Gene conversion tracts in Saccharomyces cerevisiae can be extremely short and highly directional

Abstract

Gene conversion is a common outcome of double-strand break (DSB) repair in yeast. Prior studies revealed that DSB-induced gene conversion tracts are often short (<53 bp), unidirectional, and biased toward promoter-proximal (5') markers. In those studies, broken ends had short, non-homologous termini. For the present study we created plasmid x chromosome, chromosomal direct repeat and allelic recombination substrates in which donor alleles carried mutant HO sites (HOinc--not cleaved) at the same position as cleavable HO sites in recipient alleles. In these substrates, broken ends are almost completely homologous to donor alleles, differing only at the three HOinc mutations. These mutations serve as markers very close to, or within, the four-base overhang produced by HO nuclease. We identified extremely short tracts (<12 bp) and many tracts were highly directional, extending <2 bp on one side of the DSB. We thought that terminal homology would promote bidirectional tracts, but found instead that unidirectional tracts were more frequent. Interestingly, substrates with terminal homology displayed enhanced 3' conversion, and in several cases conversion bias was reversed toward 3' markers. These results are discussed in relation to factors that may influence tract length and directionality, including heteroduplex DNA formation, transcription, replication and mismatch repair.

Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion

“…The findings from this and other recent plant mitochondrial studies (15,31) are consistent with the overall gene conversion literature (12,13) in suggesting that most gene conversions in plant mitochondrial genomes are relatively short, ranging from several to a few hundred nucleotides in length. This, together with the very low rates of apparent point mutations in most plant mitochondrial genomes (23), means that most plant-to-plant HGT-driven conversions will be difficult to detect with confidence.…”

“…However, gene conversion often involves short tracts of DNA and can, therefore, be difficult to detect (12,13). Indeed, using a recombination search algorithm developed specifically for plant mitochondrial genomes (14), nine putative cases of short-patch gene conversion of native, functional plant mitochondrial atp1 genes by homologous atpA genes of chloroplast origin were described just last year (15), despite most of the relevant gene sequences having been published years ago.…”

MuDR Transposase Increases the Frequency of Meiotic Crossovers in the Vicinity of a Mu Insertion in the Maize a1 Gene

“…Although in plants the mechanisms underlying meiotic recombination are not as well understream of the Mu1 insertion site that lacks polymorphisms between the parental alleles of crosses 1 and 2. stood, it is thought that they are at least similar to those that occur in yeast. Support for this view comes from This would be consistent with the finding that in mice and yeast, gene conversion tracts can be Ͻ100 bp the isolation of plant homologs of many of the yeast genes involved in DSB processing and meiotic recombi- (Sweetser et al 1994;Elliott et al 1998;Palmer et al 2003).…”

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

“…The latter scenario would require that gene conversion acts on relatively short stretches of nucleotides in plant mitochondrial genomes, because we observed numerous cases where editing sites were lost by C-to-T substitution with no change at nearby sites. So-called ''microconversions'' are known to occur between short stretches of homologous sequence in other genomes and organisms (Wheeler et al 1990;Semple and Wolfe 1999;Palmer et al 2003), while recent evidence indicates that microconversion (presumably DNA mediated) readily occurs in plant mitochondrial genomes (Hao and Palmer 2009; our unpublished data). Singlenucleotide substitutions at editing sites (independent of retroprocessing) and gene conversion with cDNA from partially edited transcripts would be expected to further reduce the clustering of lost editing sites.…”