1
|
Tang S, Koo J, Pourhosseinzadeh M, Nguyen E, Liu N, Ma C, Lu H, Lee M, Hunter N. Synaptonemal complex protects double-Holliday junctions during meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.14.613089. [PMID: 39314413 PMCID: PMC11419148 DOI: 10.1101/2024.09.14.613089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Chromosomal linkages formed through crossover recombination are essential for accurate segregation of homologous chromosomes during meiosis1. DNA events of recombination are spatially and functionally linked to structural components of meiotic chromosomes2. Imperatively, biased resolution of double-Holliday junction (dHJ) intermediates into crossovers3,4 occurs within the synaptonemal complex (SC), the meiosis-specific structure that mediates homolog synapsis during the pachytene stage5,6. However, the SC's role in crossing over remains unclear. Here we show that SC promotes crossover-specific resolution by protecting dHJs from unscheduled and aberrant resolution. When key SC components are conditionally inactivated during pachytene, dHJs are resolved into noncrossover products by Sgs1-Top3-Rmi1 (STR), the yeast ortholog of the human BLM complex7. Cohesin, the core component of SC lateral elements, plays a primary role in chromatin organization and is required to maintain both SCs and crossover recombination complexes (CRCs) during pachytene. SC central region component Zip1 is required to maintain CRCs even when dHJs are stabilized by inactivating STR. Reciprocally, SC stability requires continuous presence of CRCs, an unanticipated interdependence with important implications for SC dynamics. In conclusion, through hierarchical and interdependent functions of its key components, the SC enables crossover-specific dHJ resolution and thereby ensures the linkage and segregation of homologous chromosomes.
Collapse
Affiliation(s)
- Shangming Tang
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer Koo
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Mohammad Pourhosseinzadeh
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Emerald Nguyen
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Natalie Liu
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Christopher Ma
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Hanyu Lu
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Monica Lee
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, CA, USA
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, CA, USA
- Department of Molecular & Cellular Biology, University of California, Davis, Davis, CA, USA
| |
Collapse
|
2
|
Huang PC, Hong S, Mimitou EP, Kim KP, Murakami H, Keeney S. Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589955. [PMID: 38659928 PMCID: PMC11042300 DOI: 10.1101/2024.04.17.589955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
DNA double-strand breaks (DSBs) are nucleolytically processed to generate single-stranded DNA tails for homologous recombination. In Saccharomyces cerevisiae meiosis, this 5'-to-3' resection involves initial nicking by the Mre11-Rad50-Xrs2 complex (MRX) plus Sae2, then exonucleolytic digestion by Exo1. Chromatin remodeling adjacent to meiotic DSBs is thought to be necessary for resection, but the relevant remodeling activity was unknown. Here we show that the SWI/SNF-like ATPase Fun30 plays a major, non-redundant role in resecting meiotic DSBs. A fun30 null mutation shortened resection tract lengths almost as severely as an exo1-nd (nuclease-dead) mutation, and resection was further shortened in the fun30 exo1-nd double mutant. Fun30 associates with chromatin in response to meiotic DSBs, and the constitutive positioning of nucleosomes governs resection endpoint locations in the absence of Fun30. We infer that Fun30 directly promotes both the MRX- and Exo1-dependent steps in resection, possibly by removing nucleosomes from broken chromatids. Moreover, we found that the extremely short resection in the fun30 exo1-nd double mutant is accompanied by compromised interhomolog recombination bias, leading to defects in recombination and chromosome segregation. Thus, this study also provides insight about the minimal resection lengths needed for robust recombination.
Collapse
Affiliation(s)
- Pei-Ching Huang
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Soogil Hong
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Eleni P. Mimitou
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Keun P. Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
- Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 06974, South Korea
| | - Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10021
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| |
Collapse
|
3
|
Altmannova V, Spirek M, Orlic L, Jēkabsons A, Clarence T, Henggeler A, Mlcouskova J, Chaleil RA, Matos J, Krejci L. The role of bivalent ions in the regulation of D-loop extension mediated by DMC1 during meiotic recombination. iScience 2022; 25:105439. [PMID: 36388968 PMCID: PMC9641244 DOI: 10.1016/j.isci.2022.105439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/06/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
During meiosis, programmed DNA double-strand breaks (DSBs) are repaired by homologous recombination. DMC1, a conserved recombinase, plays a central role in this process. DMC1 promotes DNA strand exchange between homologous chromosomes, thus creating the physical linkage between them. Its function is regulated not only by several accessory proteins but also by bivalent ions. Here, we show that whereas calcium ions in the presence of ATP cause a conformational change within DMC1, stimulating its DNA binding and D-loop formation, they inhibit the extension of the invading strand within the D-loop. Based on structural studies, we have generated mutants of two highly conserved amino acids - E162 and D317 - in human DMC1, which are deficient in calcium regulation. In vivo studies of their yeast homologues further showed that they exhibit severe defects in meiosis, thus emphasizing the importance of calcium ions in the regulation of DMC1 function and meiotic recombination.
Collapse
Affiliation(s)
- Veronika Altmannova
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | - Mario Spirek
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | - Lucija Orlic
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9 1030 Vienna, Austria
| | - Atis Jēkabsons
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | - Tereza Clarence
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Adrian Henggeler
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9 1030 Vienna, Austria
| | - Jarmila Mlcouskova
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
| | | | - Joao Matos
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9 1030 Vienna, Austria
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
- International Clinical Research Center, St. Anne’s University Hospital, Brno 65691, Czech Republic
- National Center for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| |
Collapse
|
4
|
Ahuja JS, Harvey CS, Wheeler DL, Lichten M. Repeated strand invasion and extensive branch migration are hallmarks of meiotic recombination. Mol Cell 2021; 81:4258-4270.e4. [PMID: 34453891 PMCID: PMC8541907 DOI: 10.1016/j.molcel.2021.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/09/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Currently favored models for meiotic recombination posit that both noncrossover and crossover recombination are initiated by DNA double-strand breaks but form by different mechanisms: noncrossovers by synthesis-dependent strand annealing and crossovers by formation and resolution of double Holliday junctions centered around the break. This dual mechanism hypothesis predicts different hybrid DNA patterns in noncrossover and crossover recombinants. We show that these predictions are not upheld, by mapping with unprecedented resolution parental strand contributions to recombinants at a model locus. Instead, break repair in both noncrossovers and crossovers involves synthesis-dependent strand annealing, often with multiple rounds of strand invasion. Crossover-specific double Holliday junction formation occurs via processes involving branch migration as an integral feature, one that can be separated from repair of the break itself. These findings reveal meiotic recombination to be a highly dynamic process and prompt a new view of the relationship between crossover and noncrossover recombination.
Collapse
Affiliation(s)
- Jasvinder S Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Catherine S Harvey
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David L Wheeler
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| |
Collapse
|
5
|
Lee MS, Higashide MT, Choi H, Li K, Hong S, Lee K, Shinohara A, Shinohara M, Kim KP. The synaptonemal complex central region modulates crossover pathways and feedback control of meiotic double-strand break formation. Nucleic Acids Res 2021; 49:7537-7553. [PMID: 34197600 PMCID: PMC8287913 DOI: 10.1093/nar/gkab566] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 12/27/2022] Open
Abstract
The synaptonemal complex (SC) is a proteinaceous structure that mediates homolog engagement and genetic recombination during meiosis. In budding yeast, Zip-Mer-Msh (ZMM) proteins promote crossover (CO) formation and initiate SC formation. During SC elongation, the SUMOylated SC component Ecm11 and the Ecm11-interacting protein Gmc2 facilitate the polymerization of Zip1, an SC central region component. Through physical recombination, cytological, and genetic analyses, we found that ecm11 and gmc2 mutants exhibit chromosome-specific defects in meiotic recombination. CO frequencies on a short chromosome (chromosome III) were reduced, whereas CO and non-crossover frequencies on a long chromosome (chromosome VII) were elevated. Further, in ecm11 and gmc2 mutants, more double-strand breaks (DSBs) were formed on a long chromosome during late prophase I, implying that the Ecm11–Gmc2 (EG) complex is involved in the homeostatic regulation of DSB formation. The EG complex may participate in joint molecule (JM) processing and/or double-Holliday junction resolution for ZMM-dependent CO-designated recombination. Absence of the EG complex ameliorated the JM-processing defect in zmm mutants, suggesting a role for the EG complex in suppressing ZMM-independent recombination. Our results suggest that the SC central region functions as a compartment for sequestering recombination-associated proteins to regulate meiosis specificity during recombination.
Collapse
Affiliation(s)
- Min-Su Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Mika T Higashide
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hyungseok Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Ke Li
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.,Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan
| | - Soogil Hong
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Miki Shinohara
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.,Graduate School of Agriculture, Kindai University, Nara 631-8505, Japan.,Agricultural Technology and Innovation Research Institute, Kindai University, Nara 631-8505, Japan
| | - Keun P Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| |
Collapse
|
6
|
Piazza A, Rajput P, Heyer WD. Physical and Genetic Assays for the Study of DNA Joint Molecules Metabolism and Multi-invasion-Induced Rearrangements in S. cerevisiae. Methods Mol Biol 2021; 2153:535-554. [PMID: 32840803 DOI: 10.1007/978-1-0716-0644-5_36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA double-strand breaks (DSBs) are genotoxic lesions that can be repaired in a templated fashion by homologous recombination (HR). HR is a complex pathway that involves the formation of DNA joint molecules (JMs) containing heteroduplex DNA. Various types of JMs are formed throughout the pathway, including displacement loops (D-loops), multi-invasions (MI), and double Holliday junction intermediates. Dysregulation of JM metabolism in various mutant contexts revealed the propensity of HR to generate repeat-mediated chromosomal rearrangements. Specifically, we recently identified MI-induced rearrangements (MIR), a tripartite recombination mechanism initiated by one end of a DSB that exploits repeated regions to generate rearrangements between intact chromosomal regions. MIR occurs upon MI-JM processing by endonucleases and is suppressed by JM disruption activities. Here, we detail two assays: a physical assay for JM detection in Saccharomyces cerevisiae cells and genetic assays to determine the frequency of MIR in various chromosomal contexts. These assays enable studying the regulation of the HR pathway and the consequences of their defects for genomic instability by MIR.
Collapse
Affiliation(s)
- Aurèle Piazza
- Spatial Regulation of Genomes, Institut Pasteur, UMR3525 CNRS, Paris, France.,Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA.,Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, Lyon, France
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, USA. .,Department of Molecular and Cellular Biology, University of California, Davis, CA, USA.
| |
Collapse
|
7
|
Bhagwat NR, Owens SN, Ito M, Boinapalli JV, Poa P, Ditzel A, Kopparapu S, Mahalawat M, Davies OR, Collins SR, Johnson JR, Krogan NJ, Hunter N. SUMO is a pervasive regulator of meiosis. eLife 2021; 10:57720. [PMID: 33502312 PMCID: PMC7924959 DOI: 10.7554/elife.57720] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Protein modification by SUMO helps orchestrate the elaborate events of meiosis to faithfully produce haploid gametes. To date, only a handful of meiotic SUMO targets have been identified. Here, we delineate a multidimensional SUMO-modified meiotic proteome in budding yeast, identifying 2747 conjugation sites in 775 targets, and defining their relative levels and dynamics. Modified sites cluster in disordered regions and only a minority match consensus motifs. Target identities and modification dynamics imply that SUMOylation regulates all levels of chromosome organization and each step of meiotic prophase I. Execution-point analysis confirms these inferences, revealing functions for SUMO in S-phase, the initiation of recombination, chromosome synapsis and crossing over. K15-linked SUMO chains become prominent as chromosomes synapse and recombine, consistent with roles in these processes. SUMO also modifies ubiquitin, forming hybrid oligomers with potential to modulate ubiquitin signaling. We conclude that SUMO plays diverse and unanticipated roles in regulating meiotic chromosome metabolism. Most mammalian, yeast and other eukaryote cells have two sets of chromosomes, one from each parent, which contain all the cell’s DNA. Sex cells – like the sperm and egg – however, have half the number of chromosomes and are formed by a specialized type of cell division known as meiosis. At the start of meiosis, each cell replicates its chromosomes so that it has twice the amount of DNA. The cell then undergoes two rounds of division to form sex cells which each contain only one set of chromosomes. Before the cell divides, the two duplicated sets of chromosomes pair up and swap sections of their DNA. This exchange allows each new sex cell to have a unique combination of DNA, resulting in offspring that are genetically distinct from their parents. This complex series of events is tightly regulated, in part, by a protein called the 'small ubiquitin-like modifier' (or SUMO for short), which attaches itself to other proteins and modifies their behavior. This process, known as SUMOylation, can affect a protein’s stability, where it is located in the cell and how it interacts with other proteins. However, despite SUMO being known as a key regulator of meiosis, only a handful of its protein targets have been identified. To gain a better understanding of what SUMO does during meiosis, Bhagwat et al. set out to find which proteins are targeted by SUMO in budding yeast and to map the specific sites of modification. The experiments identified 2,747 different sites on 775 different proteins, suggesting that SUMO regulates all aspects of meiosis. Consistently, inactivating SUMOylation at different times revealed SUMO plays a role at every stage of meiosis, including the replication of DNA and the exchanges between chromosomes. In depth analysis of the targeted proteins also revealed that SUMOylation targets different groups of proteins at different stages of meiosis and interacts with other protein modifications, including the ubiquitin system which tags proteins for destruction. The data gathered by Bhagwat et al. provide a starting point for future research into precisely how SUMO proteins control meiosis in yeast and other organisms. In humans, errors in meiosis are the leading cause of pregnancy loss and congenital diseases. Most of the proteins identified as SUMO targets in budding yeast are also present in humans. So, this research could provide a platform for medical advances in the future. The next step is to study mammalian models, such as mice, to confirm that the regulation of meiosis by SUMO is the same in mammals as in yeast.
Collapse
Affiliation(s)
- Nikhil R Bhagwat
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Shannon N Owens
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Masaru Ito
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jay V Boinapalli
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Philip Poa
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Alexander Ditzel
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Srujan Kopparapu
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Meghan Mahalawat
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Owen Richard Davies
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sean R Collins
- Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States
| | - Jeffrey R Johnson
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Nevan J Krogan
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, United States
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California Davis, Davis, United States.,Department of Microbiology & Molecular Genetics, University of California Davis, Davis, United States.,Department of Molecular & Cellular Biology, University of California Davis, Davis, United States
| |
Collapse
|
8
|
Abstract
The ribosomal RNA (rDNA) sequence is the most abundant repetitive element in the budding yeast genome and forms a tandem cluster of ~100-200 copies. Cells frequently change their rDNA copy number, making rDNA the most unstable region in the budding yeast genome. The rDNA region experiences programmed replication fork arrest and subsequent formation of DNA double-strand breaks (DSBs), which are the main drivers of rDNA instability. The rDNA region offers a unique system to understand the mechanisms that respond to replication fork arrest as well as the mechanisms that regulate repeat instability. This chapter describes three methods to assess rDNA instability.
Collapse
|
9
|
Shah SS, Hartono S, Piazza A, Som V, Wright W, Chédin F, Heyer WD. Rdh54/Tid1 inhibits Rad51-Rad54-mediated D-loop formation and limits D-loop length. eLife 2020; 9:59112. [PMID: 33185188 PMCID: PMC7695457 DOI: 10.7554/elife.59112] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023] Open
Abstract
Displacement loops (D-loops) are critical intermediates formed during homologous recombination. Rdh54 (a.k.a. Tid1), a Rad54 paralog in Saccharomyces cerevisiae, is well-known for its role with Dmc1 recombinase during meiotic recombination. Yet contrary to Dmc1, Rdh54/Tid1 is also present in somatic cells where its function is less understood. While Rdh54/Tid1 enhances the Rad51 DNA strand invasion activity in vitro, it is unclear how it interplays with Rad54. Here, we show that Rdh54/Tid1 inhibits D-loop formation by Rad51 and Rad54 in an ATPase-independent manner. Using a novel D-loop Mapping Assay, we further demonstrate that Rdh54/Tid1 uniquely restricts the length of Rad51-Rad54-mediated D-loops. The alterations in D-loop properties appear to be important for cell survival and mating-type switch in haploid yeast. We propose that Rdh54/Tid1 and Rad54 compete for potential binding sites within the Rad51 filament, where Rdh54/Tid1 acts as a physical roadblock to Rad54 translocation, limiting D-loop formation and D-loop length.
Collapse
Affiliation(s)
- Shanaya Shital Shah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - Stella Hartono
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Aurèle Piazza
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,CR CNRS UMR5239, Team Genome Mechanics, Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon 46, Lyon, France
| | - Vanessa Som
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States
| | - William Wright
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Mammoth Biosciences, South San Francisco, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.,Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| |
Collapse
|
10
|
Woo TT, Chuang CN, Higashide M, Shinohara A, Wang TF. Dual roles of yeast Rad51 N-terminal domain in repairing DNA double-strand breaks. Nucleic Acids Res 2020; 48:8474-8489. [PMID: 32652040 PMCID: PMC7470947 DOI: 10.1093/nar/gkaa587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 01/17/2023] Open
Abstract
Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20–30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 h. We report that the NH2-terminal domain (NTD; residues 1–66) of Rad51 has dual functions for repairing DSBs during vegetative growth and meiosis. Firstly, Rad51-NTD exhibits autonomous expression-enhancing activity for high-level production of native Rad51 and when fused to exogenous β-galactosidase in vivo. Secondly, Rad51-NTD is an S/T-Q cluster domain (SCD) harboring three putative Mec1/Tel1 target sites. Mec1/Tel1-dependent phosphorylation antagonizes the proteasomal degradation pathway, increasing the half-life of Rad51 from ∼30 min to ≥180 min. Our results evidence a direct link between homologous recombination and DDR modulated by Rad51 homeostasis.
Collapse
Affiliation(s)
- Tai-Ting Woo
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Ning Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Mika Higashide
- Laboratory of Genome-Chromosome Functions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Japan
| | - Akira Shinohara
- Laboratory of Genome-Chromosome Functions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Japan
| | - Ting-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
11
|
Reitz D, Grubb J, Bishop DK. A mutant form of Dmc1 that bypasses the requirement for accessory protein Mei5-Sae3 reveals independent activities of Mei5-Sae3 and Rad51 in Dmc1 filament stability. PLoS Genet 2019; 15:e1008217. [PMID: 31790385 PMCID: PMC6907854 DOI: 10.1371/journal.pgen.1008217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 12/12/2019] [Accepted: 11/15/2019] [Indexed: 12/16/2022] Open
Abstract
During meiosis, homologous recombination repairs programmed DNA double-stranded breaks. Meiotic recombination physically links the homologous chromosomes (“homologs”), creating the tension between them that is required for their segregation. The central recombinase in this process is Dmc1. Dmc1’s activity is regulated by its accessory factors including the heterodimeric protein Mei5-Sae3 and Rad51. We use a gain-of-function dmc1 mutant, dmc1-E157D, that bypasses Mei5-Sae3 to gain insight into the role of this accessory factor and its relationship to mitotic recombinase Rad51, which also functions as a Dmc1 accessory protein during meiosis. We find that Mei5-Sae3 has a role in filament formation and stability, but not in the bias of recombination partner choice that favors homolog over sister chromatids. Analysis of meiotic recombination intermediates suggests that Mei5-Sae3 and Rad51 function independently in promoting filament stability. In spite of its ability to load onto single-stranded DNA and carry out recombination in the absence of Mei5-Sae3, recombination promoted by the Dmc1 mutant is abnormal in that it forms foci in the absence of DNA breaks, displays unusually high levels of multi-chromatid and intersister joint molecule intermediates, as well as high levels of ectopic recombination products. We use super-resolution microscopy to show that the mutant protein forms longer foci than those formed by wild-type Dmc1. Our data support a model in which longer filaments are more prone to engage in aberrant recombination events, suggesting that filament lengths are normally limited by a regulatory mechanism that functions to prevent recombination-mediated genome rearrangements. During meiosis, two rounds of division follow a single round of DNA replication to create the gametes for biparental reproduction. The first round of division requires that the homologous chromosomes become physically linked to one another to create the tension that is necessary for their segregation. This linkage is achieved through DNA recombination between the two homologous chromosomes, followed by resolution of the recombination intermediate into a crossover. Central to this process is the meiosis-specific recombinase Dmc1, and its accessory factors, which provide important regulatory functions to ensure that recombination is accurate, efficient, and occurs predominantly between homologous chromosomes, and not sister chromatids. To gain insight into the regulation of Dmc1 by its accessory factors, we mutated Dmc1 such that it was no longer dependent on its accessory factor Mei5-Sae3. Our analysis reveals that Dmc1 accessory factors Mei5-Sae3 and Rad51 have independent roles in stabilizing Dmc1 filaments. Furthermore, we find that although Rad51 is required for promoting recombination between homologous chromosomes, Mei5-Sae3 is not. Lastly, we show that our Dmc1 mutant forms abnormally long filaments, and high levels of aberrant recombination intermediates and products. These findings suggest that filaments are actively maintained at short lengths to prevent deleterious genome rearrangements.
Collapse
Affiliation(s)
- Diedre Reitz
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Jennifer Grubb
- Department of Radiation and Cellular Oncology, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Douglas K. Bishop
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Radiation and Cellular Oncology, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| |
Collapse
|
12
|
Kaur H, Gn K, Lichten M. Unresolved Recombination Intermediates Cause a RAD9-Dependent Cell Cycle Arrest in Saccharomyces cerevisiae. Genetics 2019; 213:805-818. [PMID: 31562181 PMCID: PMC6827386 DOI: 10.1534/genetics.119.302632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023] Open
Abstract
In Saccharomyces cerevisiae, the conserved Sgs1-Top3-Rmi1 helicase-decatenase regulates homologous recombination by limiting accumulation of recombination intermediates that are crossover precursors. In vitro studies have suggested that this may be due to dissolution of double-Holliday junction joint molecules by Sgs1-driven convergent junction migration and Top3-Rmi1 mediated strand decatenation. To ask whether dissolution occurs in vivo, we conditionally depleted Sgs1 and/or Rmi1 during return to growth (RTG), a procedure where recombination intermediates formed during meiosis are resolved when cells resume the mitotic cell cycle. Sgs1 depletion during RTG delayed joint molecule resolution, but, ultimately, most were resolved and cells divided normally. In contrast, Rmi1 depletion resulted in delayed and incomplete joint molecule resolution, and most cells did not divide. rad9 ∆ mutation restored cell division in Rmi1-depleted cells, indicating that the DNA damage checkpoint caused this cell cycle arrest. Restored cell division in Rmi1-depleted rad9 ∆ cells frequently produced anucleate cells, consistent with the suggestion that persistent recombination intermediates prevented chromosome segregation. Our findings indicate that Sgs1-Top3-Rmi1 acts in vivo, as it does in vitro, to promote recombination intermediate resolution by dissolution. They also indicate that, in the absence of Top3-Rmi1 activity, unresolved recombination intermediates persist and activate the DNA damage response, which is usually thought to be activated by much earlier DNA damage-associated lesions.
Collapse
Affiliation(s)
- Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Krishnaprasad Gn
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892
| |
Collapse
|
13
|
Hunt LJ, Ahmed EA, Kaur H, Ahuja JS, Hulme L, Chou TC, Lichten M, Goldman ASH. S. cerevisiae Srs2 helicase ensures normal recombination intermediate metabolism during meiosis and prevents accumulation of Rad51 aggregates. Chromosoma 2019; 128:249-265. [PMID: 31069484 PMCID: PMC6823294 DOI: 10.1007/s00412-019-00705-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/04/2019] [Accepted: 04/24/2019] [Indexed: 01/06/2023]
Abstract
We investigated the meiotic role of Srs2, a multi-functional DNA helicase/translocase that destabilises Rad51-DNA filaments and is thought to regulate strand invasion and prevent hyper-recombination during the mitotic cell cycle. We find that Srs2 activity is required for normal meiotic progression and spore viability. A significant fraction of srs2 mutant cells progress through both meiotic divisions without separating the bulk of their chromatin, although in such cells sister centromeres often separate. Undivided nuclei contain aggregates of Rad51 colocalised with the ssDNA-binding protein RPA, suggesting the presence of persistent single-strand DNA. Rad51 aggregate formation requires Spo11-induced DSBs, Rad51 strand-invasion activity and progression past the pachytene stage of meiosis, but not the DSB end-resection or the bias towards interhomologue strand invasion characteristic of normal meiosis. srs2 mutants also display altered meiotic recombination intermediate metabolism, revealed by defects in the formation of stable joint molecules. We suggest that Srs2, by limiting Rad51 accumulation on DNA, prevents the formation of aberrant recombination intermediates that otherwise would persist and interfere with normal chromosome segregation and nuclear division.
Collapse
Affiliation(s)
- Laura J Hunt
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Emad A Ahmed
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK.,Immunology and Molecular Physiology Lab., Zoology Department, Faculty of Science, Assiut University, Markaz El-Fath, 71515, Egypt
| | - Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA.,Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, 78229, USA
| | - Jasvinder S Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Lydia Hulme
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Ta-Chung Chou
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK.,All First Tech Co., Ltd, 32467, No 146-2. Hung Chun Road, Ping Zhen Dist, Taoyuan City, Taiwan
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Alastair S H Goldman
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, S10 2TN, UK. .,Faculty of Life Sciences, The University of Bradford, Bradford, BD7 1AZ, UK.
| |
Collapse
|
14
|
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.
Collapse
|
15
|
Li D, Roca M, Yuecel R, Lorenz A. Immediate visualization of recombination events and chromosome segregation defects in fission yeast meiosis. Chromosoma 2019; 128:385-396. [PMID: 30739171 PMCID: PMC6823302 DOI: 10.1007/s00412-019-00691-y] [Citation(s) in RCA: 5] [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: 11/01/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 02/07/2023]
Abstract
Schizosaccharomyces pombe, also known as fission yeast, is an established model for studying chromosome biological processes. Over the years, research employing fission yeast has made important contributions to our knowledge about chromosome segregation during meiosis, as well as meiotic recombination and its regulation. Quantification of meiotic recombination frequency is not a straightforward undertaking, either requiring viable progeny for a genetic plating assay, or relying on laborious Southern blot analysis of recombination intermediates. Neither of these methods lends itself to high-throughput screens to identify novel meiotic factors. Here, we establish visual assays novel to Sz. pombe for characterizing chromosome segregation and meiotic recombination phenotypes. Genes expressing red, yellow, and/or cyan fluorophores from spore-autonomous promoters have been integrated into the fission yeast genomes, either close to the centromere of chromosome 1 to monitor chromosome segregation, or on the arm of chromosome 3 to form a genetic interval at which recombination frequency can be determined. The visual recombination assay allows straightforward and immediate assessment of the genetic outcome of a single meiosis by epi-fluorescence microscopy without requiring tetrad dissection. We also demonstrate that the recombination frequency analysis can be automatized by utilizing imaging flow cytometry to enable high-throughput screens. These assays have several advantages over traditional methods for analyzing meiotic phenotypes.
Collapse
Affiliation(s)
- Dmitriy Li
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Iain Fraser Cytometry Centre (IFCC), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Marianne Roca
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, 06230, Villefranche-sur-Mer, France
| | - Raif Yuecel
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
- Iain Fraser Cytometry Centre (IFCC), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK.
| |
Collapse
|
16
|
Dynamic Processing of Displacement Loops during Recombinational DNA Repair. Mol Cell 2019; 73:1255-1266.e4. [PMID: 30737186 DOI: 10.1016/j.molcel.2019.01.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/08/2018] [Accepted: 01/03/2019] [Indexed: 12/22/2022]
Abstract
Displacement loops (D-loops) are pivotal intermediates of homologous recombination (HR), a universal DNA double strand break (DSB) repair pathway. We developed a versatile assay for the physical detection of D-loops in vivo, which enabled studying the kinetics of their formation and defining the activities controlling their metabolism. Nascent D-loops are detected within 2 h of DSB formation and extended in a delayed fashion in a genetic system designed to preclude downstream repair steps. The majority of nascent D-loops are disrupted by two pathways: one supported by the Srs2 helicase and the other by the Mph1 helicase and the Sgs1-Top3-Rmi1 helicase-topoisomerase complex. Both pathways operate without significant overlap and are delineated by the Rad54 paralog Rdh54 in an ATPase-independent fashion. This study uncovers a layer of quality control of HR relying on nascent D-loop dynamics.
Collapse
|
17
|
Muller H, Scolari VF, Agier N, Piazza A, Thierry A, Mercy G, Descorps-Declere S, Lazar-Stefanita L, Espeli O, Llorente B, Fischer G, Mozziconacci J, Koszul R. Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi-C. Mol Syst Biol 2018; 14:e8293. [PMID: 30012718 PMCID: PMC6047084 DOI: 10.15252/msb.20188293] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/29/2022] Open
Abstract
In chromosome conformation capture experiments (Hi-C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn-HiC design). In the Syn-HiC region, Hi-C signal-to-noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact frequencies, allowing to propose a robust definition of a Hi-C experiment resolution. The redesigned region is also distinguishable from its native homologous counterpart in an otherwise isogenic diploid strain. As a proof of principle, we tracked homologous chromosomes during meiotic prophase in synchronized and pachytene-arrested cells and captured important features of their spatial reorganization, such as chromatin restructuration into arrays of Rec8-delimited loops, centromere declustering, individualization, and pairing. Overall, we illustrate the promises held by redesigning genomic regions to explore complex biological questions.
Collapse
Affiliation(s)
- Héloïse Muller
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Vittore F Scolari
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Nicolas Agier
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Aurèle Piazza
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Agnès Thierry
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Guillaume Mercy
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Stéphane Descorps-Declere
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Luciana Lazar-Stefanita
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| | - Olivier Espeli
- Centre Interdisciplinaire de Recherche en Biologie, Collège de France, UMR-CNRS 7241, INSERM U1050, Paris, France
| | - Bertrand Llorente
- Cancer Research Center of Marseille, CNRS UMR7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Gilles Fischer
- Laboratory of Computational and Quantitative Biology, CNRS, Institut de Biologie Paris-Seine, Sorbonne Université, Paris, France
| | - Julien Mozziconacci
- Theoretical Physics for Condensed Matter Lab, CNRS UMR 7600, Sorbonne Universités, UPMC University Paris 06, Paris, France
| | - Romain Koszul
- Department Genomes and Genetics, Groupe Régulation Spatiale des Génomes, Institut Pasteur, Paris, France
- CNRS, UMR 3525, Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, Paris, France
| |
Collapse
|
18
|
Kaur H, Ahuja JS, Lichten M. Methods for Controlled Protein Depletion to Study Protein Function during Meiosis. Methods Enzymol 2018; 601:331-357. [PMID: 29523238 PMCID: PMC10798147 DOI: 10.1016/bs.mie.2017.11.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins with potential roles in meiotic recombination often have essential or important functions during the mitotic cell cycle. In addition, proteins may have different functions at different times during meiosis. In such cases, it can be challenging to precisely determine protein function during meiosis using null or hypomorphic mutants. One example is the Sgs1-Top3-Rmi1 helicase-decatenase complex, which is required for normal vegetative growth and genome stability. In such cases, conditional loss-of-function mutants can be useful. In this chapter, we describe the construction of two types of conditional mutants, meiotic depletion alleles and auxin-induced degradation alleles, that allow protein depletion specifically during budding yeast meiosis, and illustrate their use with Sgs1. We also describe a modified method for the isolation of meiotic recombination intermediates that combines previous psoralen cross-linking and cetyltrimethylammonium bromide isolation methods.
Collapse
Affiliation(s)
- Hardeep Kaur
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Jasvinder S Ahuja
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.
| |
Collapse
|
19
|
Abstract
Homologous recombination is fundamental to sexual reproduction, facilitating accurate segregation of homologous chromosomes at the first division of meiosis, and creating novel allele combinations that fuel evolution. Following initiation of meiotic recombination by programmed DNA double-strand breaks (DSBs), homologous pairing and DNA strand exchange form joint molecule (JM) intermediates that are ultimately resolved into crossover and noncrossover repair products. Physical monitoring of the DNA steps of meiotic recombination in Saccharomyces cerevisiae (budding yeast) cultures undergoing synchronous meiosis has provided seminal insights into the molecular basis of meiotic recombination and affords a powerful tool for dissecting the molecular roles of recombination factors. This chapter describes a suit of electrophoretic and Southern hybridization techniques used to detect and quantify the DNA intermediates of meiotic recombination at recombination hotspots in budding yeast. DSBs and recombination products (crossovers and noncrossovers) are resolved using one-dimensional electrophoresis and distinguished by restriction site polymorphisms between the parental chromosomes. Psoralen cross-linking is used to stabilize branched JMs, which are resolved from linear species by native/native two-dimensional electrophoresis. Native/denaturing two-dimensional electrophoresis is employed to determine the component DNA strands of JMs and to measure the processing of DSBs. These techniques are generally applicable to any locus where the frequency of recombination is high enough to detect intermediates by Southern hybridization.
Collapse
Affiliation(s)
- Shannon Owens
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, United States; University of California, Davis, Davis, CA, United States; Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Shangming Tang
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, United States; University of California, Davis, Davis, CA, United States; Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Neil Hunter
- Howard Hughes Medical Institute, University of California, Davis, Davis, CA, United States; University of California, Davis, Davis, CA, United States.
| |
Collapse
|
20
|
Sasaki M, Kobayashi T. Ctf4 Prevents Genome Rearrangements by Suppressing DNA Double-Strand Break Formation and Its End Resection at Arrested Replication Forks. Mol Cell 2017; 66:533-545.e5. [PMID: 28525744 DOI: 10.1016/j.molcel.2017.04.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/20/2017] [Accepted: 04/26/2017] [Indexed: 12/19/2022]
Abstract
Arrested replication forks lead to DNA double-strand breaks (DSBs), which are a major source of genome rearrangements. Yet DSB repair in the context of broken forks remains poorly understood. Here we demonstrate that DSBs that are formed at arrested forks in the budding yeast ribosomal RNA gene (rDNA) locus are normally repaired by pathways dependent on the Mre11-Rad50-Xrs2 complex but independent of HR. HR is also dispensable for DSB repair at stalled forks at tRNA genes. In contrast, in cells lacking the core replisome component Ctf4, DSBs are formed more frequently, and these DSBs undergo end resection and HR-mediated repair that is prone to rDNA hyper-amplification; this highlights Ctf4 as a key regulator of DSB end resection at arrested forks. End resection also occurs during physiological rDNA amplification even in the presence of Ctf4. Suppression of end resection is thus important for protecting DSBs at arrested forks from chromosome rearrangements.
Collapse
MESH Headings
- DNA Breaks, Double-Stranded
- DNA Repair
- DNA Replication
- DNA, Fungal/biosynthesis
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Endodeoxyribonucleases/genetics
- Endodeoxyribonucleases/metabolism
- Exodeoxyribonucleases/genetics
- Exodeoxyribonucleases/metabolism
- Gene Rearrangement
- Microbial Viability
- Mutation
- Nucleic Acid Conformation
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Replication Origin
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Time Factors
Collapse
Affiliation(s)
- Mariko Sasaki
- Laboratory of Genome Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
21
|
The Nucleoporin Nup2 Contains a Meiotic-Autonomous Region that Promotes the Dynamic Chromosome Events of Meiosis. Genetics 2017; 206:1319-1337. [PMID: 28455351 DOI: 10.1534/genetics.116.194555] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
Meiosis is a specialized cellular program required to create haploid gametes from diploid parent cells. Homologous chromosomes pair, synapse, and recombine in a dynamic environment that accommodates gross chromosome reorganization and significant chromosome motion, which are critical for normal chromosome segregation. In Saccharomyces cerevisiae, Ndj1 is a meiotic telomere-associated protein required for physically attaching telomeres to proteins embedded in the nuclear envelope. In this study, we identified additional proteins that act at the nuclear periphery from meiotic cell extracts, including Nup2, a nonessential nucleoporin with a known role in tethering interstitial chromosomal loci to the nuclear pore complex. We found that deleting NUP2 affects meiotic progression and spore viability, and gives increased levels of recombination intermediates and products. We identified a previously uncharacterized 125 aa region of Nup2 that is necessary and sufficient for its meiotic function, thus behaving as a meiotic autonomous region (MAR). Nup2-MAR forms distinct foci on spread meiotic chromosomes, with a subset overlapping with Ndj1 foci. Localization of Nup2-MAR to meiotic chromosomes does not require Ndj1, nor does Ndj1 localization require Nup2, suggesting these proteins function in different pathways, and their interaction is weak or indirect. Instead, several severe synthetic phenotypes are associated with the nup2Δ ndj1Δ double mutant, including delayed turnover of recombination joint molecules, and a failure to undergo nuclear divisions without also arresting the meiotic program. These data suggest Nup2 and Ndj1 support partially overlapping functions that promote two different levels of meiotic chromosome organization necessary to withstand a dynamic stage of the eukaryotic life cycle.
Collapse
|
22
|
Coordination of Double Strand Break Repair and Meiotic Progression in Yeast by a Mek1-Ndt80 Negative Feedback Loop. Genetics 2017; 206:497-512. [PMID: 28249986 DOI: 10.1534/genetics.117.199703] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 02/25/2017] [Indexed: 11/18/2022] Open
Abstract
During meiosis, homologous chromosomes are physically connected by crossovers and sister chromatid cohesion. Interhomolog crossovers are generated by the highly regulated repair of programmed double strand breaks (DSBs). The meiosis-specific kinase Mek1 is critical for this regulation. Mek1 downregulates the mitotic recombinase Rad51, indirectly promoting interhomolog strand invasion by the meiosis-specific recombinase Dmc1. Mek1 also promotes the formation of crossovers that are distributed throughout the genome by interference and is the effector kinase for a meiosis-specific checkpoint that delays entry into Meiosis I until DSBs have been repaired. The target of this checkpoint is a meiosis-specific transcription factor, Ndt80, which is necessary to express the polo-like kinase CDC5 and the cyclin CLB1 thereby allowing completion of recombination and meiotic progression. This work shows that Mek1 and Ndt80 negatively feedback on each other such that when DSB levels are high, Ndt80 is inactive due to high levels of Mek1 activity. As DSBs are repaired, chromosomes synapse and Mek1 activity is reduced below a threshold that allows activation of Ndt80. Ndt80 transcription of CDC5 results in degradation of Red1, a meiosis-specific protein required for Mek1 activation, thereby abolishing Mek1 activity completely. Elimination of Mek1 kinase activity allows Rad51-mediated repair of any remaining DSBs. In this way, cells do not enter Meiosis I until recombination is complete and all DSBs are repaired.
Collapse
|
23
|
Mek1 Down Regulates Rad51 Activity during Yeast Meiosis by Phosphorylation of Hed1. PLoS Genet 2016; 12:e1006226. [PMID: 27483004 PMCID: PMC4970670 DOI: 10.1371/journal.pgen.1006226] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/08/2016] [Indexed: 11/24/2022] Open
Abstract
During meiosis, programmed double strand breaks (DSBs) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I. In many organisms, there are two strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required for interhomolog (IH) bias. This bias requires the presence, but not the strand exchange activity of Rad51, while Dmc1 is responsible for the bulk of meiotic recombination. How these activities are regulated is less well established. In dmc1Δ mutants, Rad51 is actively inhibited, thereby resulting in prophase arrest due to unrepaired DSBs triggering the meiotic recombination checkpoint. This inhibition is dependent upon the meiosis-specific kinase Mek1 and occurs through two different mechanisms that prevent complex formation with the Rad51 accessory factor Rad54: (i) phosphorylation of Rad54 by Mek1 and (ii) binding of Rad51 by the meiosis-specific protein Hed1. An open question has been why inhibition of Mek1 affects Hed1 repression of Rad51. This work shows that Hed1 is a direct substrate of Mek1. Phosphorylation of Hed1 at threonine 40 helps suppress Rad51 activity in dmc1Δ mutants by promoting Hed1 protein stability. Rad51-mediated recombination occurring in the absence of Hed1 phosphorylation results in a significant increase in non-exchange chromosomes despite wild-type levels of crossovers, confirming previous results indicating a defect in crossover assurance. We propose that Rad51 function in meiosis is regulated in part by the coordinated phosphorylation of Rad54 and Hed1 by Mek1. Sexual reproduction requires the formation of haploid gametes by a highly conserved, specialized cell division called meiosis. Failures in meiotic chromosome segregation lead to chromosomally imbalanced gametes that cause infertility and birth defects such as Trisomy 21 in humans. Meiotic crossovers, initiated by programmed double strand breaks (DSBs), are critical for proper chromosome segregation. Interhomolog strand invasion requires the presence of Rad51, and the strand invasion activity of the meiosis-specific recombinase Dmc1. The meiosis-specific kinase, Mek1, is a key regulator of meiotic recombination, promoting interhomolog strand invasion and recombination pathway choice. Rad51 activity during meiosis is inhibited by preventing the Rad51 protein from forming complexes with an accessory factor, Rad54, in two ways: (1) Mek1 phosphorylation of Rad54 and (2) binding of Rad51 by a meiosis-specific protein, Hed1. Why inactivation of Mek1 affects Hed1-mediated repression of Rad51 was previously unknown. This work demonstrates that Mek1 regulates the ability of Hed1 to inhibit Rad51 by direct phosphorylation of Hed1. Therefore in meiosis, Rad51 activity is regulated in part by the coordinated phosphorylation of both Rad54 and Hed1 by Mek1.
Collapse
|
24
|
Chen X, Suhandynata RT, Sandhu R, Rockmill B, Mohibullah N, Niu H, Liang J, Lo HC, Miller DE, Zhou H, Börner GV, Hollingsworth NM. Phosphorylation of the Synaptonemal Complex Protein Zip1 Regulates the Crossover/Noncrossover Decision during Yeast Meiosis. PLoS Biol 2015; 13:e1002329. [PMID: 26682552 PMCID: PMC4684282 DOI: 10.1371/journal.pbio.1002329] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/16/2015] [Indexed: 12/02/2022] Open
Abstract
Interhomolog crossovers promote proper chromosome segregation during meiosis and are formed by the regulated repair of programmed double-strand breaks. This regulation requires components of the synaptonemal complex (SC), a proteinaceous structure formed between homologous chromosomes. In yeast, SC formation requires the "ZMM" genes, which encode a functionally diverse set of proteins, including the transverse filament protein, Zip1. In wild-type meiosis, Zmm proteins promote the biased resolution of recombination intermediates into crossovers that are distributed throughout the genome by interference. In contrast, noncrossovers are formed primarily through synthesis-dependent strand annealing mediated by the Sgs1 helicase. This work identifies a conserved region on the C terminus of Zip1 (called Zip1 4S), whose phosphorylation is required for the ZMM pathway of crossover formation. Zip1 4S phosphorylation is promoted both by double-strand breaks (DSBs) and the meiosis-specific kinase, MEK1/MRE4, demonstrating a role for MEK1 in the regulation of interhomolog crossover formation, as well as interhomolog bias. Failure to phosphorylate Zip1 4S results in meiotic prophase arrest, specifically in the absence of SGS1. This gain of function meiotic arrest phenotype is suppressed by spo11Δ, suggesting that it is due to unrepaired breaks triggering the meiotic recombination checkpoint. Epistasis experiments combining deletions of individual ZMM genes with sgs1-md zip1-4A indicate that Zip1 4S phosphorylation functions prior to the other ZMMs. These results suggest that phosphorylation of Zip1 at DSBs commits those breaks to repair via the ZMM pathway and provides a mechanism by which the crossover/noncrossover decision can be dynamically regulated during yeast meiosis.
Collapse
Affiliation(s)
- Xiangyu Chen
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Ray T. Suhandynata
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Rima Sandhu
- Center for Gene Regulation in Health and Disease and Department of Biological Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Beth Rockmill
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Neeman Mohibullah
- Molecular Biology Program, Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York City, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York City, New York, United States of America
| | - Hengyao Niu
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana, United States of America
| | - Jason Liang
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California, United States of America
- Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Hsiao-Chi Lo
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Danny E. Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Huilin Zhou
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California, United States of America
- Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - G. Valentin Börner
- Center for Gene Regulation in Health and Disease and Department of Biological Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Nancy M. Hollingsworth
- Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| |
Collapse
|
25
|
Tang S, Wu MKY, Zhang R, Hunter N. Pervasive and essential roles of the Top3-Rmi1 decatenase orchestrate recombination and facilitate chromosome segregation in meiosis. Mol Cell 2015; 57:607-621. [PMID: 25699709 DOI: 10.1016/j.molcel.2015.01.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/03/2014] [Accepted: 01/12/2015] [Indexed: 11/30/2022]
Abstract
The Bloom's helicase ortholog, Sgs1, plays central roles to coordinate the formation and resolution of joint molecule intermediates (JMs) during meiotic recombination in budding yeast. Sgs1 can associate with type-I topoisomerase Top3 and its accessory factor Rmi1 to form a conserved complex best known for its unique ability to decatenate double-Holliday junctions. Contrary to expectations, we show that the strand-passage activity of Top3-Rmi1 is required for all known functions of Sgs1 in meiotic recombination, including channeling JMs into physiological crossover and noncrossover pathways, and suppression of non-allelic recombination. We infer that Sgs1 always functions in the context of the Sgs1-Top3-Rmi1 complex to regulate meiotic recombination. In addition, we reveal a distinct late role for Top3-Rmi1 in resolving recombination-dependent chromosome entanglements to allow segregation at anaphase. Surprisingly, Sgs1 does not share this essential role of Top3-Rmi1. These data reveal an essential and pervasive role for the Top3-Rmi1 decatenase during meiosis.
Collapse
Affiliation(s)
- Shangming Tang
- Howard Hughes Medical Institute and the Departments of Microbiology & Molecular Genetics, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Michelle Ka Yan Wu
- Howard Hughes Medical Institute and the Departments of Microbiology & Molecular Genetics, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Ruoxi Zhang
- Howard Hughes Medical Institute and the Departments of Microbiology & Molecular Genetics, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Neil Hunter
- Howard Hughes Medical Institute and the Departments of Microbiology & Molecular Genetics, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA.
| |
Collapse
|
26
|
Abstract
Double-strand breaks (DSBs) threaten chromosome integrity. The most accurate repair of DSBs is by homologous recombination (HR), catalyzed by recombination proteins such as Rad51. Three papers in this issue of Molecular Cell (Fasching et al., 2015; Kaur et al., 2015; Tang et al., 2015) now reveal the role of three of these proteins in budding yeast: Sgs1 (BLM homolog), Top3 (TOPIIIα homolog), and Rmi1. They demonstrate several steps where all three proteins act together, and find additional functions of the Top3-Rmi1 subcomplex that are critical for the completion of meiosis.
Collapse
Affiliation(s)
- James E Haber
- Rosenstiel Basic Medical Sciences Research Center and Department of Biology, Brandeis University, Waltham, MA 02454, USA.
| |
Collapse
|
27
|
Robinson NP. Analysis of branched DNA replication and recombination intermediates from prokaryotic cells by two-dimensional (2D) native-native agarose gel electrophoresis. Methods Mol Biol 2014; 1054:45-61. [PMID: 23913284 DOI: 10.1007/978-1-62703-565-1_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Branched DNA molecules are generated by the essential processes of replication and recombination. Owing to their distinctive extended shapes, these intermediates migrate differently from linear double-stranded DNA under certain electrophoretic conditions. However, these branched species exist in the cell at much low abundance than the bulk linear DNA. Consequently, branched molecules cannot be visualized by conventional electrophoresis and ethidium bromide staining. Two-dimensional native-native agarose electrophoresis has therefore been developed as a method to facilitate the separation and visualization of branched replication and recombination intermediates. A wide variety of studies have employed this technique to examine branched molecules in eukaryotic, archaeal, and bacterial cells, providing valuable insights into how DNA is duplicated and repaired in all three domains of life.
Collapse
|
28
|
Lao JP, Tang S, Hunter N. Native/Denaturing two-dimensional DNA electrophoresis and its application to the analysis of recombination intermediates. Methods Mol Biol 2014; 1054:105-20. [PMID: 23913287 DOI: 10.1007/978-1-62703-565-1_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Two-dimensional (2D) gel electrophoresis employs distinct electrophoretic conditions to better resolve complex mixtures of molecules. In combination with Southern analysis, 2D agarose gel electrophoresis is routinely employed to detect and analyze DNA intermediates that arise during the replication and repair of chromosomes. By separating intermediates into their component single-strands, native/denaturing 2D gels can reveal structure that is not apparent under native conditions alone. Here, we describe a general method for native/denaturing two-dimensional gel electrophoresis and its application to understanding the DNA strand-composition of recombination intermediates formed during meiosis.
Collapse
Affiliation(s)
- Jessica P Lao
- Howard Hughes Medical Institute and the Departments of Microbiology & Molecular Genetics, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, Davis, CA, USA
| | | | | |
Collapse
|
29
|
Liu Y, Gaines WA, Callender T, Busygina V, Oke A, Sung P, Fung JC, Hollingsworth NM. Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks. PLoS Genet 2014; 10:e1004005. [PMID: 24465215 PMCID: PMC3900393 DOI: 10.1371/journal.pgen.1004005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022] Open
Abstract
Interhomolog recombination plays a critical role in promoting proper meiotic chromosome segregation but a mechanistic understanding of this process is far from complete. In vegetative cells, Rad51 is a highly conserved recombinase that exhibits a preference for repairing double strand breaks (DSBs) using sister chromatids, in contrast to the conserved, meiosis-specific recombinase, Dmc1, which preferentially repairs programmed DSBs using homologs. Despite the different preferences for repair templates, both Rad51 and Dmc1 are required for interhomolog recombination during meiosis. This paradox has recently been explained by the finding that Rad51 protein, but not its strand exchange activity, promotes Dmc1 function in budding yeast. Rad51 activity is inhibited in dmc1Δ mutants, where the failure to repair meiotic DSBs triggers the meiotic recombination checkpoint, resulting in prophase arrest. The question remains whether inhibition of Rad51 activity is important during wild-type meiosis, or whether inactivation of Rad51 occurs only as a result of the absence of DMC1 or checkpoint activation. This work shows that strains in which mechanisms that down-regulate Rad51 activity are removed exhibit reduced numbers of interhomolog crossovers and noncrossovers. A hypomorphic mutant, dmc1-T159A, makes less stable presynaptic filaments but is still able to mediate strand exchange and interact with accessory factors. Combining dmc1-T159A with up-regulated Rad51 activity reduces interhomolog recombination and spore viability, while increasing intersister joint molecule formation. These results support the idea that down-regulation of Rad51 activity is important during meiosis to prevent Rad51 from competing with Dmc1 for repair of meiotic DSBs.
Collapse
Affiliation(s)
- Yan Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - William A. Gaines
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Tracy Callender
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Valeria Busygina
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ashwini Oke
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Jennifer C. Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| |
Collapse
|
30
|
Lichten M. Tetrad, random spore, and molecular analysis of meiotic segregation and recombination. Methods Mol Biol 2014; 1205:13-28. [PMID: 25213236 DOI: 10.1007/978-1-4939-1363-3_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The power of Saccharomyces cerevisiae as an experimental organism derives from its genetic tractability. Mutant variants can be isolated or constructed and phenotypically characterized with relative ease. In addition, the ability to recover and characterize all four products of meiosis, as haploid spores in a tetrad ascus, greatly facilitates determining the allelic composition of variants, measuring linkage relationships between alleles, and constructing new allele combinations for the analysis of genetic interactions. Saccharomyces cerevisiae also is a preeminent model organism for the study of meiotic recombination, by analysis of tetrads, by analysis of populations of single spores (often called random spore analysis), and by direct monitoring of recombination at the DNA level. This chapter contains methods for tetrad dissection, for random spore preparation, and for preparing DNA for molecular analysis from liquid cultures undergoing synchronous meiosis.
Collapse
Affiliation(s)
- Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, Building 37, Room 6124, 37 Convent Drive MSC4260, Bethesda, MD, 20892-4260, USA,
| |
Collapse
|
31
|
Xaver M, Huang L, Chen D, Klein F. Smc5/6-Mms21 prevents and eliminates inappropriate recombination intermediates in meiosis. PLoS Genet 2013; 9:e1004067. [PMID: 24385936 PMCID: PMC3873250 DOI: 10.1371/journal.pgen.1004067] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 11/13/2013] [Indexed: 01/05/2023] Open
Abstract
Repairing broken chromosomes via joint molecule (JM) intermediates is hazardous and therefore strictly controlled in most organisms. Also in budding yeast meiosis, where production of enough crossovers via JMs is imperative, only a subset of DNA breaks are repaired via JMs, closely regulated by the ZMM pathway. The other breaks are repaired to non-crossovers, avoiding JM formation, through pathways that require the BLM/Sgs1 helicase. “Rogue” JMs that escape the ZMM pathway and BLM/Sgs1 are eliminated before metaphase by resolvases like Mus81-Mms4 to prevent chromosome nondisjunction. Here, we report the requirement of Smc5/6-Mms21 for antagonizing rogue JMs via two mechanisms; destabilizing early intermediates and resolving JMs. Elimination of the Mms21 SUMO E3-ligase domain leads to transient JM accumulation, depending on Mus81-Mms4 for resolution. Absence of Smc6 leads to persistent rogue JMs accumulation, preventing chromatin separation. We propose that the Smc5/6-Mms21 complex antagonizes toxic JMs by coordinating helicases and resolvases at D-Loops and HJs, respectively. Homologous recombination allows repair of DNA breaks from intact templates of identical sequence by a “copy-and-paste” like mechanism. However, the double Holliday Junction (dHJ) is a hazardous intermediate that can form during homologous recombination, if single stranded DNA from both ends of a lesion pair with the template. Once the primary lesion is eliminated, the dHJ connects the chromosomes stably and if unresolved can prevent segregation during cell division. In order to prevent chromosome non-disjunction, resolvases will cut any HJ before division. However, genomes contain many multi-copy DNA sequences as transposons or repetitive elements. If dHJs form between such non-allelic loci, cleavage by resolvases can result in chromosome translocations and deletions. Therefore, stabilization of dHJs is sought to be avoided in the first instance by anti-recombinogenic helicases on early intermediates. Analysis of Smc5/6-Mms21 mutants in meiosis revealed that it antagonizes unregulated dHJs both by prevention and resolution. Elimination of the Mms21 SUMO E3-ligase domain leads to inappropriate dHJ accumulation still resolved by Mus81-Mms4. Disruption of the whole complex results in persistent dHJ accumulation and dysfunction of resolvases, preventing chromatin segregation. These results provide a first unified view on the function of Smc5/6-Mms21 as an antagonist of dangerous dHJs.
Collapse
Affiliation(s)
- Martin Xaver
- Max Perutz Laboratories, Chromosome Biology, University of Vienna, Vienna Biocenter, Vienna, Austria
- * E-mail: (MX); (FK)
| | - Lingzhi Huang
- Max Perutz Laboratories, Chromosome Biology, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Doris Chen
- Max Perutz Laboratories, Chromosome Biology, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Franz Klein
- Max Perutz Laboratories, Chromosome Biology, University of Vienna, Vienna Biocenter, Vienna, Austria
- * E-mail: (MX); (FK)
| |
Collapse
|
32
|
Mazón G, Symington LS. Mph1 and Mus81-Mms4 prevent aberrant processing of mitotic recombination intermediates. Mol Cell 2013; 52:63-74. [PMID: 24119400 DOI: 10.1016/j.molcel.2013.09.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/13/2013] [Accepted: 08/23/2013] [Indexed: 10/26/2022]
Abstract
Homology-dependent repair of double-strand breaks (DSBs) from nonsister templates has the potential to generate loss of heterozygosity or genome rearrangements. Here we show that the Saccharomyces cerevisiae Mph1 helicase prevents crossovers between ectopic sequences by removing substrates for Mus81-Mms4 or Rad1-Rad10 cleavage. A role for Yen1 is only apparent in the absence of Mus81. Cells lacking Mph1 and the three nucleases are highly defective in the repair of a single DSB, suggesting that the recombination intermediates that accumulate cannot be processed by the Sgs1-Top3-Rmi1 complex (STR). Consistent with this hypothesis, ectopic joint molecules (JMs) accumulate transiently in the mph1Δ mutant and persistently when Mus81 is eliminated. Furthermore, the ectopic JMs formed in the mus81Δ mutant contain a single Holliday junction (HJ) explaining why STR is unable to process them. We suggest that Mph1 and Mus81-Mms4 recognize an early strand exchange intermediate and direct repair to noncrossover or crossover outcomes, respectively.
Collapse
Affiliation(s)
- Gerard Mazón
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | | |
Collapse
|
33
|
Zhang Y, Saini N, Sheng Z, Lobachev KS. Genome-wide screen reveals replication pathway for quasi-palindrome fragility dependent on homologous recombination. PLoS Genet 2013; 9:e1003979. [PMID: 24339793 PMCID: PMC3855049 DOI: 10.1371/journal.pgen.1003979] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/12/2013] [Indexed: 02/07/2023] Open
Abstract
Inverted repeats capable of forming hairpin and cruciform structures present a threat to chromosomal integrity. They induce double strand breaks, which lead to gross chromosomal rearrangements, the hallmarks of cancers and hereditary diseases. Secondary structure formation at this motif has been proposed to be the driving force for the instability, albeit the mechanisms leading to the fragility are not well-understood. We carried out a genome-wide screen to uncover the genetic players that govern fragility of homologous and homeologous Alu quasi-palindromes in the yeast Saccharomyces cerevisiae. We found that depletion or lack of components of the DNA replication machinery, proteins involved in Fe-S cluster biogenesis, the replication-pausing checkpoint pathway, the telomere maintenance complex or the Sgs1-Top3-Rmi1 dissolvasome augment fragility at Alu-IRs. Rad51, a component of the homologous recombination pathway, was found to be required for replication arrest and breakage at the repeats specifically in replication-deficient strains. These data demonstrate that Rad51 is required for the formation of breakage-prone secondary structures in situations when replication is compromised while another mechanism operates in DSB formation in replication-proficient strains. Inverted repeats are found in many eukaryotic genomes including humans. They have a potential to cause chromosomal breakage and rearrangements that contribute to genome polymorphism and the development of diseases. Instability of inverted repeats is accounted for by their propensity to adopt DNA secondary structures that is negatively affected by the distance between the repeats and level of sequence divergence. However, the genetic factors that promote the abnormal structure formation or affect the ability of the repeats to break are largely unknown. Here, using a genome-wide screen we identified 38 mutants that destabilize imperfect human inverted Alu repeats and predispose them to breakage. The proteins that are required to maintain repeat stability belong to the core of the DNA replication machinery and to the accessory proteins that help replication fork to move through the difficult templates. Remarkably, when replication machinery is compromised, the proteins involved in homologous recombination promote the formation of secondary structures and replication block thereby triggering breakage at the inverted repeats. These results reveal a powerful pathway for the destabilization of chromosomes containing inverted repeats that requires the activity of homologous recombination.
Collapse
Affiliation(s)
- Yu Zhang
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Natalie Saini
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Ziwei Sheng
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
| |
Collapse
|
34
|
Lilienthal I, Kanno T, Sjögren C. Inhibition of the Smc5/6 complex during meiosis perturbs joint molecule formation and resolution without significantly changing crossover or non-crossover levels. PLoS Genet 2013; 9:e1003898. [PMID: 24244180 PMCID: PMC3820751 DOI: 10.1371/journal.pgen.1003898] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/04/2013] [Indexed: 11/19/2022] Open
Abstract
Meiosis is a specialized cell division used by diploid organisms to form haploid gametes for sexual reproduction. Central to this reductive division is repair of endogenous DNA double-strand breaks (DSBs) induced by the meiosis-specific enzyme Spo11. These DSBs are repaired in a process called homologous recombination using the sister chromatid or the homologous chromosome as a repair template, with the homolog being the preferred substrate during meiosis. Specific products of inter-homolog recombination, called crossovers, are essential for proper homolog segregation at the first meiotic nuclear division in budding yeast and mice. This study identifies an essential role for the conserved Structural Maintenance of Chromosomes (SMC) 5/6 protein complex during meiotic recombination in budding yeast. Meiosis-specific smc5/6 mutants experience a block in DNA segregation without hindering meiotic progression. Establishment and removal of meiotic sister chromatid cohesin are independent of functional Smc6 protein. smc6 mutants also have normal levels of DSB formation and repair. Eliminating DSBs rescues the segregation block in smc5/6 mutants, suggesting that the complex has a function during meiotic recombination. Accordingly, smc6 mutants accumulate high levels of recombination intermediates in the form of joint molecules. Many of these joint molecules are formed between sister chromatids, which is not normally observed in wild-type cells. The normal formation of crossovers in smc6 mutants supports the notion that mainly inter-sister joint molecule resolution is impaired. In addition, return-to-function studies indicate that the Smc5/6 complex performs its most important functions during joint molecule resolution without influencing crossover formation. These results suggest that the Smc5/6 complex aids primarily in the resolution of joint molecules formed outside of canonical inter-homolog pathways. Most eukaryotic cells are diploid, which means that they contain two copies of each chromosome – one from each parent. In order to preserve the chromosome number from generation to generation, diploid organisms employ a process called meiosis to form gametes containing only one copy of each chromosome. During sexual reproduction, two gametes (sperm and eggs in mammals) fuse to form a zygote with the same chromosome number as the parents. This zygote will develop into a new organism that has genetic characteristics unique from, but still related to, both parents. The reduction of chromosome number and the reshuffling of genetic traits during meiosis depend on the repair of naturally occurring DNA breaks. Improper break repair during meiosis may block meiosis altogether or form genetically instable gametes, leading to fertility problems or defects in the offspring. The study presented here demonstrates the importance of the evolutionarily conserved Smc5/6 protein complex in upholding the integrity of meiotic repair processes. Our results show that cells deficient in components of the Smc5/6 complex lead to inviable meiotic products. Cells lacking functional Smc5/6 complex are unable to direct DNA repair to the proper template and accumulate abnormal repair intermediates, which inhibit the reductive division.
Collapse
Affiliation(s)
- Ingrid Lilienthal
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Takaharu Kanno
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Camilla Sjögren
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
35
|
Migrating bubble during break-induced replication drives conservative DNA synthesis. Nature 2013; 502:389-92. [PMID: 24025772 PMCID: PMC3804423 DOI: 10.1038/nature12584] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 08/20/2013] [Indexed: 11/08/2022]
Abstract
The repair of chromosomal double strand breaks (DSBs) is crucial for the maintenance of genomic integrity. However, the repair of DSBs can also destabilize the genome by causing mutations and chromosomal rearrangements, the driving forces for carcinogenesis and hereditary diseases. Break-induced replication (BIR) is one of the DSB repair pathways that is highly prone to genetic instability. BIR proceeds by invasion of one broken end into a homologous DNA sequence followed by replication that can copy hundreds of kilobases of DNA from a donor molecule all the way through its telomere. The resulting repaired chromosome comes at a great cost to the cell, as BIR promotes mutagenesis, loss of heterozygosity, translocations, and copy number variations, all hallmarks of carcinogenesis. BIR uses most known replication proteins to copy large portions of DNA, similar to S-phase replication. It has therefore been suggested that BIR proceeds by semiconservative replication; however, the model of a bona fide, stable replication fork contradicts the known instabilities associated with BIR such as a 1,000-fold increase in mutation rate compared to normal replication. Here we demonstrate that in budding yeast the mechanism of replication during BIR is significantly different from S-phase replication, as it proceeds via an unusual bubble-like replication fork that results in conservative inheritance of the new genetic material. We provide evidence that this atypical mode of DNA replication, dependent on Pif1 helicase, is responsible for the marked increase in BIR-associated mutations. We propose that the BIR mode of synthesis presents a powerful mechanism that can initiate bursts of genetic instability in eukaryotes, including humans.
Collapse
|
36
|
Zakharyevich K, Tang S, Ma Y, Hunter N. Delineation of joint molecule resolution pathways in meiosis identifies a crossover-specific resolvase. Cell 2012; 149:334-47. [PMID: 22500800 DOI: 10.1016/j.cell.2012.03.023] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/31/2012] [Accepted: 03/27/2012] [Indexed: 11/18/2022]
Abstract
At the final step of homologous recombination, Holliday junction-containing joint molecules (JMs) are resolved to form crossover or noncrossover products. The enzymes responsible for JM resolution in vivo remain uncertain, but three distinct endonucleases capable of resolving JMs in vitro have been identified: Mus81-Mms4(EME1), Slx1-Slx4(BTBD12), and Yen1(GEN1). Using physical monitoring of recombination during budding yeast meiosis, we show that all three endonucleases are capable of promoting JM resolution in vivo. However, in mms4 slx4 yen1 triple mutants, JM resolution and crossing over occur efficiently. Paradoxically, crossing over in this background is strongly dependent on the Blooms helicase ortholog Sgs1, a component of a well-characterized anticrossover activity. Sgs1-dependent crossing over, but not JM resolution per se, also requires XPG family nuclease Exo1 and the MutLγ complex Mlh1-Mlh3. Thus, Sgs1, Exo1, and MutLγ together define a previously undescribed meiotic JM resolution pathway that produces the majority of crossovers in budding yeast and, by inference, in mammals.
Collapse
Affiliation(s)
- Kseniya Zakharyevich
- Department of Microbiology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | | | | | | |
Collapse
|
37
|
Steinacher R, Osman F, Dalgaard JZ, Lorenz A, Whitby MC. The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability. Genes Dev 2012; 26:594-602. [PMID: 22426535 DOI: 10.1101/gad.184663.111] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bidirectionally moving DNA replication forks merge at termination sites composed of accidental or programmed DNA-protein barriers. If merging fails, then regions of unreplicated DNA can result in the breakage of DNA during mitosis, which in turn can give rise to genome instability. Despite its importance, little is known about the mechanisms that promote the final stages of fork merging in eukaryotes. Here we show that the Pif1 family DNA helicase Pfh1 plays a dual role in promoting replication fork termination. First, it facilitates replication past DNA-protein barriers, and second, it promotes the merging of replication forks. A failure of these processes in Pfh1-deficient cells results in aberrant chromosome segregation and heightened genome instability.
Collapse
Affiliation(s)
- Roland Steinacher
- Department of Biochemistry, University of Oxford, Oxford OX13QU, United Kingdom
| | | | | | | | | |
Collapse
|
38
|
Analysis of meiotic recombination intermediates by two-dimensional gel electrophoresis. Methods Mol Biol 2011; 745:99-116. [PMID: 21660691 DOI: 10.1007/978-1-61779-129-1_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
During meiosis, programmed double strand breaks give rise to crossover and non-crossover recombination products. Meiotic recombination products are formed via several branched intermediates, including single end invasions and double Holliday junctions. Two-dimensional gel electrophoresis provides a sensitive and specific approach for detecting branched recombination intermediates, determining their genetic requirements, and enriching intermediates for further analysis. Here, we describe analysis of branched recombination intermediates in the yeast Saccharomyces cerevisiae by two-dimensional gel electrophoresis. We also provide an introduction to meiotic time-course procedures, stabilization of branched DNA molecules by interstrand crosslinking, extraction of genomic DNA from meiotic cultures, and quantitative analysis of two-dimensional gel blots.
Collapse
|
39
|
Zakharyevich K, Ma Y, Tang S, Hwang PYH, Boiteux S, Hunter N. Temporally and biochemically distinct activities of Exo1 during meiosis: double-strand break resection and resolution of double Holliday junctions. Mol Cell 2010; 40:1001-15. [PMID: 21172664 PMCID: PMC3061447 DOI: 10.1016/j.molcel.2010.11.032] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 09/21/2010] [Accepted: 10/21/2010] [Indexed: 01/09/2023]
Abstract
The Rad2/XPG family nuclease, Exo1, functions in a variety of DNA repair pathways. During meiosis, Exo1 promotes crossover recombination and thereby facilitates chromosome segregation at the first division. Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs). Nucleolytic resection of DSBs generates long 3' single-strand tails that undergo strand exchange with a homologous chromosome to form joint molecule (JM) intermediates. We show that meiotic DSB resection is dramatically reduced in exo1Δ mutants and test the idea that Exo1-catalyzed resection promotes crossing over by facilitating formation of crossover-specific JMs called double Holliday junctions (dHJs). Contrary to this idea, dHJs form at wild-type levels in exo1Δ mutants, implying that Exo1 has a second function that promotes resolution of dHJs into crossovers. Surprisingly, the dHJ resolution function of Exo1 is independent of its nuclease activities but requires interaction with the putative endonuclease complex, Mlh1-Mlh3. Thus, the DSB resection and procrossover functions of Exo1 during meiosis involve temporally and biochemically distinct activities.
Collapse
Affiliation(s)
- Kseniya Zakharyevich
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Yunmei Ma
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Shangming Tang
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Patty Yi-Hwa Hwang
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| | - Serge Boiteux
- CEA SDV/IRCM UMR217 CNRS Radiobiologie Moléculaire et Cellulaire, CEA Fontenay aux Roses, France
| | - Neil Hunter
- Howard Hughes Medical Institute and the Departments of Microbiology, Molecular & Cellular Biology and Cell Biology & Human Anatomy, University of California Davis, One Shields Ave., Davis, CA 95616, USA
| |
Collapse
|
40
|
Darmon E, Eykelenboom JK, Lincker F, Jones LH, White M, Okely E, Blackwood JK, Leach DR. E. coli SbcCD and RecA control chromosomal rearrangement induced by an interrupted palindrome. Mol Cell 2010; 39:59-70. [PMID: 20603075 PMCID: PMC3315005 DOI: 10.1016/j.molcel.2010.06.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 02/19/2010] [Accepted: 04/09/2010] [Indexed: 11/01/2022]
Abstract
Survival and genome stability are critical characteristics of healthy cells. DNA palindromes pose a threat to genome stability and have been shown to participate in a reaction leading to the formation of inverted chromosome duplications centered around themselves. There is considerable interest in the mechanism of this rearrangement given its likely contribution to genome instability in cancer cells. This study shows that formation of large inverted chromosome duplications can be observed in the chromosome of Escherichia coli. They are formed at the site of a 246 bp interrupted DNA palindrome in the absence of the hairpin nuclease SbcCD and the recombination protein RecA. The genetic requirements for this spontaneous rearrangement are consistent with a pathway involving DNA degradation and hairpin formation, as opposed to a cruciform cleavage pathway. Accordingly, the formation of palindrome-dependent hairpin intermediates can be induced by an adjacent DNA double-stand break.
Collapse
Affiliation(s)
- Elise Darmon
- Institute of Cell Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, UK
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Callender TL, Hollingsworth NM. Mek1 suppression of meiotic double-strand break repair is specific to sister chromatids, chromosome autonomous and independent of Rec8 cohesin complexes. Genetics 2010; 185:771-82. [PMID: 20421598 PMCID: PMC2900162 DOI: 10.1534/genetics.110.117523] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/21/2010] [Indexed: 11/18/2022] Open
Abstract
During meiosis, recombination is directed to occur between homologous chromosomes to create connections necessary for proper segregation at meiosis I. Partner choice is determined at the time of strand invasion and is mediated by two recombinases: Rad51 and the meiosis-specific Dmc1. In budding yeast, interhomolog bias is created in part by the activity of a meiosis-specific kinase, Mek1, which is localized to the protein cores of condensed sister chromatids. Analysis of meiotic double-strand break (DSB) repair in haploid and disomic haploid strains reveals that Mek1 suppresses meiotic intersister DSB repair by working directly on sister chromatids. Rec8 cohesin complexes are not required, however, either for suppression of intersister DSB repair or for the repair itself. Regulation of DSB repair in meiosis is chromosome autonomous such that unrepaired breaks on haploid chromosomes do not prevent interhomolog repair between disomic homologs. The pattern of DSB repair in haploids containing Dmc1 and/or Rad51 indicates that Mek1 acts on Rad51-specific recombination processes.
Collapse
Affiliation(s)
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215
| |
Collapse
|
42
|
Double Holliday junctions are intermediates of DNA break repair. Nature 2010; 464:937-41. [PMID: 20348905 PMCID: PMC2851831 DOI: 10.1038/nature08868] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 01/27/2010] [Indexed: 01/27/2023]
Abstract
Repair of DNA double-strand-breaks (DSBs) by homologous recombination is crucial for cell proliferation and tumor suppression. However, despite its importance, the molecular intermediates of mitotic DSB-repair remain undefined. The double Holliday Junction (dHJ), presupposed to be the central intermediate for more than 25 years1, has only been identified during meiotic recombination2. Moreover, evidence has accumulated for alternative, dHJ-independent mechanisms3–6, raising the possibility that dHJs are not formed during DSB-repair in mitotically cycling cells. Here we identify intermediates of DSB-repair using a budding yeast assay system designed to mimic physiological DSB repair. This system utilizes diploid cells and provides the possibility for allelic recombination either between sister-chromatids or between homologs, as well as direct comparison with meiotic recombination at the same locus. In mitotically cycling cells, we detect inter-homolog Joint Molecule (JM) intermediates whose size and strand-composition are identical to the canonical dHJ structures observed in meiosis2. However, in contrast to meiosis, JMs between sister chromatids form in preference to those between homologs. Moreover, JMs appear to represent a minor pathway of DSB repair in mitotic cells, being detected at ~10-fold lower levels (per DSB) than during meiotic recombination. Thus, although dHJs are identified as intermediates of DSB-promoted recombination in both mitotic and meiotic cells, their formation is distinctly regulated according to the specific dictates of the two cellular programs.
Collapse
|