Chromosomal Rearrangements Occur in S Chromosomal Rearrangements Occur in S. cerevisiae rfa1 Mutator Mutants Due to Mutagenic Lesions Processed by Double-Strand-Break Repair  Clark Chen, Keiko Umezu, Richard D. Kolodner  Molecular Cell  Volume 2, Issue 1, Pages 9-22 (July 1998) DOI: 10.1016/S1097-2765(00)80109-4

Figure 1 PCR Analysis of Deletion Formation at the CAN1 Locus (a) Amplification of CAN1 from 20 rfa1-t29 Canr mutants. (b) Amplification of RFA1 from the same rfa1-t29 Canr mutants. (c) Amplification of ORFs surrounding CAN1 (YEL063c) in a rfa1-t29 rad51 Canr mutant (TR51C4). (m), mutant DNA sample; (W), wild-type DNA sample. Analyses of YEL066w and YEL070w were performed in different experiments (data not shown). (d) Amplification of CAN1 from 20 rad51 Canr mutants. (e) Amplification of CAN1 from 20 rfa1-t29 rad51 Canr mutants. (f) Amplification of RFA1 from the same rfa1-t29 rad51 Canr mutants. (g) Amplification of CAN1 from 20 rfa1-t29 rad52 Canr mutants. (h) Amplification of CAN1 from 20 rfa1-t29 rad10 Canr mutants. (L), Lambda HindIII molecular weight marker; (K), Kb molecular weight marker. Molecular Cell 1998 2, 9-22DOI: (10.1016/S1097-2765(00)80109-4)

Figure 2 rad10, -51, and -52 Mutations Enhance the Growth Defect Caused by rfa1-t29 (a–c) The strain RDKY2491 rfa1-t29 was crossed to RDKY2629 rad51::URA3 (a), RDKY2712 rad52::URA3 (b), and RDKY2347 rad10::HIS3 (c). The resulting tetrads were dissected and genotyped as described in the Experimental Procedures. Genotypes are indicated as: (+), wild-type allele; (−), mutant allele; (0), no growth. (d and e) Spores from a single tetrad in the RDKY2491 × RDKY2347 cross were grown in liquid YPD to stationary phase. Cells were diluted, and 10 μl aliquots were spotted onto two YPD plates. One plate was incubated at 30°C (d), while the other at 37°C (e). Molecular Cell 1998 2, 9-22DOI: (10.1016/S1097-2765(00)80109-4)

Figure 3 Model for Formation of Gross Rearrangements in rfa1-t29 Defects in RFA result in the eventual generation of DSBs (step [a]). The DSBs are processed by bidirectional 5′-3′ exonuclease degradation, leading to the exposure of short stretches of complementary sequences (step [b]). These DSBs are processed by a variety of repair mechanisms, all of which compete for the available substrate. The most efficient repair pathway to act on these DSBs is homologous recombination (step [c]), which is unlikely to be mutagenic. In the absence of homologous recombination, DSBs are shunted into mutagenic repair pathways such as single-strand annealing (SSA, step [d]). Intrachromosomal SSA would give rise to deletions or inversions whereas interchromosomal SSA results in reciprocal translocations. An alternate mechanism by which deletion/translocation could be formed is shown in step (e), where the 3′ single-stranded DNA of a broken chromosome end invades a second chromosome at the site of complementary sequences. Subsequent break-induced replication (BIR) results, copying the second chromosome from the insertion site to the telomere. Depending on the orientation of the complementary sequence relative to the invading end, deletion, nonreciprocal translocation, or inversion events could result. Additional DSB repair pathways that do not seem to participate in the generation of gross rearrangements observed in this study, such as nonhomologous end joining (NHEJ) and DNA religation, are indicated in step (f). Molecular Cell 1998 2, 9-22DOI: (10.1016/S1097-2765(00)80109-4)