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A role for synaptonemal complex in meiotic mismatch repair

Citation

Oke, Ashwini; MacQueen, Amy (2021), A role for synaptonemal complex in meiotic mismatch repair, Dryad, Dataset, https://doi.org/10.7272/Q6R78CG5

Abstract

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.

Methods

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).

Usage Notes

allEventList.xls
Contains informattion about each recombination event in a tetrad. There is one file each for mother and daughter tetrad (m_ or d_)
    Grp: Unique ID for the recombination event that can be cross referenced across different files
    Tet: Tetrad number
    Chr: Chromosome number
    Pos: Eventb position (midpoint in bp)
    Lenth: Length of gene conversion tract (bp)
    Spores: Spores (1,2,3 or 4) involved in the recombination event
    start_out, start_in, end_in, end_out: positions of genotype switch used to detect the recombination event
    Event_type: Type of recombination event

eventsWithPMS.txt
Contains a list of all events in a tetrad that have at least one PMS
    Grp: Event ID
    Tet: Tetrad (1=m, 0=d)
    Chr: Chromosome number
    Event_type: Type of recombination event
    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
    gc_length_m: Length of gene conversion tract (bp) in mother tetrad
    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
    gc_length_d: Length of gene conversion tract (bp) in daughter tetrad
    pms_count: number of PMS SNPs within the tract
    pms_list: list of PMS coordinates
    gc_length: gene conversion tract calculated using the outermost conversion SNPs

Snps.txt
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)
    Chromosome
    Position
    <spaceholder>
    spore1 genotype (0=S96, 1=YJM)
    spore2 genotype
    spore3 genotype
    spore4 genotype