al. 1982). Gene conversion is the nonreciprocal transfer of information from a DNA duplex to a homologous duplex. DSB-induced gene conversion has two hallmark features: broken alleles are preferentially converted, and nearly all conversion tracts are continuous (reviewed in Petes et al. 1991). Although the DSB or gap-repair model (Szostak et al. 1983) easily explains these features, studies of meiotic recombinat
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