1
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Estrem B, Davis RE, Wang J. End resection and telomere healing of DNA double-strand breaks during nematode programmed DNA elimination. Nucleic Acids Res 2024; 52:8913-8929. [PMID: 38953168 DOI: 10.1093/nar/gkae579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/24/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well characterized, little is known regarding the DSBs that fragment nematode chromosomes. Here, we used embryos from the human and pig parasitic nematode Ascaris to characterize the DSBs. Using END-seq, we demonstrate that DSBs are introduced before mitosis, followed by extensive end resection. The resection profile is unique for each break site, and the resection generates 3'-overhangs before the addition of neotelomeres. Interestingly, telomere healing occurs much more frequently on retained DSB ends than on eliminated ends. This biased repair of the DSB ends may be due to the sequestration of the eliminated DNA into micronuclei, preventing neotelomere formation at their ends. Additional DNA breaks occur within the eliminated DNA in both Ascaris and Parascaris, ensuring chromosomal breakage and providing a fail-safe mechanism for PDE. Overall, our data indicate that telomere healing of DSBs is specific to the break sites responsible for nematode PDE.
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Affiliation(s)
- Brandon Estrem
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jianbin Wang
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, USA
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2
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Diagouraga B, Tambones I, Carivenc C, Bechara C, Nadal M, de Massy B, le Maire A, Robert T. The TOPOVIBL meiotic DSB formation protein: new insights from its biochemical and structural characterization. Nucleic Acids Res 2024; 52:8930-8946. [PMID: 38966985 DOI: 10.1093/nar/gkae587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
The TOPOVIL complex catalyzes the formation of DNA double strand breaks (DSB) that initiate meiotic homologous recombination, an essential step for chromosome segregation and genetic diversity during gamete production. TOPOVIL is composed of two subunits (SPO11 and TOPOVIBL) and is evolutionarily related to the archaeal TopoVI topoisomerase complex. SPO11 is the TopoVIA subunit orthologue and carries the DSB formation catalytic activity. TOPOVIBL shares homology with the TopoVIB ATPase subunit. TOPOVIBL is essential for meiotic DSB formation, but its molecular function remains elusive, partly due to the lack of biochemical studies. Here, we purified TOPOVIBLΔC25 and characterized its structure and mode of action in vitro. Our structural analysis revealed that TOPOVIBLΔC25 adopts a dynamic conformation in solution and our biochemical study showed that the protein remains monomeric upon incubation with ATP, which correlates with the absence of ATP binding. Moreover, TOPOVIBLΔC25 interacted with DNA, with a preference for some geometries, suggesting that TOPOVIBL senses specific DNA architectures. Altogether, our study identified specific TOPOVIBL features that might help to explain how TOPOVIL function evolved toward a DSB formation activity in meiosis.
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Affiliation(s)
- Boubou Diagouraga
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Izabella Tambones
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Coralie Carivenc
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Chérine Bechara
- Institut de Génomique Fonctionnelle (IGF), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Marc Nadal
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Department of Life Sciences, Université Paris Cité, Paris, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Univ Montpellier, CNRS, 34090 Montpellier, France
| | - Albane le Maire
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Thomas Robert
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
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3
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Tamai T, Reginato G, Ojiri R, Morita I, Avrutis A, Cejka P, Shinohara M, Sugimoto K. Sae2 controls Mre11 endo- and exonuclease activities by different mechanisms. Nat Commun 2024; 15:7221. [PMID: 39174552 PMCID: PMC11341764 DOI: 10.1038/s41467-024-51493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 08/09/2024] [Indexed: 08/24/2024] Open
Abstract
DNA double-strand breaks (DSBs) must be repaired to ensure cell survival and genomic integrity. In yeast, the Mre11-Rad50-Xrs2 complex (MRX) collaborates with Sae2 to initiate DSB repair. Sae2 stimulates two MRX nuclease activities, endonuclease and 3'-5' exonuclease. However, how Sae2 controls the two nuclease activities remains enigmatic. Using a combined genetic and biochemical approach, we identified a separation-of-function rad50 mutation, rad50-C47, that causes a defect in Sae2-dependent MRX 3'-5' exonuclease activity, but not endonuclease activity. We found that both the endo- and 3'-5' exonuclease activities are essential to release Spo11 from DNA ends, whereas only the endonuclease activity is required for hairpin removal. We also uncovered that MRX-Sae2 endonuclease introduces a cleavage at defined distances from the Spo11-blocked end with gradually decreasing efficiency. Our findings demonstrate that Sae2 stimulates the MRX endo- and exonuclease activities via Rad50 by different mechanisms, ensuring diverse actions of MRX-Sae2 nuclease at DNA ends.
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Affiliation(s)
- Tomoki Tamai
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Giordano Reginato
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland
| | - Ryusei Ojiri
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Issei Morita
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan
| | - Alexandra Avrutis
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA
| | - Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500, Bellinzona, Switzerland.
| | - Miki Shinohara
- Faculty of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara City, Nara, 631-8505, Japan.
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ, 07103, USA.
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4
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Kim S, Yamada S, Li T, Canasto-Chibuque C, Kim JH, Marcet-Ortega M, Xu J, Eng DY, Feeney L, Petrini JHJ, Keeney S. The MRE11-RAD50-NBS1 complex both starts and extends DNA end resection in mouse meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.17.608390. [PMID: 39185212 PMCID: PMC11343206 DOI: 10.1101/2024.08.17.608390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Nucleolytic resection of DNA ends is critical for homologous recombination, but its mechanism is not fully understood, particularly in mammalian meiosis. Here we examine roles of the conserved MRN complex (MRE11, RAD50, and NBS1) through genome-wide analysis of meiotic resection in mice with various MRN mutations, including several that cause chromosomal instability in humans. Meiotic DSBs form at elevated levels but remain unresected if Mre11 is conditionally deleted, thus MRN is required for both resection initiation and regulation of DSB numbers. Resection lengths are reduced to varying degrees in MRN hypomorphs or if MRE11 nuclease activity is attenuated in a conditional nuclease-dead Mre11 model. These findings unexpectedly establish that MRN is needed for longer-range extension of resection, not just resection initiation. Finally, resection defects are additively worsened by combining MRN and Exo1 mutations, and mice that are unable to initiate resection or have greatly curtailed resection lengths experience catastrophic spermatogenic failure. Our results elucidate multiple functions of MRN in meiotic recombination, uncover unanticipated relationships between short- and long-range resection, and establish the importance of resection for mammalian meiosis.
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5
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Aithal R, Nangalia K, Spirek M, Chen D, Klein F, Krejci L. Physical interaction with Spo11 mediates the localisation of Mre11 to chromatin in meiosis and promotes its nuclease activity. Nucleic Acids Res 2024; 52:4328-4343. [PMID: 38407383 PMCID: PMC11077076 DOI: 10.1093/nar/gkae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Meiotic recombination is of central importance for the proper segregation of homologous chromosomes, but also for creating genetic diversity. It is initiated by the formation of double-strand breaks (DSBs) in DNA catalysed by evolutionarily conserved Spo11, together with additional protein partners. Difficulties in purifying the Spo11 protein have limited the characterization of its biochemical properties and of its interactions with other DSB proteins. In this study, we have purified fragments of Spo11 and show for the first time that Spo11 can physically interact with Mre11 and modulates its DNA binding, bridging, and nuclease activities. The interaction of Mre11 with Spo11 requires its far C-terminal region, which is in line with the severe meiotic phenotypes of various mre11 mutations located at the C-terminus. Moreover, calibrated ChIP for Mre11 shows that Spo11 promotes Mre11 recruitment to chromatin, independent of DSB formation. A mutant deficient in Spo11 interaction severely reduces the association of Mre11 with meiotic chromatin. Consistent with the reduction of Mre11 foci in this mutant, it strongly impedes DSB formation, leading to spore death. Our data provide evidence that physical interaction between Spo11 and Mre11, together with end-bridging, promote normal recruitment of Mre11 to hotspots and DSB formation.
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Affiliation(s)
- Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Kuldeep Nangalia
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030Vienna, Austria
| | - Mario Spirek
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Doris Chen
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030Vienna, Austria
| | - Franz Klein
- Department of Chromosome Biology, Center for Molecular Biology, University of Vienna
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Dr.-Bohr-Gasse 9, 1030Vienna, Austria
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Department of Biology, Masaryk University, Brno, Czech Republic
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6
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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.
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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
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7
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López Ruiz LM, Johnson D, Gittens WH, Brown GGB, Allison RM, Neale MJ. Meiotic prophase length modulates Tel1-dependent DNA double-strand break interference. PLoS Genet 2024; 20:e1011140. [PMID: 38427688 PMCID: PMC10936813 DOI: 10.1371/journal.pgen.1011140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 03/13/2024] [Accepted: 01/17/2024] [Indexed: 03/03/2024] Open
Abstract
During meiosis, genetic recombination is initiated by the formation of many DNA double-strand breaks (DSBs) catalysed by the evolutionarily conserved topoisomerase-like enzyme, Spo11, in preferred genomic sites known as hotspots. DSB formation activates the Tel1/ATM DNA damage responsive (DDR) kinase, locally inhibiting Spo11 activity in adjacent hotspots via a process known as DSB interference. Intriguingly, in S. cerevisiae, over short genomic distances (<15 kb), Spo11 activity displays characteristics of concerted activity or clustering, wherein the frequency of DSB formation in adjacent hotspots is greater than expected by chance. We have proposed that clustering is caused by a limited number of sub-chromosomal domains becoming primed for DSB formation. Here, we provide evidence that DSB clustering is abolished when meiotic prophase timing is extended via deletion of the NDT80 transcription factor. We propose that extension of meiotic prophase enables most cells, and therefore most chromosomal domains within them, to reach an equilibrium state of similar Spo11-DSB potential, reducing the impact that priming has on estimates of coincident DSB formation. Consistent with this view, when Tel1 is absent but Ndt80 is present and thus cells are able to rapidly exit meiotic prophase, genome-wide maps of Spo11-DSB formation are skewed towards pericentromeric regions and regions that load pro-DSB factors early-revealing regions of preferential priming-but this effect is abolished when NDT80 is deleted. Our work highlights how the stochastic nature of Spo11-DSB formation in individual cells within the limited temporal window of meiotic prophase can cause localised DSB clustering-a phenomenon that is exacerbated in tel1Δ cells due to the dual roles that Tel1 has in DSB interference and meiotic prophase checkpoint control.
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Affiliation(s)
- Luz María López Ruiz
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Dominic Johnson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - William H. Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - George G. B. Brown
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rachal M. Allison
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Matthew J. Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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8
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Chen L, Weir JR. The molecular machinery of meiotic recombination. Biochem Soc Trans 2024; 52:379-393. [PMID: 38348856 PMCID: PMC10903461 DOI: 10.1042/bst20230712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Meiotic recombination, a cornerstone of eukaryotic diversity and individual genetic identity, is essential for the creation of physical linkages between homologous chromosomes, facilitating their faithful segregation during meiosis I. This process requires that germ cells generate controlled DNA lesions within their own genome that are subsequently repaired in a specialised manner. Repair of these DNA breaks involves the modulation of existing homologous recombination repair pathways to generate crossovers between homologous chromosomes. Decades of genetic and cytological studies have identified a multitude of factors that are involved in meiotic recombination. Recent work has started to provide additional mechanistic insights into how these factors interact with one another, with DNA, and provide the molecular outcomes required for a successful meiosis. Here, we provide a review of the recent developments with a focus on protein structures and protein-protein interactions.
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Affiliation(s)
- Linda Chen
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - John R Weir
- Structural Biochemistry of Meiosis Group, Friedrich Miescher Laboratory, Max-Planck-Ring 9, 72076 Tübingen, Germany
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9
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Lee ED, Kempes CP, West GB. Idea engines: Unifying innovation & obsolescence from markets & genetic evolution to science. Proc Natl Acad Sci U S A 2024; 121:e2312468120. [PMID: 38306477 PMCID: PMC10861874 DOI: 10.1073/pnas.2312468120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/04/2023] [Indexed: 02/04/2024] Open
Abstract
Innovation and obsolescence describe dynamics of ever-churning and adapting social and biological systems, concepts that encompass field-specific formulations. We formalize the connection with a reduced model of the dynamics of the "space of the possible" (e.g., technologies, mutations, theories) to which agents (e.g., firms, organisms, scientists) couple as they grow, die, and replicate. We predict three regimes: The space is finite, ever growing, or a Schumpeterian dystopia in which obsolescence drives the system to collapse. We reveal a critical boundary at which the space of the possible fluctuates dramatically in size, displaying recurrent periods of minimal and of veritable diversity. When the space is finite, corresponding to physically realizable systems, we find surprising structure. This structure predicts a taxonomy for the density of agents near and away from the innovative frontier that we compare with distributions of firm productivity, COVID diversity, and citation rates for scientific publications. Our minimal model derived from first principles aligns with empirical examples, implying a follow-the-leader dynamic in firm cost efficiency and biological evolution, whereas scientific progress reflects consensus that waits on old ideas to go obsolete. Our theory introduces a fresh and empirically testable framework for unifying innovation and obsolescence across fields.
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10
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Ahuja JS, Sandhu R, Huang L, Klein F, Börner GV. Temporal and Functional Relationship between Synaptonemal Complex Morphogenesis and Recombination during Meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575218. [PMID: 38260343 PMCID: PMC10802607 DOI: 10.1101/2024.01.11.575218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
During prophase of meiosis I, programmed double strand breaks (DSBs) are processed into crossovers, a critical requirement for segregation of homologous chromosomes (homologs) and genome haploidization in sexually reproducing organisms. Crossovers form via homologous recombination in close temporospatial association with morphogenesis of the synaptonemal complex (SC), a proteinaceous structure that connects paired homologs along their length during the pachytene stage. Synapsis and recombination are a paradigm for the interplay between higher order chromosome structure and DNA metabolism, yet their temporal and functional relationship remains poorly understood. Probing linkage between these processes in budding yeast, we show that SC assembly is associated with a distinct threshold number of unstable D-loops. The transition from bona fide paranemic D-loops to plectonemic DSB single end invasions (SEIs) is completed during midpachynema, when the SC is fully assembled. Double Holliday junctions (dHJs) form at the time of desynapsis and are resolved into crossovers during diplonema. The SC central element component Zip1 shepherds recombination through three transitions, including DSB first end strand exchange and second end capture, as well as dHJ resolution. Zip1 mediates SEI formation independent of its polymerization whereas precocious Zip1 assembly interferes with double Holliday junction resolution. Together, our findings indicate that the synaptonemal complex controls recombination while assembled but also beyond its disassembly, possibly by establishing spatial constraints at recombination sites.
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11
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Hinch R, Donnelly P, Hinch AG. Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science 2023; 382:eadh2531. [PMID: 38033082 PMCID: PMC7615360 DOI: 10.1126/science.adh2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 12/02/2023]
Abstract
Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading to de novo mutation in one in four sperm and one in 12 eggs. Its impact on indels and structural variants is even higher, with 100- to 1300-fold increases in rates per break. We uncovered new mutational signatures and footprints relative to break sites, which implicate unexpected biochemical processes and error-prone DNA repair mechanisms, including translesion synthesis and end joining in meiotic break repair. We provide evidence that these mechanisms drive mutagenesis in human germ lines and lead to disruption of hundreds of genes genome wide.
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Affiliation(s)
- Robert Hinch
- Big Data Institute, University of Oxford; Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford; Oxford, UK
- Genomics plc; Oxford, UK
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12
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Abstract
The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.
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Affiliation(s)
- Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA;
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13
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Yu Y, Wang J, Liu K, Zheng Z, Arter M, Bouuaert CC, Pu S, Patel DJ, Keeney S. Cryo-EM structure of the Spo11 core complex bound to DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.31.564985. [PMID: 37961437 PMCID: PMC10634984 DOI: 10.1101/2023.10.31.564985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The DNA double-strand breaks that initiate meiotic recombination are formed by topoisomerase relative Spo11, supported by conserved auxiliary factors. Because high-resolution structural data are lacking, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-EM structures at up to 3.3 Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104, and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3'-OH and first 5' overhanging nucleotide, definitively establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.
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Affiliation(s)
- You Yu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Juncheng Wang
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Kaixian Liu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Zhi Zheng
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Meret Arter
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Corentin Claeys Bouuaert
- 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
| | - Stephen Pu
- 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
| | - Dinshaw J. Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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14
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Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
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Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
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15
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Erenpreisa J, Vainshelbaum NM, Lazovska M, Karklins R, Salmina K, Zayakin P, Rumnieks F, Inashkina I, Pjanova D, Erenpreiss J. The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer. Int J Mol Sci 2023; 24:11660. [PMID: 37511419 PMCID: PMC10380301 DOI: 10.3390/ijms241411660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.
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Affiliation(s)
| | | | - Marija Lazovska
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Roberts Karklins
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Juris Erenpreiss
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
- Clinic iVF-Riga, Zala 1, LV-1010 Riga, Latvia
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16
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Sun Y, Xu X, Lin L, Xu K, Zheng Y, Ren C, Tao H, Wang X, Zhao H, Tu W, Bai X, Wang J, Huang Q, Li Y, Chen H, Li H, Bo X. A graph neural network-based interpretable framework reveals a novel DNA fragility-associated chromatin structural unit. Genome Biol 2023; 24:90. [PMID: 37095580 PMCID: PMC10124043 DOI: 10.1186/s13059-023-02916-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation. RESULTS Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation. CONCLUSIONS Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.
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Affiliation(s)
- Yu Sun
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xiang Xu
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Lin Lin
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Kang Xu
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Yang Zheng
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Chao Ren
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Huan Tao
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Xu Wang
- 4Paradigm Inc, Beijing, China
| | | | | | - Xuemei Bai
- The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Junting Wang
- The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Qiya Huang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaru Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, China.
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17
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Mazur AK, Gladyshev E. C-DNA may facilitate homologous DNA pairing. Trends Genet 2023:S0168-9525(23)00023-9. [PMID: 36804168 DOI: 10.1016/j.tig.2023.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/17/2023]
Abstract
Recombination-independent homologous pairing represents a prominent yet largely enigmatic feature of chromosome biology. As suggested by studies in the fungus Neurospora crassa, this process may be based on the direct pairing of homologous DNA molecules. Theoretical search for the DNA structures consistent with those genetic results has led to an all-atom model in which the B-DNA conformation of the paired double helices is strongly shifted toward C-DNA. Coincidentally, C-DNA also features a very shallow major groove that could permit initial homologous contacts without atom-atom clashes. The hereby conjectured role of C-DNA in homologous pairing should encourage the efforts to discover its biological functions and may also clarify the mechanism of recombination-independent recognition of DNA homology.
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Affiliation(s)
- Alexey K Mazur
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, Paris, France; Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
| | - Eugene Gladyshev
- Institut Pasteur, Université Paris Cité, Group Fungal Epigenomics, Paris, France.
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18
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Kawashima Y, Oda AH, Hikida Y, Ohta K. Chromosome-dependent aneuploid formation in Spo11-less meiosis. Genes Cells 2023; 28:129-148. [PMID: 36530025 PMCID: PMC10107155 DOI: 10.1111/gtc.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/21/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Deficiency in meiotic recombination leads to aberrant chromosome disjunction during meiosis, often resulting in the lethality of gametes or genetic disorders due to aneuploidy formation. Budding yeasts lacking Spo11, which is essential for initiation of meiotic recombination, produce many inviable spores in meiosis, while very rarely all sets of 16 chromosomes are coincidentally assorted into gametes to form viable spores. We induced meiosis in a spo11∆ diploid, in which homolog pairs can be distinguished by single nucleotide polymorphisms and determined whole-genome sequences of their exceptionally viable spores. We detected no homologous recombination in the viable spores of spo11∆ diploid. Point mutations were fewer in spo11∆ than in wild-type. We observed spo11∆ viable spores carrying a complete diploid set of homolog pairs or haploid spores with a complete haploid set of homologs but with aneuploidy in some chromosomes. In the latter, we found the chromosome-dependence in the aneuploid incidence, which was positively and negatively influenced by the chromosome length and the impact of dosage-sensitive genes, respectively. Selection of aneuploidy during meiosis II or mitosis after spore germination was also chromosome dependent. These results suggest a pathway by which specific chromosomes are more prone to cause aneuploidy, as observed in Down syndrome.
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Affiliation(s)
- Yuri Kawashima
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Arisa H Oda
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasushi Hikida
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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19
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Tian M, Cai X, Liu Y, Liucong M, Howard-Till R. A practical reference for studying meiosis in the model ciliate Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:595-608. [PMID: 37078080 PMCID: PMC10077211 DOI: 10.1007/s42995-022-00149-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 09/28/2022] [Indexed: 05/03/2023]
Abstract
Meiosis is a critical cell division program that produces haploid gametes for sexual reproduction. Abnormalities in meiosis are often causes of infertility and birth defects (e.g., Down syndrome). Most organisms use a highly specialized zipper-like protein complex, the synaptonemal complex (SC), to guide and stabilize pairing of homologous chromosomes in meiosis. Although the SC is critical for meiosis in many eukaryotes, there are organisms that perform meiosis without a functional SC. However, such SC-less meiosis is poorly characterized. To understand the features of SC-less meiosis and its adaptive significance, the ciliated protozoan Tetrahymena was selected as a model. Meiosis research in Tetrahymena has revealed intriguing aspects of the regulatory programs utilized in its SC-less meiosis, yet additional efforts are needed for obtaining an in-depth comprehension of mechanisms that are associated with the absence of SC. Here, aiming at promoting a wider application of Tetrahymena for meiosis research, we introduce basic concepts and core techniques for studying meiosis in Tetrahymena and then suggest future directions for expanding the current Tetrahymena meiosis research toolbox. These methodologies could be adopted for dissecting meiosis in poorly characterized ciliates that might reveal novel features. Such data will hopefully provide insights into the function of the SC and the evolution of meiosis from a unique perspective. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00149-8.
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Affiliation(s)
- Miao Tian
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
- Institute of Human Genetics, CNRS, University of Montpellier, 34090 Montpellier, France
| | - Xia Cai
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yujie Liu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Mingmei Liucong
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Rachel Howard-Till
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA USA
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20
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Continuous double-strand break induction and their differential processing sustain chiasma formation during Caenorhabditis elegans meiosis. Cell Rep 2022; 40:111403. [PMID: 36170820 DOI: 10.1016/j.celrep.2022.111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/01/2022] [Accepted: 09/01/2022] [Indexed: 11/22/2022] Open
Abstract
Faithful chromosome segregation into gametes depends on Spo11-induced DNA double-strand breaks (DSBs). These yield single-stranded 3' tails upon resection to promote crossovers (COs). While early Mre11-dependent end resection is the predominant pathway in most organisms, Exo1 or Dna2/BLM can also contribute to the efficient processing of meiotic DSBs. Although its enzymatic activity has been thoroughly dissected, the temporal dynamics underlying Spo11 activity have remained mostly elusive. We show that, in Caenorhabditis elegans, SPO-11-mediated DSB induction takes place throughout early meiotic prophase I until mid-late pachynema. We find that late DSBs are essential for CO formation and are preferentially processed by EXO-1 and DNA-2 in a redundant fashion. Further, EXO-1-DNA-2-mediated resection ensures completion of conservative DSB repair and discourages activation of KU-dependent end joining. Taken together, our data unveil important temporal aspects of DSB induction and identify previously unknown functional implications for EXO-1-DNA-2-mediated resection activity in C. elegans.
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21
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Anqi Y, Saina Y, Chujie C, Yanfei Y, Xiangwei T, Jiajia M, Jiaojiao X, Maoliang R, Bin C. Regulation of DNA methylation during the testicular development of Shaziling pigs. Genomics 2022; 114:110450. [PMID: 35995261 DOI: 10.1016/j.ygeno.2022.110450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
DNA methylation is one of the key epigenetic regulatory mechanisms in development and spermatogenesis. However, the dynamic regulatory mechanisms of genome-wide DNA methylation during testicular development remain largely unknown. Herein, we generated a single-base resolution DNA methylome and transcriptome atlas of precocious porcine testicular tissues across three developmental stages (1, 75, and 150 days old). The results showed that the dynamic methylation patterns were directly related to the expression of the DNMT3A gene. Conjoint analysis revealed a negative regulatory pattern between promoter methylation and the positive regulation of 3'-untranslated region (3'UTR) methylation. Mechanistically, the decrease in promoter methylation affected the upregulation of meiosis-related genes, such as HORMAD1, SPO11, and SYCE1. Demethylation in the 3'UTR induced the downregulation of the INHBA gene and knockdown of INHBA inhibited cell proliferation by reducing the synthesis of activin A. These findings contribute to exploring the regulatory mechanisms of DNA methylation in testicular development.
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Affiliation(s)
- Yang Anqi
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yan Saina
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Chen Chujie
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yin Yanfei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Tang Xiangwei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ma Jiajia
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Xiang Jiaojiao
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ran Maoliang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
| | - Chen Bin
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
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22
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Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
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23
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Raina VB, Schoot Uiterkamp M, Vader G. Checkpoint control in meiotic prophase: Idiosyncratic demands require unique characteristics. Curr Top Dev Biol 2022; 151:281-315. [PMID: 36681474 DOI: 10.1016/bs.ctdb.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromosomal transactions such as replication, recombination and segregation are monitored by cell cycle checkpoint cascades. These checkpoints ensure the proper execution of processes that are needed for faithful genome inheritance from one cell to the next, and across generations. In meiotic prophase, a specialized checkpoint monitors defining events of meiosis: programmed DNA break formation, followed by dedicated repair through recombination based on interhomolog (IH) crossovers. This checkpoint shares molecular characteristics with canonical DNA damage checkpoints active during somatic cell cycles. However, idiosyncratic requirements of meiotic prophase have introduced unique features in this signaling cascade. In this review, we discuss the unique features of the meiotic prophase checkpoint. While being related to canonical DNA damage checkpoint cascades, the meiotic prophase checkpoint also shows similarities with the spindle assembly checkpoint (SAC) that guards chromosome segregation. We highlight these emerging similarities in the signaling logic of the checkpoints that govern meiotic prophase and chromosome segregation, and how thinking of these similarities can help us better understand meiotic prophase control. We also discuss work showing that, when aberrantly expressed, components of the meiotic prophase checkpoint might alter DNA repair fidelity and chromosome segregation in cancer cells. Considering checkpoint function in light of demands imposed by the special characteristics of meiotic prophase helps us understand checkpoint integration into the meiotic cell cycle machinery.
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Affiliation(s)
- Vivek B Raina
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York City, NY, United States
| | - Maud Schoot Uiterkamp
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gerben Vader
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
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24
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Lorenz A, Mpaulo SJ. Gene conversion: a non-Mendelian process integral to meiotic recombination. Heredity (Edinb) 2022; 129:56-63. [PMID: 35393552 PMCID: PMC9273591 DOI: 10.1038/s41437-022-00523-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 12/30/2022] Open
Abstract
Meiosis is undoubtedly the mechanism that underpins Mendelian genetics. Meiosis is a specialised, reductional cell division which generates haploid gametes (reproductive cells) carrying a single chromosome complement from diploid progenitor cells harbouring two chromosome sets. Through this process, the hereditary material is shuffled and distributed into haploid gametes such that upon fertilisation, when two haploid gametes fuse, diploidy is restored in the zygote. During meiosis the transient physical connection of two homologous chromosomes (one originally inherited from each parent) each consisting of two sister chromatids and their subsequent segregation into four meiotic products (gametes), is what enables genetic marker assortment forming the core of Mendelian laws. The initiating events of meiotic recombination are DNA double-strand breaks (DSBs) which need to be repaired in a certain way to enable the homologous chromosomes to find each other. This is achieved by DSB ends searching for homologous repair templates and invading them. Ultimately, the repair of meiotic DSBs by homologous recombination physically connects homologous chromosomes through crossovers. These physical connections provided by crossovers enable faithful chromosome segregation. That being said, the DSB repair mechanism integral to meiotic recombination also produces genetic transmission distortions which manifest as postmeiotic segregation events and gene conversions. These processes are non-reciprocal genetic exchanges and thus non-Mendelian.
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Affiliation(s)
- Alexander Lorenz
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK.
| | - Samantha J Mpaulo
- Institute of Medical Sciences (IMS), University of Aberdeen, Aberdeen, UK
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25
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Lukaszewicz A, Lange J, Keeney S, Jasin M. De novo deletions and duplications at recombination hotspots in mouse germlines. Cell 2021; 184:5970-5984.e18. [PMID: 34793701 PMCID: PMC8616837 DOI: 10.1016/j.cell.2021.10.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/10/2021] [Accepted: 10/27/2021] [Indexed: 11/23/2022]
Abstract
Numerous DNA double-strand breaks (DSBs) arise during meiosis to initiate homologous recombination. These DSBs are usually repaired faithfully, but here, we uncover a distinct type of mutational event in which deletions form via joining of ends from two closely spaced DSBs (double cuts) within a single hotspot or at adjacent hotspots on the same or different chromatids. Deletions occur in normal meiosis but are much more frequent when DSB formation is dysregulated in the absence of the ATM kinase. Events between chromosome homologs point to multi-chromatid damage and aborted gap repair. Some deletions contain DNA from other hotspots, indicating that double cutting at distant sites creates substrates for insertional mutagenesis. End joining at double cuts can also yield tandem duplications or extrachromosomal circles. Our findings highlight the importance of DSB regulation and reveal a previously hidden potential for meiotic mutagenesis that is likely to affect human health and genome evolution.
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Affiliation(s)
- Agnieszka Lukaszewicz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Memorial Sloan Kettering Cancer Center, Howard Hughes Medical Institute, New York, NY 10065, USA.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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26
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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: 24] [Impact Index Per Article: 8.0] [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.
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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.
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27
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Abstract
The specialized two-stage meiotic cell division program halves a cell's chromosome complement in preparation for sexual reproduction. This reduction in ploidy requires that in meiotic prophase, each pair of homologous chromosomes (homologs) identify one another and form physical links through DNA recombination. Here, we review recent advances in understanding the complex morphological changes that chromosomes undergo during meiotic prophase to promote homolog identification and crossing over. We focus on the structural maintenance of chromosomes (SMC) family cohesin complexes and the meiotic chromosome axis, which together organize chromosomes and promote recombination. We then discuss the architecture and dynamics of the conserved synaptonemal complex (SC), which assembles between homologs and mediates local and global feedback to ensure high fidelity in meiotic recombination. Finally, we discuss exciting new advances, including mechanisms for boosting recombination on particular chromosomes or chromosomal domains and the implications of a new liquid crystal model for SC assembly and structure. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sarah N Ur
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA; ,
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA; , .,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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28
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Johnson D, Crawford M, Cooper T, Claeys Bouuaert C, Keeney S, Llorente B, Garcia V, Neale MJ. Concerted cutting by Spo11 illuminates meiotic DNA break mechanics. Nature 2021; 594:572-576. [PMID: 34108687 PMCID: PMC7611867 DOI: 10.1038/s41586-021-03389-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Genetic recombination arises during meiosis through the repair of DNA double-strand breaks (DSBs) that are created by Spo11, a topoisomerase-like protein1,2. Spo11 DSBs form preferentially in nucleosome-depleted regions termed hotspots3,4, yet how Spo11 engages with its DNA substrate to catalyse DNA cleavage is poorly understood. Although most recombination events are initiated by a single Spo11 cut, here we show in Saccharomyces cerevisiae that hyperlocalized, concerted Spo11 DSBs separated by 33 to more than 100 base pairs also form, which we term 'double cuts'. Notably, the lengths of double cuts vary with a periodicity of 10.5 base pairs, which is conserved in yeast and mice. This finding suggests a model in which the orientation of adjacent Spo11 molecules is fixed relative to the DNA helix-a proposal supported by the in vitro DNA-binding properties of the Spo11 core complex. Deep sequencing of meiotic progeny identifies recombination scars that are consistent with repair initiated from gaps generated by adjacent Spo11 DSBs. Collectively, these results revise our present understanding of the mechanics of Spo11-DSB formation and expand on the original concepts of gap repair during meiosis to include DNA gaps that are generated by Spo11 itself.
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Affiliation(s)
- Dominic Johnson
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Margaret Crawford
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Tim Cooper
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Corentin Claeys Bouuaert
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louvain Institute of Biomolecular Science and Technology, Louvain-la-Neuve, Belgium
| | - Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bertrand Llorente
- Cancer Research Centre of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France
| | - Valerie Garcia
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
- Cancer Research Centre of Marseille, CNRS, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, France.
| | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.
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