DOI: 10.7272/q6r78cg5
title: A role for synaptonemal complex in meiotic mismatch repair

description: During meiosis a large subset of interhomolog recombination repair
 intermediates form within the physical context of the synaptonemal complex
 (SC), a protein-rich structure assembled at the interface of aligned
 homologous chromosomes. However, the functional relationship between SC
 structure and homologous recombination remains poorly defined. In prior
 work we determined that tripartite SC is dispensable for recombination
 in S. cerevisiae; SC central element proteins Ecm11 and Gmc2
 instead limit the number of recombination events. Here we report that
 while dispensable for recombination per se, SC central element
 proteins influence the processing of interhomolog recombination
 intermediates in a manner that minimizes errors in mismatch correction.
 Failure to correct mis-paired bases within heteroduplex at meiotic
 recombination sites leads to genotypically sectored colonies (post meiotic
 segregation events) arising from mitotic proliferation of
 mismatch-containing spores. We discovered an increase in post-meiotic
 segregation at the THR1 locus in cells lacking Ecm11 or
 Gmc2, or in the SC-deficient but crossover
 recombination-proficient zip1[Δ21-163] mutant.
 High-throughput sequencing of octad meiotic products revealed a
 genome-wide increase in recombination events with uncorrected mismatches
 in ecm11 mutants relative to wild type. Meiotic cells
 missing Ecm11 also display longer gene conversion tracts, but tract length
 alone does not account for the higher frequency of uncorrected mismatches.
 Interestingly, the per-nucleotide mismatch frequency is elevated
 in ecm11 mutants when analyzing all gene conversion
 tracts, but is similar between wild type and ecm11 if
 one considers only those events with uncorrected mismatches. Our data
 suggest that a subset of recombination events is similarly susceptible to
 mismatch repair errors in both wild type
 and ecm11 strains, but
 in ecm11 mutants many more recombination events fall
 into this inefficient repair category. Finally, we observe elevated
 post-meiotic segregation at THR1 in mutants with a dual
 deficiency in MutSγ-mediated crossover recombination and SC assembly, but
 not in the mlh3 mutant, which lacks MutSγ crossovers but
 has abundant SC. We propose that SC structure promotes efficient mismatch
 repair of joint molecule recombination intermediates resolved via both
 MutSγ-associated and MutSγ-independent pathways, and is the molecular
 basis for elevated post-meiotic segregation in both MutSγ
 crossover-proficient (ecm11, gmc2) and MutSγ crossover-deficient (msh4,
 zip3) strains.
description: The ReCombine software package (ANDERSON et al. 2011; OKE et al.
 2014) was used on Fastq files from Illumina’s Casava pipeline to align all
 sequences to reference genomes, genotype markers, and designate CO and NCO
 locations for each mother or daughter “tetrad” component of the octad.
 Recombination events were compared between each pair of mother and
 daughter spores and mismatches were identified using a custom R script.
 Indels were removed.  Statistical tests were performed using GraphPad
 Prism software (www.graphpad.com).
description: allEventList.xls<br> Contains informattion about each
 recombination event in a tetrad. There is one file each for mother and
 daughter tetrad (m_ or d_)<br>     Grp: Unique ID for the
 recombination event that can be cross referenced across different
 files<br>     Tet: Tetrad number<br>     Chr: Chromosome
 number<br>     Pos: Eventb position (midpoint in bp)<br>   
  Lenth: Length of gene conversion tract (bp)<br>     Spores: Spores
 (1,2,3 or 4) involved in the recombination event<br>     start_out,
 start_in, end_in, end_out: positions of genotype switch used to detect the
 recombination event<br>     Event_type: Type of recombination
 event eventsWithPMS.txt<br> Contains a list of
 all events in a tetrad that have at least one PMS<br>     Grp: Event
 ID<br>     Tet: Tetrad (1=m, 0=d)<br>     Chr: Chromosome
 number<br>     Event_type: Type of recombination event<br>   
  start_out_m, start_in_m, end_in_m, end_out_m: positions of genotype
 switch used to detect the recombination event from mother tetrad<br>
     gc_length_m: Length of gene conversion tract (bp) in mother
 tetrad<br>     start_out_d, start_in_d, end_in_d, end_out_d:
 positions of genotype switch used to detect the recombination event from
 daughter tetrad<br>     gc_length_d: Length of gene conversion tract
 (bp) in daughter tetrad<br>     pms_count: number of PMS SNPs within
 the tract<br>     pms_list: list of PMS coordinates<br>   
  gc_length: gene conversion tract calculated using the outermost
 conversion SNPs Snps.txt<br> Contains the
 genotypes for all sequenced SNPs for each of the four spores in a tetrad.
  There is one file each for mother and daughter tetrad (m or d)<br>
     Chromosome<br>     Position<br>   
  &lt;spaceholder&gt;<br>     spore1 genotype (0=S96,
 1=YJM)<br>     spore2 genotype<br>     spore3
 genotype<br>     spore4 genotype