During Saccharomyces cerevisiae mating-type switching, an HO endonuclease-induced double-strand break (DSB) at MAT is repaired by recombining with one of two donors, HMLα or HMR a, located at opposite ends of chromosome III. MAT a cells preferentially recombine with HMLα; this decision depends on the Recombination Enhancer (RE), located about 17 kb to the right of HML. In MATα cells, HML is rarely used and RE is bound by the MATα2-Mcm1 corepressor, which prevents the binding of other proteins to RE. In contrast, in MAT a cells, RE is bound by multiple copies of Fkh1 and a single copy of Swi4/Swi6. We report here that, when RE is replaced with four LexA operators in MAT a cells, 95% of cells use HMR for repair, but expression of a LexA-Fkh1 fusion protein strongly increases HML usage. A LexA-Fkh1 truncation, containing only Fkh1's phosphothreonine-binding FHA domain, restores HML usage to 90%. A LexA-FHA-R80A mutant lacking phosphothreonine binding fails to increase HML usage. The LexA-FHA fusion protein associates with chromatin in a 10-kb interval surrounding the HO cleavage site at MAT, but only after DSB induction. This association occurs even in a donorless strain lacking HML. We propose that the FHA domain of Fkh1 regulates donor preference by physically interacting with phosphorylated threonine residues created on proteins bound near the DSB, thus positioning HML close to the DSB at MAT. Donor preference is independent of Mec1/ATR and Tel1/ATM checkpoint protein kinases but partially depends on casein kinase II. RE stimulates the strand invasion step of interchromosomal recombination even for non-MAT sequences. We also find that when RE binds to the region near the DSB at MAT a then Mec1 and Tel1 checkpoint kinases are not only able to phosphorylate histone H2A (γ-H2AX) around the DSB but can also promote γ-H2AX spreading around the RE region.

Mating-type gene switching in Saccharomyces cerevisiae has provided one of the best-studied examples of DNA double-strand break (DSB)-induced recombination in mitotic cells. Recombination is initiated by cleavage of the MAT locus with the sequence-specific HO endonuclease. The ends of the DSB can recombine with one of two silenced and heterochromatic donor loci, HML and HMR, located near the extremities of the same chromosome (Fig. 1A). Gene conversion occurs without crossing-over, often resulting in the replacement of MAT-Ya or -Y␣ sequences that regulate whether cells will be a-or ␣-mating type (Strathern 1989;Haber 1992Haber , 1998a2002). In most strains of S. cerevisiae, HML carries Y␣ sequences (HML␣), whereas HMR carries Ya (HMRa). One of the remarkable aspects of this process is the phenomenon of donor preference, in which MATa cells preferentially recombine with HML␣, ensuring that recombination will usually result in a change of mating type; similarly, MAT␣ cells preferentially select HMRa (Klar et al. 1982;Weiler and Broach 1992;Wu and Haber 1995;. Donor selection depends on the location of the sequences but not their content, as MATa cells will preferentially recombine with HMLa even versus HMR␣ (Weiler and Broach 1992). Moreover, MATa's choice of a left-arm donor occurs even if the entire HML region is replaced by HMR (Weiler and Broach 1992) or if the donor is placed at other locations along the left arm (Wu and Haber 1995). MAT␣ cells continue to choose a right-arm donor even if HMR is replaced by HML sequences, again regardless of whether the donor carries Ya or Y␣ .The control of donor preference depends on a small cis-acting sequence, the recombination enhancer (RE), which acts as a locus-control region to control recombination along the entire left arm of chromosome III . RE lies in a 2.5-kb intergenic region. It is located ∼29 kb from the left end of chromosome III (i.e., 17 kb centromere-proximal to HML) between KAR4 and SPB1 genes, but it retains its ability to influence donor choice even if it is inserted 43 kb further toward the centromere (G.-F. Richard and J.E. Haber, unpubl.). Deletion of the entire RE region causes a profound change in MATa donor preference, so that HML is used only 10% of the time, compared with 85%-90% when RE is present (Wu and Haber 1996). These studies indi- Cold Spring Harbor Laboratory Press on May 9, 2018 -Published by genesdev.cshlp.org Downloaded from

Recombination events between non-identical sequences most often involve heteroduplex DNA intermediates that are subjected to mismatch repair. The well-characterized long-patch mismatch repair process, controlled in eukaryotes by bacterial MutS and MutL orthologs, is the major system involved in repair of mispaired bases. Here we present evidence for an alternative short-patch mismatch repair pathway that operates on a broad spectrum of mismatches. In msh2 mutants lacking the long-patch repair system, sequence analysis of recombination tracts resulting from exchanges between similar but non-identical (homeologous) parental DNAs showed the occurrence of short-patch repair events that can involve <12 nucleotides. Such events were detected both in mitotic and in meiotic recombinants. Con®rming the existence of a distinct short-patch repair activity, we found in a recombination assay involving homologous alleles that closely spaced mismatches are repaired independently with high ef®ciency in cells lacking MSH2 or PMS1. We show that this activity does not depend on genes required for nucleotide excision repair and thus differs from the short-patch mismatch repair described in Schizosaccharomyces pombe.