mlh3 mutations in baker’s yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide

Al-Sweel, Najla; Raghavan, Vandana; Dutta, Abhishek; Ajith, V. P.; Vietro, Luigi Di; N, Khondakar; Manhart, Carol M.; Surtees, Jennifer A.; Nishant, K. T.; Alani, Eric

doi:10.1371/journal.pgen.1006974

Cited by 37 publications

(50 citation statements)

References 97 publications

(230 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in pch2∆ mlh3∆ double mutants, COs were reduced 20-35% relative to pch2∆ MLH3 ( Figure 3B; average pch2∆ mlh3∆/pch2∆ = 74 ± 7%), as was previously observed for inserts at URA3 and HIS4 (MEDHI et al 2016). A quantitatively similar MutLg-dependence has also been observed for Spo11-initiated COs in pch2∆ mutants, both genome-wide (pch2∆ mlh3∆ / pch2∆ = 73% (CHAKRABORTY et al 2017) and for individual genetic intervals (pch2∆ / pch2∆ mlh3∆ = 75%, calculated from combined data of NISHANT et al 2008;ZANDERS AND ALANI 2009;AL-SWEEL et al 2017;CHAKRABORTY et al 2017). Thus, the absence of Pch2 increases the MutLg-dependence of VDEinitiated COs at many loci, while decreasing the MutLg-dependence of VDE-initiated COs at HIS4 and of Spo11-initiated COs.…”

Section: Increased Mlh3-dependence Of Vde-initiated Cos In Pch2∆ Mutantssupporting

confidence: 83%

“…In contrast to what was seen for VRS inserts at HIS4, where COs were reduced dramatically in mlh3∆ mutants (to ~40% of wild-type levels), COs in the same sequences inserted at all other loci were only modestly affected, with COs in mlh3∆ ranging from ~80% to ~115% of wild type (mean = 91 ± 12%; Figure 2D); NCOs were similarly unaffected ( Figure 2E, F). These results indicate that, in contrast to Spo11-initiated COs, which are reduced about 2-fold in mlh3∆ mutants (WANG et al 1999;KHAZANEHDARI AND BORTS 2000;KIRKPATRICK et al 2000;TSUBOUCHI AND OGAWA 2000;HOFFMANN et al 2003;ARGUESO et al 2004;NISHANT et al 2008;AL-SWEEL et al 2017;CHAKRABORTY et al 2017), most COs at the VDE break sites are formed independent of MutLg, irrespective of the chromosome size, distance from centromere or telomere, or Hop1-enrichment in their vicinity. Thus, at most insert loci in otherwise wild-type cells, VDE-initiated recombination differs from Spo11-initiated recombination and more closely resembles mitotic recombination, in that NCOs are in excess over COs (ESPOSITO 1978;LICHTEN AND HABER 1989;IRA et al 2003;DAYANI et al 2011) and, with the exception of those formed in inserts at HIS4, VDE-initiated COs are largely MutLg-independent.…”

Section: Vde-initiated Cos Are Mlh3-independent At Most Insert Sitesmentioning

confidence: 88%

“…Meiotic DSBs are also important for homolog colocalization, pairing and synapsis (KEENEY et al 1997;ROMANIENKO AND CAMERINI-OTERO 2000;BAUDAT et al 2013). Current thinking is that most DSBs are repaired either by a synthesis-dependent strand annealing pathway that forms non-crossovers (NCOs), or by a pathway that forms double Holiday junction (dHJ) intermediates that are resolved as crossovers (COs) by the MutLg (Mlh1-Mlh3 and Exo1) meiosis-specific resolvase (SCHWACHA AND KLECKNER 1994;WANG et al 1999;KHAZANEHDARI AND BORTS 2000;KIRKPATRICK et al 2000;TSUBOUCHI AND OGAWA 2000;ALLERS AND LICHTEN 2001b;ALLERS AND LICHTEN 2001a;HOFFMANN et al 2003;ARGUESO et al 2004;BISHOP AND ZICKLER 2004;NISHANT et al 2008;ZAKHARYEVICH et al 2010;AL-SWEEL et al 2017). In budding yeast, COs and NCOs are formed at similar levels, suggesting that roughly equal fractions of DSBs are repaired by these two pathways (MARTINI et al 2006;MANCERA et al 2008).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Noncanonical contributions of MutLγ to VDE-initiated crossovers duringSaccharomyces cerevisiaemeiosis

Shodhan

Medhi

Lichten

2019

Preprint

View full text Add to dashboard Cite

In Saccharomyces cerevisiae, the meiosis-specific axis proteins Hop1 and Red1 are present nonuniformly across the genome. In a previous study, the meiosis-specific VMA1-derived endonuclease (VDE) was used to examine Spo11-independent recombination in a recombination reporter inserted in a Hop1/Red1-enriched region (HIS4) and in a Hop1/Red1-poor region (URA3). VDE-initiated crossovers at HIS4 were mostly dependent on Mlh3, a component of the MutLg meiotic recombination intermediate resolvase, while VDE-initiated crossovers at URA3 were mostly Mlh3-independent. These differences were abolished in the absence of the chromosome axis remodeler Pch2, and crossovers at both loci become partly Mlh3-dependent. To test the generality of these observations, we examined inserts at six additional loci that differed in terms of Hop1/Red1 enrichment, chromosome size, and distance from centromeres and telomeres. All six loci behaved similarly to URA3: the vast majority of VDE-initiated crossovers were Mlh3-independent. This indicates that, counter to previous suggestions, meiotic chromosome axis protein enrichment is not a primary determinant of which recombination pathway gives rise to crossovers during VDE-initiated meiotic recombination. In pch2∆ mutants, the fraction of VDE-induced crossovers that were Mlh3dependent increased to levels previously observed for Spo11-initiated crossovers in pch2∆, indicating that Pch2-dependent processes play an important role in controlling the distribution of factors necessary for MutLg-dependent crossovers.

show abstract

Section: Increased Mlh3-dependence Of Vde-initiated Cos In Pch2∆ Mutantssupporting

confidence: 83%

Section: Vde-initiated Cos Are Mlh3-independent At Most Insert Sitesmentioning

confidence: 88%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Noncanonical contributions of MutLγ to VDE-initiated crossovers duringSaccharomyces cerevisiaemeiosis

Shodhan

Medhi

Lichten

2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Molecular incompatibilities between certain alleles of the CO formation or CO interference machinery may account for these cross-specific differences. To investigate this hypothesis further, we analysed the frequency and distribution of COs within a mlh3 Δ S288c x YJM789 background containing a functional copy of the SK1 MLH3 allele ( SK1-MLH3 ) 45 . Surprisingly, introduction of the SK1 MLH3 allele is sufficient to reduce the global strength of CO interference and produce a CO distribution identical to that of S288c x SK1 wild type (p = 0.91; Two-sample KS Test) (Supplementary Fig.…”

Section: Supplementary Discussionmentioning

confidence: 99%

Mismatch repair disturbs meiotic class I crossover control

Cooper

Crawford

Hunt

et al. 2018

Preprint

View full text Add to dashboard Cite

11Sequence divergence, mediated by the anti-recombinogenic activity of mismatch repair (MMR), forms a potent 12 barrier to meiotic recombination and in turn the formation of viable gametes 1-5 . However, exactly how MMR 13 jeopardizes meiotic success is unclear. Here we utilize a combination of S. cerevisiae genetics, genome-wide 14 mapping of recombination and computational modelling to demonstrate that MMR unexpectedly influences the 15 global distribution of recombination through preferential suppression of interfering crossovers (COs) at regions of 16 greater sequence divergence. As a result, inactivation of MMR not only increases the rate of recombination, as 17 previously observed, but also, paradoxically, the strength of CO interference. Our observations reveal a new 18 mechanism by which MMR spatially sculpts the meiotic landscape-linking CO control to the mechanisms that 19 can reproductively isolate a population, and highlighting how genomes may become meiotically incompatible at 20 the molecular level, dependent upon interactions of the primary DNA sequence. 21 22 the majority of COs formed (~70-85% within S. cerevisiae), are dispersed evenly along each chromosome by 31 means of CO interference-a process that suppresses the formation of COs in proximity to one another. A 32 subpopulation of recombination events alternatively resolve as non-interfering class II COs dependent upon 33 Mus81-Mms4, Yen1 or Slx1-Slx4. Homologous recombination, the process responsible for CO formation, 34 requires a repair template with near-perfect homology 8 . By contrast, recombination between polymorphic, 35 homoeologous substrates is markedly inefficient, leading to reduced rates of meiotic CO formation, reduced spore 36 viability and increased chromosomal non-disjunction during meiosis I within hybrid strains of S. cerevisiae-37 phenotypes linked to incipient speciation and which are largely reversed within MMR-deficient strains 1-4 . Despite 38 characterization of this anti-recombinogenic activity, a detailed analysis of how MMR alters meiotic recombination 39 on a genome-wide level has not yet been achieved. 40 41 In order to investigate the impact sequence divergence has upon CO formation, we mapped recombination ( Fig. 42 1a, Methods) within six wild type and 13 MMR-defective msh2Δ meioses-obtained from a cross of two widely 43 utilized laboratory isolates: S288c and SK1 3,9 (~65,000 SNPs, ~4,000 high confidence INDELs, ~0.57% 44 divergence). Additionally, we re-analyzed datasets comprising 51 wild type 10,11 and four msh2Δ tetrads 12 from a 45 S96 x YJM789 cross of S. cerevisiae (~0.6% divergence). On average, we identified 74.3 ±5.4 and 105.9 ±7.8 46 COs per meiosis within our SK1 x S288c wild type and msh2Δ samples respectively, corresponding to a significant 47 50 YJM789 than S288c x SK1 (91.4 vs. 74.3 COs per wild type meiosis)-suggesting that cross-specific differences 51 may exist. 52 53 To investigate any possible effect of Msh2 on CO patterning, we calculated the distribution of inter-cro...

show abstract

“…In budding yeast, the endonuclease Mlh1-Mlh3 interacts with Sc Msh4-Msh5 to resolve dHJs, although how the asymmetry in resolution occurs is not understood, particularly because the junctions form hundreds of bps apart from each other. One proposed model for MutSg function is the stabilization of dHJs to prevent dissolution before resolution by MutLg (20,31,73). Fishel and co-workers have proposed that multiple MutSg complexes form sliding clamps around the junction site, potentially facilitating asymmetric resolution of the junctions (31), whereas others have suggested that the polymerization of Mlh1-Mlh3 enables asymmetric junction resolution (27).…”

Section: Discussionmentioning

confidence: 99%

MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination

Lahiri

Hingorani

et al. 2018

Biophysical Journal

View full text Add to dashboard Cite

In many organisms, MutSg plays a role in meiotic recombination, facilitating crossover formation between homologous chromosomes. Failure to form crossovers leads to improper segregation of chromosomes and aneuploidy, which in humans result in infertility and birth defects. To improve current understanding of MutSg function, this study investigates the binding affinities and structures of MutSg in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSg protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3 0 overhangs, single-stranded (ss) forks, and the displacement loop with nanomolar affinity. The weakest binding affinities are detected for an intact duplex and open-junction construct. Similar to the human protein, Sc Msh4-Msh5 exhibits the highest affinity for the HJ with a K d < 0.4 nM in solution. Energy-transfer experiments further demonstrate that DNA structure is modulated by the binding interaction with the largest changes associated with substrates containing an ss end. Upon binding, Sc Msh4-Msh5 displaces the ss away from the duplex in most of the ss-containing intermediates, potentially enabling the binding of RPA and other proteins. In the case of the junction-like intermediates, Msh4-Msh5 binding either stabilizes the existing stacked structure or induces formation of the stacked X conformation. Significantly, we find that upon binding, Msh4-Msh5 stacks an open-junction construct to the same extent as the standard junction. Stabilization of the junction in the stacked conformation is generally refractory to branch migration, which is consistent with a potential role for MutSg to stabilize HJs and prevent branch migration until resolution by MutLg. The different binding modalities observed suggest that Msh4-Msh5 not only binds to and stabilizes stacked junctions but also participates in meiotic recombination before junction formation through the stabilization of single-end invasion intermediates.

show abstract

mlh3 mutations in baker’s yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide

Cited by 37 publications

References 97 publications

Noncanonical contributions of MutLγ to VDE-initiated crossovers duringSaccharomyces cerevisiaemeiosis

Noncanonical contributions of MutLγ to VDE-initiated crossovers duringSaccharomyces cerevisiaemeiosis

Mismatch repair disturbs meiotic class I crossover control

MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination

Contact Info

Product

Resources

About