Mus81 and Yen1 Promote Reciprocal Exchange during Mitotic Recombination to Maintain Genome Integrity in Budding Yeast  Chu Kwen Ho, Gerard Mazón, Alicia F. Lam, Lorraine S. Symington  Molecular Cell  Volume 40, Issue 6, Pages 988-1000 (December 2010) DOI: 10.1016/j.molcel.2010.11.016 Copyright © 2010 Elsevier Inc. Terms and Conditions

Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 1 Model for Repair of DSBs by Homologous Recombination See main text for details. STR, Sgs1-Top3-Rmi1. Scissors indicate sites of HJ cleavage; dual cleavages in the same plane generate noncrossovers, whereas cleavages in opposite planes result in crossover products. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 2 Genetic Assay for DSB-Induced Gene Conversion and Associated LOH (A) Schematic of the diploid strain; the I-SceI cut site was inserted 950 bp upstream of the NdeI site, which is mutated on the other homolog (shown by ∗). (B) Colonies formed after 1 hr of I-SCEI induction in the wild-type strain. ade2 mutants accumulate a red pigment resulting in red colonies, whereas Ade+ recombinants form white colonies. (C) Repair of DSBs in G2 can occur by short tract or long tract gene conversion to produce ADE2 or ade2-n recombinants. (D) Crossovers associated with gene conversion can be detected if the two participating chromatids segregate to opposite poles during mitosis. If the crossover chromatids segregate to the same daughter cell, heterozygosity for Nat and Hph is maintained (not shown). Break-induced replication results in homozygosis of the Nat marker and is detected regardless of the chromatid segregations. See also Figures S1 and S2 and Table S3. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 3 Mus81 and Yen1 Are Required for Reciprocal Exchange (A) Distribution of recombinant colony types in wild-type (WT), mus81Δ, yen1Δ, and mus81Δ yen1Δ diploids. (B–D) Percent events for each strain among the red/white sectored (B), red (C), and white (D) colonies. See also Figures S1 and S2 and Tables S1–S3. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 4 The Elevated BIR and Residual Crossovers in the mus81Δ yen1Δ Mutant Are Pol32 Dependent (A) Distribution of recombinant colony types in wild-type (WT) and pol32Δ diploids. (B) Percent of each type of recombination event among the red/white-sectored colonies for each strain is shown. See also Tables S1–S3. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 5 MUS81 and YEN1 Are Required for MMS and HU Resistance and Prevent Accumulation of Joint Molecules (A) Overlapping roles of MUS81 and YEN1 in MMS and HU resistance. Ten-fold serial dilutions of log-phase cultures were spotted onto plates containing the indicated amounts of MMS or HU. (B) Doubling times of the indicated haploid (1N) and diploid (2N) strains. (C) Cell-cycle progression of cells synchronized in G1 with α factor and released in media containing 0.03% MMS. One hour after damage induction, cells were washed and transferred to MMS-free medium with α factor to arrest at the next cell cycle before resuming replication. (D) Western blot of protein samples from cells harboring an HA-epitope tagged Rad53 after 1 hr exposure to 0.03%MMS (+) or to buffer only (–). Rad53 was detected with α-HA. (E) PFGE analysis of samples of DNA from cells recovering after a 0.03% MMS treatment for 1 hr. PFGE gels were transferred to nylon membranes and hybridized with probes against chromosomes III and XV. (F) Quantitation of the percent unresolved chromosomes (indicative of joint molecules). Error bars show standard deviation from three trials; ∗p < 0.05 and ∗∗p < 0.005 compared to the amount of unresolved chromosomes in wild-type. See also Figures S3 and S4 and Table S3. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 6 The mus81Δ and mus81Δ yen1Δ Mutants Exhibit Increased Spontaneous LOH and Chromosome Loss/Gain (A) Assay for spontaneous LOH. Spontaneous loss of the URA3 marker can occur by mitotic recombination or by chromosome loss. (B and C) The rates of mitotic recombination (B) and chromosome loss (C) were calculated for the indicated genetic backgrounds. Error bars indicate the standard deviations. (D) Assay for chromosome mis-segregation using the ade2 direct repeats. (E) Relative Ade+ Ura+/Ade+ cosegregation rates for the indicated strains. Error bars indicate the standard deviations. (F) Schematic showing alternative pathways that could lead to the accumulation of joint molecules in G2/M. See also Figure S5 and Table S3. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions

Figure 7 Models for Mus81 and Yen1 Resolution of Recombination Intermediates (A) The 3′ end of the strand invasion intermediate is extended by DNA Pol δ and then displaced to form a NCO or cleaved by Mus81 to generate a CO. If the D loop undergoes reverse branch migration to form a dHJ, dissolution by STR will generate a NCO; resolution by Yen1 (or possibly Mus81) generates NCO or CO products. In the absence of Mus81, Yen1 is predicted to cleave HJs that are fully ligated or formed by reversed branch migration. Cleavage of the HJ without cleavage of the leading end of the D loop might channel the intermediate to BIR. In the absence of Mus81 and Yen1, BIR might occur by a migrating D loop intermediate, or the unresolved structures persist until mitosis. (B) An unresolved recombination intermediate (shown as a single HJ) might be broken during mitosis if the centromeres segregate to opposite poles. Segregation of one centric fragment with an intact chromatid might result in BIR in the next cell cycle (this would probably occur in S/G2, but only one chromatid is shown for simplicity), resulting in homozygosis of the Nat or Hph marker. If both chromatids were broken during mitosis, then BIR in the two daughter cells would result in products indistinguishable from a reciprocal crossover. Molecular Cell 2010 40, 988-1000DOI: (10.1016/j.molcel.2010.11.016) Copyright © 2010 Elsevier Inc. Terms and Conditions