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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Crickard JB, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. Genetics 2024; 227:iyae066. [PMID: 38657110 PMCID: PMC11228845 DOI: 10.1093/genetics/iyae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024] Open
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80% of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates to perform its role in crossover resolution. We performed a gene dosage screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3. Specifically, we looked for genes whose lowered dosage reduced meiotic crossing over using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. To our surprise we identified genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and in vivo. Partial complementation of Mlh3 crossover functions was observed when MLH3 was expressed under the control of the CLB1 promoter (NDT80 regulon), suggesting that Mlh3 function can be provided late in meiotic prophase at some functional cost. A model for how Dmc1 could facilitate Mlh1-Mlh3's role in crossover resolution is presented.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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2
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Medina-Rivera M, Phelps S, Sridharan M, Becker J, Lamb N, Kumar C, Sutton M, Bielinsky A, Balakrishnan L, Surtees J. Elevated MSH2 MSH3 expression interferes with DNA metabolism in vivo. Nucleic Acids Res 2023; 51:12185-12206. [PMID: 37930834 PMCID: PMC10711559 DOI: 10.1093/nar/gkad934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023] Open
Abstract
The Msh2-Msh3 mismatch repair (MMR) complex in Saccharomyces cerevisiae recognizes and directs repair of insertion/deletion loops (IDLs) up to ∼17 nucleotides. Msh2-Msh3 also recognizes and binds distinct looped and branched DNA structures with varying affinities, thereby contributing to genome stability outside post-replicative MMR through homologous recombination, double-strand break repair (DSBR) and the DNA damage response. In contrast, Msh2-Msh3 promotes genome instability through trinucleotide repeat (TNR) expansions, presumably by binding structures that form from single-stranded (ss) TNR sequences. We previously demonstrated that Msh2-Msh3 binding to 5' ssDNA flap structures interfered with Rad27 (Fen1 in humans)-mediated Okazaki fragment maturation (OFM) in vitro. Here we demonstrate that elevated Msh2-Msh3 levels interfere with DNA replication and base excision repair in vivo. Elevated Msh2-Msh3 also induced a cell cycle arrest that was dependent on RAD9 and ELG1 and led to PCNA modification. These phenotypes also required Msh2-Msh3 ATPase activity and downstream MMR proteins, indicating an active mechanism that is not simply a result of Msh2-Msh3 DNA-binding activity. This study provides new mechanistic details regarding how excess Msh2-Msh3 can disrupt DNA replication and repair and highlights the role of Msh2-Msh3 protein abundance in Msh2-Msh3-mediated genomic instability.
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Affiliation(s)
- Melisa Medina-Rivera
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Samantha Phelps
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Madhumita Sridharan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jordan Becker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Charanya Kumar
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Mark D Sutton
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
| | - Anja Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo NY, 14203, USA
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3
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Pannafino G, Chen JJ, Mithani V, Payero L, Gioia M, Brooks Crickard J, Alani E. The Dmc1 recombinase physically interacts with and promotes the meiotic crossover functions of the Mlh1-Mlh3 endonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566911. [PMID: 38014100 PMCID: PMC10680668 DOI: 10.1101/2023.11.13.566911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The accurate segregation of homologous chromosomes during the Meiosis I reductional division in most sexually reproducing eukaryotes requires crossing over between homologs. In baker's yeast approximately 80 percent of meiotic crossovers result from Mlh1-Mlh3 and Exo1 acting to resolve double-Holliday junction (dHJ) intermediates in a biased manner. Little is known about how Mlh1-Mlh3 is recruited to recombination intermediates and whether it interacts with other meiotic factors prior to its role in crossover resolution. We performed a haploinsufficiency screen in baker's yeast to identify novel genetic interactors with Mlh1-Mlh3 using sensitized mlh3 alleles that disrupt the stability of the Mlh1-Mlh3 complex and confer defects in mismatch repair but do not disrupt meiotic crossing over. We identified several genetic interactions between MLH3 and DMC1, the recombinase responsible for recombination between homologous chromosomes during meiosis. We then showed that Mlh3 physically interacts with Dmc1 in vitro and at times in meiotic prophase when Dmc1 acts as a recombinase. Interestingly, restricting MLH3 expression to roughly the time of crossover resolution resulted in a mlh3 null-like phenotype for crossing over. Our data are consistent with a model in which Dmc1 nucleates a polymer of Mlh1-Mlh3 to promote crossing over.
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Affiliation(s)
- Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Viraj Mithani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA 14853
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4
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Feng H, Bavister G, Gribble KE, Mark Welch DB. Highly efficient CRISPR-mediated gene editing in a rotifer. PLoS Biol 2023; 21:e3001888. [PMID: 37478130 PMCID: PMC10395877 DOI: 10.1371/journal.pbio.3001888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/09/2023] [Indexed: 07/23/2023] Open
Abstract
Rotifers have been studied in the laboratory and field for over 100 years in investigations of microevolution, ecological dynamics, and ecotoxicology. In recent years, rotifers have emerged as a model system for modern studies of the molecular mechanisms of genome evolution, development, DNA repair, aging, life history strategy, and desiccation tolerance. However, a lack of gene editing tools and transgenic strains has limited the ability to link genotype to phenotype and dissect molecular mechanisms. To facilitate genetic manipulation and the creation of reporter lines in rotifers, we developed a protocol for highly efficient, transgenerational, CRISPR-mediated gene editing in the monogonont rotifer Brachionus manjavacas by microinjection of Cas9 protein and synthetic single-guide RNA into the vitellaria of young amictic (asexual) females. To demonstrate the efficacy of the method, we created knockout mutants of the developmental gene vasa and the DNA mismatch repair gene mlh3. More than half of mothers survived injection and produced offspring. Genotyping these offspring and successive generations revealed that most carried at least 1 CRISPR-induced mutation, with many apparently mutated at both alleles. In addition, we achieved precise CRISPR-mediated knock-in of a stop codon cassette in the mlh3 locus, with half of injected mothers producing F2 offspring with an insertion of the cassette. Thus, this protocol produces knockout and knock-in CRISPR/Cas9 editing with high efficiency, to further advance rotifers as a model system for biological discovery.
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Affiliation(s)
- Haiyang Feng
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Gemma Bavister
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Kristin E Gribble
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - David B Mark Welch
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
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5
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Gioia M, Payero L, Salim S, Fajish V. G, Farnaz AF, Pannafino G, Chen JJ, Ajith VP, Momoh S, Scotland M, Raghavan V, Manhart CM, Shinohara A, Nishant KT, Alani E. Exo1 protects DNA nicks from ligation to promote crossover formation during meiosis. PLoS Biol 2023; 21:e3002085. [PMID: 37079643 PMCID: PMC10153752 DOI: 10.1371/journal.pbio.3002085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/02/2023] [Accepted: 03/17/2023] [Indexed: 04/21/2023] Open
Abstract
In most sexually reproducing organisms crossing over between chromosome homologs during meiosis is essential to produce haploid gametes. Most crossovers that form in meiosis in budding yeast result from the biased resolution of double Holliday junction (dHJ) intermediates. This dHJ resolution step involves the actions of Rad2/XPG family nuclease Exo1 and the Mlh1-Mlh3 mismatch repair endonuclease. Here, we provide genetic evidence in baker's yeast that Exo1 promotes meiotic crossing over by protecting DNA nicks from ligation. We found that structural elements in Exo1 that interact with DNA, such as those required for the bending of DNA during nick/flap recognition, are critical for its role in crossing over. Consistent with these observations, meiotic expression of the Rad2/XPG family member Rad27 partially rescued the crossover defect in exo1 null mutants, and meiotic overexpression of Cdc9 ligase reduced the crossover levels of exo1 DNA-binding mutants to levels that approached the exo1 null. In addition, our work identified a role for Exo1 in crossover interference. Together, these studies provide experimental evidence for Exo1-protected nicks being critical for the formation of meiotic crossovers and their distribution.
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Affiliation(s)
- Michael Gioia
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Lisette Payero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sagar Salim
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Ghanim Fajish V.
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Amamah F. Farnaz
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Jun Jie Chen
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - V. P. Ajith
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Sherikat Momoh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michelle Scotland
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Vandana Raghavan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Carol M. Manhart
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - K. T. Nishant
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
- Center for High-Performance Computing, Indian Institute of Science Education and Research Thiruvananthapuram, Trivandrum, India
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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6
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Shodhan A, Xaver M, Wheeler D, Lichten M. Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae. Genetics 2022; 222:6649696. [PMID: 35876814 PMCID: PMC9434160 DOI: 10.1093/genetics/iyac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022] Open
Abstract
The DNA double strand breaks (DSBs) that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in Saccharomyces cerevisiae contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red1 are important for DSB formation; DSB levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with DSB levels. How axis protein levels influence DSB formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased DSBs and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in DSBs did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote DSB formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, crossovers that formed at an insert locus were only modestly reduced in the absence of MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local DSB levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.
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Affiliation(s)
- Anura Shodhan
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Martin Xaver
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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7
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Voelkel-Meiman K, Oke A, Feil A, Shames A, Fung J, MacQueen AJ. A role for synaptonemal complex in meiotic mismatch repair. Genetics 2022; 220:iyab230. [PMID: 35100397 PMCID: PMC9097268 DOI: 10.1093/genetics/iyab230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/17/2021] [Indexed: 11/14/2022] Open
Abstract
A large subset of meiotic recombination intermediates form within the physical context of synaptonemal complex (SC), but the functional relationship between SC structure and homologous recombination remains obscure. Our prior analysis of strains deficient for SC central element proteins demonstrated that tripartite SC is dispensable for interhomolog recombination in Saccharomyces cerevisiae. Here, we report that while dispensable for recombination per se, SC proteins promote efficient mismatch repair at interhomolog recombination sites. Failure to repair mismatches within heteroduplex-containing meiotic recombination intermediates leads to genotypically sectored colonies (postmeiotic segregation events). We discovered increased postmeiotic segregation at THR1 in cells lacking Ecm11 or Gmc2, or in the SC-deficient but recombination-proficient zip1[Δ21-163] mutant. High-throughput sequencing of octad meiotic products furthermore revealed a genome-wide increase in recombination events with unrepaired mismatches in ecm11 mutants relative to wildtype. Meiotic cells missing Ecm11 display longer gene conversion tracts, but tract length alone does not account for the higher frequency of unrepaired mismatches. Interestingly, the per-nucleotide mismatch frequency is elevated in ecm11 when analyzing all gene conversion tracts, but is similar between wildtype and ecm11 if considering only those events with unrepaired mismatches. Thus, in both wildtype and ecm11 strains a subset of recombination events is susceptible to a similar degree of inefficient mismatch repair, but in ecm11 mutants a larger fraction of events fall into this inefficient repair category. Finally, we observe elevated postmeiotic segregation at THR1 in mutants with a dual deficiency in MutSγ 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, and that absence of SC is the molecular basis for elevated postmeiotic segregation in both MutSγ crossover-proficient (ecm11, gmc2) and MutSγ crossover-deficient (msh4, zip3) strains.
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Affiliation(s)
- Karen Voelkel-Meiman
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Arden Feil
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Alexander Shames
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Jennifer Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, Center of Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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8
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Singh P, Fragoza R, Blengini CS, Tran TN, Pannafino G, Al-Sweel N, Schimenti KJ, Schindler K, Alani EA, Yu H, Schimenti JC. Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging. Nat Commun 2021; 12:5005. [PMID: 34408140 PMCID: PMC8373927 DOI: 10.1038/s41467-021-25028-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/20/2021] [Indexed: 01/12/2023] Open
Abstract
Embryonic aneuploidy from mis-segregation of chromosomes during meiosis causes pregnancy loss. Proper disjunction of homologous chromosomes requires the mismatch repair (MMR) genes MLH1 and MLH3, essential in mice for fertility. Variants in these genes can increase colorectal cancer risk, yet the reproductive impacts are unclear. To determine if MLH1/3 single nucleotide polymorphisms (SNPs) in human populations could cause reproductive abnormalities, we use computational predictions, yeast two-hybrid assays, and MMR and recombination assays in yeast, selecting nine MLH1 and MLH3 variants to model in mice via genome editing. We identify seven alleles causing reproductive defects in mice including female subfertility and male infertility. Remarkably, in females these alleles cause age-dependent decreases in litter size and increased embryo resorption, likely a consequence of fewer chiasmata that increase univalents at meiotic metaphase I. Our data suggest that hypomorphic alleles of meiotic recombination genes can predispose females to increased incidence of pregnancy loss from gamete aneuploidy. Proper meiotic chromosome segregation requires mismatch repair genes MLH1 and MLH3, of which variants occur in the human population. Here, the authors use computational predictions and yeast assays to select human MLH1/3 variants for modelling in mice, observing reproductive defects from abnormal levels of crossing over.
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Affiliation(s)
- Priti Singh
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA.,Preclinical Modeling Core Lab, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert Fragoza
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Tina N Tran
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Najla Al-Sweel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Kerry J Schimenti
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | | | - Eric A Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.,Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - John C Schimenti
- Dept of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA. .,Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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9
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Furman CM, Elbashir R, Pannafino G, Clark NL, Alani E. Experimental exchange of paralogous domains in the MLH family provides evidence of sub-functionalization after gene duplication. G3 (BETHESDA, MD.) 2021; 11:jkab111. [PMID: 33871573 PMCID: PMC8495741 DOI: 10.1093/g3journal/jkab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/31/2021] [Indexed: 01/24/2023]
Abstract
Baker's yeast contains a large number of duplicated genes; some function redundantly, whereas others have more specialized roles. We used the MLH family of DNA mismatch repair (MMR) proteins as a model to better understand the steps that lead to gene specialization following a gene duplication event. We focused on two highly conserved yeast MLH proteins, Pms1 and Mlh3, with Pms1 having a major role in the repair of misincorporation events during DNA replication and Mlh3 acting to resolve recombination intermediates in meiosis to form crossovers. The baker's yeast Mlh3 and Pms1 proteins are significantly diverged (19% overall identity), suggesting that an extensive number of evolutionary steps, some major, others involving subtle refinements, took place to diversify the MLH proteins. Using phylogenetic and molecular approaches, we provide evidence that all three domains (N-terminal ATP binding, linker, C-terminal endonuclease/MLH interaction) in the MLH protein family are critical for conferring pathway specificity. Importantly, mlh3 alleles in the ATP binding and endonuclease domains improved MMR functions in strains lacking the Pms1 protein and did not disrupt Mlh3 meiotic functions. This ability for mlh3 alleles to complement the loss of Pms1 suggests that an ancestral Pms1/Mlh3 protein was capable of performing both MMR and crossover functions. Our strategy for analyzing MLH pathway specificity provides an approach to understand how paralogs have evolved to support distinct cellular processes.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Gianno Pannafino
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Nathan L Clark
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84132, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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10
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Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation. Proc Natl Acad Sci U S A 2021; 118:2022704118. [PMID: 34088835 DOI: 10.1073/pnas.2022704118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In budding yeast, the MutL homolog heterodimer Mlh1-Mlh3 (MutLγ) plays a central role in the formation of meiotic crossovers. It is also involved in the repair of a subset of mismatches besides the main mismatch repair (MMR) endonuclease Mlh1-Pms1 (MutLα). The heterodimer interface and endonuclease sites of MutLγ and MutLα are located in their C-terminal domain (CTD). The molecular basis of MutLγ's dual roles in MMR and meiosis is not known. To better understand the specificity of MutLγ, we characterized the crystal structure of Saccharomyces cerevisiae MutLγ(CTD). Although MutLγ(CTD) presents overall similarities with MutLα(CTD), it harbors some rearrangement of the surface surrounding the active site, which indicates altered substrate preference. The last amino acids of Mlh1 participate in the Mlh3 endonuclease site as previously reported for Pms1. We characterized mlh1 alleles and showed a critical role of this Mlh1 extreme C terminus both in MMR and in meiotic recombination. We showed that the MutLγ(CTD) preferentially binds Holliday junctions, contrary to MutLα(CTD). We characterized Mlh3 positions on the N-terminal domain (NTD) and CTD that could contribute to the positioning of the NTD close to the CTD in the context of the full-length MutLγ. Finally, crystal packing revealed an assembly of MutLγ(CTD) molecules in filament structures. Mutation at the corresponding interfaces reduced crossover formation, suggesting that these superstructures may contribute to the oligomer formation proposed for MutLγ. This study defines clear divergent features between the MutL homologs and identifies, at the molecular level, their specialization toward MMR or meiotic recombination functions.
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11
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Roy JCL, Vitalo A, Andrew MA, Mota-Silva E, Kovalenko M, Burch Z, Nhu AM, Cohen PE, Grabczyk E, Wheeler VC, Mouro Pinto R. Somatic CAG expansion in Huntington's disease is dependent on the MLH3 endonuclease domain, which can be excluded via splice redirection. Nucleic Acids Res 2021; 49:3907-3918. [PMID: 33751106 PMCID: PMC8053082 DOI: 10.1093/nar/gkab152] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 11/18/2022] Open
Abstract
Somatic expansion of the CAG repeat tract that causes Huntington's disease (HD) is thought to contribute to the rate of disease pathogenesis. Therefore, factors influencing repeat expansion are potential therapeutic targets. Genes in the DNA mismatch repair pathway are critical drivers of somatic expansion in HD mouse models. Here, we have tested, using genetic and pharmacological approaches, the role of the endonuclease domain of the mismatch repair protein MLH3 in somatic CAG expansion in HD mice and patient cells. A point mutation in the MLH3 endonuclease domain completely eliminated CAG expansion in the brain and peripheral tissues of a HD knock-in mouse model (HttQ111). To test whether the MLH3 endonuclease could be manipulated pharmacologically, we delivered splice switching oligonucleotides in mice to redirect Mlh3 splicing to exclude the endonuclease domain. Splice redirection to an isoform lacking the endonuclease domain was associated with reduced CAG expansion. Finally, CAG expansion in HD patient-derived primary fibroblasts was also significantly reduced by redirecting MLH3 splicing to the endogenous endonuclease domain-lacking isoform. These data indicate the potential of targeting the MLH3 endonuclease domain to slow somatic CAG repeat expansion in HD, a therapeutic strategy that may be applicable across multiple repeat expansion disorders.
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Affiliation(s)
- Jennie C L Roy
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Antonia Vitalo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Marissa A Andrew
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eduarda Mota-Silva
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marina Kovalenko
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zoe Burch
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anh M Nhu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.,Center for Reproductive Genomics, Cornell University, Ithaca, NY 14853, USA
| | - Ed Grabczyk
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Ricardo Mouro Pinto
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Neurology, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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12
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Pannafino G, Alani E. Coordinated and Independent Roles for MLH Subunits in DNA Repair. Cells 2021; 10:cells10040948. [PMID: 33923939 PMCID: PMC8074049 DOI: 10.3390/cells10040948] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 02/05/2023] Open
Abstract
The MutL family of DNA mismatch repair proteins (MMR) acts to maintain genomic integrity in somatic and meiotic cells. In baker’s yeast, the MutL homolog (MLH) MMR proteins form three heterodimeric complexes, MLH1-PMS1, MLH1-MLH2, and MLH1-MLH3. The recent discovery of human PMS2 (homolog of baker’s yeast PMS1) and MLH3 acting independently of human MLH1 in the repair of somatic double-strand breaks questions the assumption that MLH1 is an obligate subunit for MLH function. Here we provide a summary of the canonical roles for MLH factors in DNA genomic maintenance and in meiotic crossover. We then present the phenotypes of cells lacking specific MLH subunits, particularly in meiotic recombination, and based on this analysis, propose a model for an independent early role for MLH3 in meiosis to promote the accurate segregation of homologous chromosomes in the meiosis I division.
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13
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Rahman MM, Mohiuddin M, Shamima Keka I, Yamada K, Tsuda M, Sasanuma H, Andreani J, Guerois R, Borde V, Charbonnier JB, Takeda S. Genetic evidence for the involvement of mismatch repair proteins, PMS2 and MLH3, in a late step of homologous recombination. J Biol Chem 2021; 295:17460-17475. [PMID: 33453991 DOI: 10.1074/jbc.ra120.013521] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease, produces the majority of crossovers during meiotic HR, but it remains elusive whether mismatch repair factors promote HR in nonmeiotic cells. We disrupted genes encoding the MLH3 and PMS2 endonucleases in the human B cell line, TK6, generating null MLH3-/- and PMS2-/- mutant cells. We also inserted point mutations into the endonuclease motif of MLH3 and PMS2 genes, generating endonuclease death MLH3DN/DN and PMS2EK/EK cells. MLH3-/- and MLH3DN/DN cells showed a very similar phenotype, a 2.5-fold decrease in the frequency of heteroallelic HR-dependent repair of restriction enzyme-induced double-strand breaks. PMS2-/- and PMS2EK/EK cells showed a phenotype very similar to that of the MLH3 mutants. These data indicate that MLH3 and PMS2 promote HR as an endonuclease. The MLH3DN/DN and PMS2EK/EK mutations had an additive effect on the heteroallelic HR. MLH3DN/DN/PMS2EK/EK cells showed normal kinetics of γ-irradiation-induced Rad51 foci but a significant delay in the resolution of Rad51 foci and a 3-fold decrease in the number of cisplatin-induced sister chromatid exchanges. The ectopic expression of the Gen1 HJ re-solvase partially reversed the defective heteroallelic HR of MLH3DN/DN/PMS2EK/EK cells. Taken together, we propose that MLH3 and PMS2 promote HR as endonucleases, most likely by processing JMs in mammalian somatic cells.
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Affiliation(s)
- Md Maminur Rahman
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mohiuddin Mohiuddin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Islam Shamima Keka
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kousei Yamada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphael Guerois
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valerie Borde
- Institut Curie, CNRS, UMR3244, PSL Research University, Paris, France
| | - Jean-Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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14
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Hayward BE, Steinbach PJ, Usdin K. A point mutation in the nuclease domain of MLH3 eliminates repeat expansions in a mouse stem cell model of the Fragile X-related disorders. Nucleic Acids Res 2020; 48:7856-7863. [PMID: 32619224 DOI: 10.1093/nar/gkaa573] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/23/2020] [Accepted: 07/02/2020] [Indexed: 12/17/2022] Open
Abstract
The Fragile X-related disorders (FXDs) are Repeat Expansion Diseases, genetic disorders that result from the expansion of a disease-specific microsatellite. In those Repeat Expansion Disease models where it has been examined, expansion is dependent on functional mismatch repair (MMR) factors, including MutLγ, a heterodimer of MLH1/MLH3, one of the three MutL complexes found in mammals and a minor player in MMR. In contrast, MutLα, a much more abundant MutL complex that is the major contributor to MMR, is either not required for expansion or plays a limited role in expansion in many model systems. How MutLγ acts to generate expansions is unclear given its normal role in protecting against microsatellite instability and while MLH3 does have an associated endonuclease activity, whether that contributes to repeat expansion is uncertain. We show here, using a gene-editing approach, that a point mutation that eliminates the endonuclease activity of MLH3 eliminates expansions in an FXD mouse embryonic stem cell model. This restricts the number of possible models for repeat expansion and supports the idea that MutLγ may be a useful druggable target to reduce somatic expansion in those disorders where it contributes to disease pathology.
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Affiliation(s)
- Bruce E Hayward
- Section on Gene Structure and Disease Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karen Usdin
- Section on Gene Structure and Disease Laboratory of Cell and Molecular Biology National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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15
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Furman CM, Elbashir R, Alani E. Expanded roles for the MutL family of DNA mismatch repair proteins. Yeast 2020; 38:39-53. [PMID: 32652606 DOI: 10.1002/yea.3512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 12/31/2022] Open
Abstract
The MutL family of DNA mismatch repair proteins plays a critical role in excising and repairing misincorporation errors during DNA replication. In many eukaryotes, members of this family have evolved to modulate and resolve recombination intermediates into crossovers during meiosis. In these organisms, such functions promote the accurate segregation of chromosomes during the meiosis I division. What alterations occurred in MutL homolog (MLH) family members that enabled them to acquire these new roles? In this review, we present evidence that the yeast Mlh1-Mlh3 and Mlh1-Mlh2 complexes have evolved novel enzymatic and nonenzymatic activities and protein-protein interactions that are critical for their meiotic functions. Curiously, even with these changes, these complexes retain backup and accessory roles in DNA mismatch repair during vegetative growth.
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Affiliation(s)
- Christopher M Furman
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ryan Elbashir
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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16
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Toledo M, Sun X, Brieño-Enríquez MA, Raghavan V, Gray S, Pea J, Milano CR, Venkatesh A, Patel L, Borst PL, Alani E, Cohen PE. A mutation in the endonuclease domain of mouse MLH3 reveals novel roles for MutLγ during crossover formation in meiotic prophase I. PLoS Genet 2019; 15:e1008177. [PMID: 31170160 PMCID: PMC6588253 DOI: 10.1371/journal.pgen.1008177] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/21/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
During meiotic prophase I, double-strand breaks (DSBs) initiate homologous recombination leading to non-crossovers (NCOs) and crossovers (COs). In mouse, 10% of DSBs are designated to become COs, primarily through a pathway dependent on the MLH1-MLH3 heterodimer (MutLγ). Mlh3 contains an endonuclease domain that is critical for resolving COs in yeast. We generated a mouse (Mlh3DN/DN) harboring a mutation within this conserved domain that is predicted to generate a protein that is catalytically inert. Mlh3DN/DN males, like fully null Mlh3-/- males, have no spermatozoa and are infertile, yet spermatocytes have grossly normal DSBs and synapsis events in early prophase I. Unlike Mlh3-/- males, mutation of the endonuclease domain within MLH3 permits normal loading and frequency of MutLγ in pachynema. However, key DSB repair factors (RAD51) and mediators of CO pathway choice (BLM helicase) persist into pachynema in Mlh3DN/DN males, indicating a temporal delay in repair events and revealing a mechanism by which alternative DSB repair pathways may be selected. While Mlh3DN/DN spermatocytes retain only 22% of wildtype chiasmata counts, this frequency is greater than observed in Mlh3-/- males (10%), suggesting that the allele may permit partial endonuclease activity, or that other pathways can generate COs from these MutLγ-defined repair intermediates in Mlh3DN/DN males. Double mutant mice homozygous for the Mlh3DN/DN and Mus81-/- mutations show losses in chiasmata close to those observed in Mlh3-/- males, indicating that the MUS81-EME1-regulated crossover pathway can only partially account for the increased residual chiasmata in Mlh3DN/DN spermatocytes. Our data demonstrate that mouse spermatocytes bearing the MLH1-MLH3DN/DN complex display the proper loading of factors essential for CO resolution (MutSγ, CDK2, HEI10, MutLγ). Despite these functions, mice bearing the Mlh3DN/DN allele show defects in the repair of meiotic recombination intermediates and a loss of most chiasmata.
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Affiliation(s)
- Melissa Toledo
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
| | - Xianfei Sun
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Miguel A. Brieño-Enríquez
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
| | - Vandana Raghavan
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Stephen Gray
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
| | - Jeffrey Pea
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
| | - Carolyn R. Milano
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
| | - Anita Venkatesh
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Lekha Patel
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
| | - Peter L. Borst
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Paula E. Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States of America
- The Center for Reproductive Genomics, Cornell University, Ithaca, NY, United States of America
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17
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Noncanonical Contributions of MutLγ to VDE-Initiated Crossovers During Saccharomyces cerevisiae Meiosis. G3-GENES GENOMES GENETICS 2019; 9:1647-1654. [PMID: 30902890 PMCID: PMC6505156 DOI: 10.1534/g3.119.400150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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 MutLγ 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 became 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, levels of meiotic chromosome axis protein enrichment alone do not determine which recombination pathway gives rise to crossovers during VDE-initiated meiotic recombination. In pch2∆ mutants, the fraction of VDE-induced crossovers that were Mlh3-dependent increased to levels previously observed for Spo11-initiated crossovers in pch2∆, indicating that Pch2-dependent processes play an important role in controlling the balance between MutLγ-dependent and MutLγ-independent crossovers.
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18
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Marsolier-Kergoat MC, Khan MM, Schott J, Zhu X, Llorente B. Mechanistic View and Genetic Control of DNA Recombination during Meiosis. Mol Cell 2019; 70:9-20.e6. [PMID: 29625041 DOI: 10.1016/j.molcel.2018.02.032] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/07/2017] [Accepted: 02/26/2018] [Indexed: 10/17/2022]
Abstract
Meiotic recombination is essential for fertility and allelic shuffling. Canonical recombination models fail to capture the observed complexity of meiotic recombinants. Here, by combining genome-wide meiotic heteroduplex DNA patterns with meiotic DNA double-strand break (DSB) sites, we show that part of this complexity results from frequent template switching during synthesis-dependent strand annealing that yields noncrossovers and from branch migration of double Holliday junction (dHJ)-containing intermediates that mainly yield crossovers. This complexity also results from asymmetric positioning of crossover intermediates relative to the initiating DSB and Msh2-independent conversions promoted by the suspected dHJ resolvase Mlh1-3 as well as Exo1 and Sgs1. Finally, we show that dHJ resolution is biased toward cleavage of the pair of strands containing newly synthesized DNA near the junctions and that this bias can be decoupled from the crossover-biased dHJ resolution. These properties are likely conserved in eukaryotes containing ZMM proteins, which includes mammals.
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Affiliation(s)
- Marie-Claude Marsolier-Kergoat
- CEA/DRF, I2BC/UMR 9198, SBIGeM, Gif-sur-Yvette, France; CNRS-UMR 7206, Éco-anthropologie et Ethnobiologie, Musée de l'Homme, 17, Place du Trocadéro et du 11 Novembre, Paris, France.
| | - Md Muntaz Khan
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Jonathan Schott
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Xuan Zhu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center and Howard Hughes Medical Institute, New York, NY, USA
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS UMR7258, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France.
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19
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Hao S, Wang R, Zhang Y, Zhan H. Prediction of Alzheimer's Disease-Associated Genes by Integration of GWAS Summary Data and Expression Data. Front Genet 2019; 9:653. [PMID: 30666269 PMCID: PMC6330278 DOI: 10.3389/fgene.2018.00653] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/03/2018] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. It is the fifth leading cause of death among elderly people. With high genetic heritability (79%), finding the disease's causal genes is a crucial step in finding a treatment for AD. Following the International Genomics of Alzheimer's Project (IGAP), many disease-associated genes have been identified; however, we do not have enough knowledge about how those disease-associated genes affect gene expression and disease-related pathways. We integrated GWAS summary data from IGAP and five different expression-level data by using the transcriptome-wide association study method and identified 15 disease-causal genes under strict multiple testing (α < 0.05), and four genes are newly identified. We identified an additional 29 potential disease-causal genes under a false discovery rate (α < 0.05), and 21 of them are newly identified. Many genes we identified are also associated with an autoimmune disorder.
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Affiliation(s)
- Sicheng Hao
- College of Computer and Information Science, Northeastern University, Boston, MA, United States
| | - Rui Wang
- College of Computer and Information Science, Northeastern University, Boston, MA, United States
| | - Yu Zhang
- Department of Neurosurgery, Heilongjiang Province Land Reclamation Headquarters General Hospital, Harbin, China
| | - Hui Zhan
- College of Electronic Engineering, Heilongjiang University, Harbin, China
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20
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Biallelic germline nonsense variant of MLH3 underlies polyposis predisposition. Genet Med 2018; 21:1868-1873. [PMID: 30573798 PMCID: PMC6752675 DOI: 10.1038/s41436-018-0405-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/03/2018] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Some 10% of familial adenomatous polyposis (FAP) and 80% of attenuated polyposis (AFAP) cases remain molecularly unexplained. We scrutinized such cases by exome-wide and targeted methods to search for novel susceptibility genes. METHODS Exome sequencing was conducted on 40 unexplained (mainly sporadic) cases with FAP or AFAP from Finland. The DNA mismatch repair (MMR) gene MLH3 (MutL Homolog 3) was pinpointed and prompted a subsequent screen of ~1000 Swedish patients referred to clinical panel sequencing for colon tumor susceptibility. RESULTS Three homozygous carriers of a truncating variant in MLH3, c.3563C>G, p.Ser1188Ter, were identified among the index cases from the Finnish series. An additional biallelic carrier of the same variant was present in the Swedish series. All four patients shared a 0.8-Mb core haplotype around MLH3, suggesting a founder variant. Colorectal polyps from variant carriers showed no instability at mono-, di-, tri-, or tetranucleotide repeats, in agreement with previous findings of a minor role of MLH3 in MMR. Multiple loci were affected by loss of heterozygosity, suggesting chromosomal instability. CONCLUSION Our results show that a biallelic nonsense variant of MLH3 underlies a novel syndrome with susceptibility to classical or attenuated adenomatous polyposis and possibly extracolonic tumors, including breast cancer.
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21
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Lahiri S, Li Y, Hingorani MM, Mukerji I. MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination. Biophys J 2018; 115:2087-2101. [PMID: 30467025 DOI: 10.1016/j.bpj.2018.10.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Accepted: 10/22/2018] [Indexed: 01/11/2023] Open
Abstract
In many organisms, MutSγ 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 MutSγ function, this study investigates the binding affinities and structures of MutSγ in complex with DNA substrates that model homologous recombination intermediates. For these studies, we overexpressed and isolated from Escherichia coli the yeast MutSγ protein Saccharomyces cerevisiae (Sc) Msh4-Msh5. Sc Msh4-Msh5 binds Holliday junction (HJ)-like substrates, 3' 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 Kd < 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 MutSγ to stabilize HJs and prevent branch migration until resolution by MutLγ. 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.
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Affiliation(s)
- Sudipta Lahiri
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Yan Li
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Manju M Hingorani
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut.
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22
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Chakraborty P, Pankajam AV, Dutta A, Nishant KT. Genome wide analysis of meiotic recombination in yeast: For a few SNPs more. IUBMB Life 2018; 70:743-752. [PMID: 29934971 PMCID: PMC6120447 DOI: 10.1002/iub.1877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/02/2018] [Indexed: 01/08/2023]
Abstract
Diploid organisms undergo meiosis to produce haploid germ cells. Crossover events during meiosis promote genetic diversity and facilitate accurate chromosome segregation. The baker's yeast Saccharomyces cerevisiae is extensively used as a model for analysis of meiotic recombination. Conventional methods for measuring recombination events in S. cerevisiae have been limited by the number and density of genetic markers. Next generation sequencing (NGS)-based analysis of hybrid yeast genomes bearing thousands of heterozygous single nucleotide polymorphism (SNP) markers has revolutionized analysis of meiotic recombination. By facilitating analysis of marker segregation in the whole genome with unprecedented resolution, this method has resulted in the generation of high-resolution recombination maps in wild-type and meiotic mutants. These studies have provided novel insights into the mechanism of meiotic recombination. In this review, we discuss the methodology, challenges, insights and future prospects of using NGS-based methods for whole genome analysis of meiotic recombination. The objective is to facilitate the use of these high through-put sequencing methods for the analysis of meiotic recombination given their power to provide significant new insights into the process. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(8):743-752, 2018.
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Affiliation(s)
- Parijat Chakraborty
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramTrivandrumIndia
| | - Ajith V. Pankajam
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramTrivandrumIndia
| | - Abhishek Dutta
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramTrivandrumIndia
| | - Koodali T. Nishant
- School of BiologyIndian Institute of Science Education and ResearchThiruvananthapuramTrivandrumIndia
- Centre for Computation Modelling and SimulationIndian Institute of Science Education and ResearchThiruvananthapuramTrivandrumIndia
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Correction: mlh3 mutations in baker’s yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide. PLoS Genet 2017; 13:e1007067. [PMID: 29065117 PMCID: PMC5655472 DOI: 10.1371/journal.pgen.1007067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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