Marker structure and recombination substrate environment influence conversion preference of broken and unbroken alleles in Saccharomyces cerevisiae

Double-strand break (DSB)-induced gene conversion was investigated using pl asmid x chromosome (P x C) and chromosomal direct-repeat recombination subs trates with markers arranged such that functional (selected) products could not arise by long-patch mismatch repair initiated from the DSB. As seen pr eviously with analogous substrates, these substrates yield products with di scontinuous conversion tracts, albeit at low frequency. Most conversion tra cts were of minimum length, suggesting that heteroduplex DNA (hDNA) is limi ting, or that co-repair imposes selective pressure against products with sn ore extensive hDNA. When functional products can arise by long-patch mismat ch repair, the broken allele is converted in nearly all products. In contra st, in the absence of long-patch mismatch repair, unbroken alleles are freq uently converted, and we show that such conversion depends on both marker s tructure (i.e., long palindromic vs. nonpalindromic insertions) and the chr omosomal environment of the recombination substrate. We propose that conver sion of unbroken alleles is largely a consequence of the segregation of unr epaired markers, and that differences in mismatch repair efficiency underli e the observed effects of marker structure and chromosome environment on al lele conversion preference.