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Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Tuncay H, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. Nat Commun 2024; 15:2941. [PMID: 38580643 PMCID: PMC10997794 DOI: 10.1038/s41467-024-47020-1] [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: 07/28/2023] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
Programmed DNA double-strand break (DSB) formation is a crucial feature of meiosis in most organisms. DSBs initiate recombination-mediated linking of homologous chromosomes, which enables correct chromosome segregation in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We uncover in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms. Both IHO1 phosphorylation and formation of axial IHO1 platforms are diminished by chemical inhibition of DBF4-dependent kinase (DDK), suggesting that DDK contributes to the control of the axial DSB-machinery. Furthermore, we show that axial IHO1 platforms are based on an interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.
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Affiliation(s)
- Ihsan Dereli
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Vladyslav Telychko
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Frantzeskos Papanikos
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Kavya Raveendran
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Jiaqi Xu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Michiel Boekhout
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Marcello Stanzione
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Benjamin Neuditschko
- Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria
| | - Naga Sailaja Imjeti
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Elizaveta Selezneva
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hasibe Tuncay
- Department of Developmental Biology, University of Hamburg, 22609, Hamburg, Germany
| | - Sevgican Demir
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Teresa Giannattasio
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Marc Gentzel
- Core Facility Mass Spectrometry & Proteomics, Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Anastasiia Bondarieva
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Michelle Stevense
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany
| | - Marco Barchi
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
- Saint Camillus International University of Health Sciences, Rome, Italy
| | - Arp Schnittger
- Department of Developmental Biology, University of Hamburg, 22609, Hamburg, Germany
| | - John R Weir
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Franz Herzog
- Institute Krems Bioanalytics, IMC University of Applied Sciences, 3500, Krems, Austria
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Attila Tóth
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Fiedlerstrasse 42, 01307, Dresden, Germany.
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Milano CR, Ur SN, Gu Y, Zhang J, Allison R, Brown G, Neale MJ, Tromer EC, Corbett KD, Hochwagen A. Chromatin binding by HORMAD proteins regulates meiotic recombination initiation. EMBO J 2024; 43:836-867. [PMID: 38332377 PMCID: PMC10907721 DOI: 10.1038/s44318-024-00034-3] [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: 05/10/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved.
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Affiliation(s)
- Carolyn R Milano
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Sarah N Ur
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Vividion Therapeutics, San Diego, CA, 92121, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jessie Zhang
- Department of Biology, New York University, New York, NY, 10003, USA
| | - Rachal Allison
- Genome Damage and Stability Centre, University of Sussex, Falmer, BN1 9RQ, UK
| | - George Brown
- Genome Damage and Stability Centre, University of Sussex, Falmer, BN1 9RQ, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Falmer, BN1 9RQ, UK
| | - Eelco C Tromer
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Andreas Hochwagen
- Department of Biology, New York University, New York, NY, 10003, USA.
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Chotiner JY, Leu NA, Yang F, Cossu IG, Guan Y, Lin H, Wang PJ. TRIP13 localizes to synapsed chromosomes and functions as a dosage-sensitive regulator of meiosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559355. [PMID: 37808842 PMCID: PMC10557606 DOI: 10.1101/2023.09.25.559355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Meiotic progression requires coordinated assembly and disassembly of protein complexes involved in chromosome synapsis and meiotic recombination. The AAA+ ATPase TRIP13 and its orthologue Pch2 are instrumental in remodeling HORMA domain proteins. Meiosis-specific HORMAD proteins are associated with unsynapsed chromosome axes but depleted from the synaptonemal complex (SC) of synapsed chromosome homologues. Here we report that TRIP13 localizes to the synapsed SC in early pachytene spermatocytes and to telomeres throughout meiotic prophase I. Loss of TRIP13 leads to meiotic arrest and thus sterility in both sexes. Trip13-null meiocytes exhibit abnormal persistence of HORMAD1 and HOMRAD2 on synapsed SC and chromosome asynapsis that preferentially affects XY and centromeric ends. These findings confirm the previously reported phenotypes of the Trip13 hypomorph alleles. Trip13 heterozygous (Trip13+/-) mice also exhibit meiotic defects that are less severe than the Trip13-null mice, showing that TRIP13 is a dosage-sensitive regulator of meiosis. Localization of TRIP13 to the synapsed SC is independent of SC axial element proteins such as REC8 and SYCP2/SYCP3. The N- or C-terminal FLAG-tagged TRIP13 proteins are functional and recapitulate the localization of native TRIP13 to SC and telomeres in knockin mice. Therefore, the evolutionarily conserved localization of TRIP13/Pch2 to the synapsed chromosomes provides an explanation for dissociation of HORMA domain proteins upon chromosome synapsis in diverse organisms.
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Affiliation(s)
- Jessica Y. Chotiner
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - N. Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Fang Yang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Isabella G. Cossu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Yongjuan Guan
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Huijuan Lin
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
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Mursalimov S, Matsumoto M, Urakubo H, Deineko E, Ohno N. Unusual nuclear structures in male meiocytes of wild-type rye as revealed by volume microscopy. ANNALS OF BOTANY 2023; 132:1159-1174. [PMID: 37490684 PMCID: PMC10809220 DOI: 10.1093/aob/mcad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023]
Abstract
BACKGROUND AND AIMS During the analysis of plant male meiocytes coming from destroyed meiocyte columns (united multicellular structures formed by male meiocytes in each anther locule), a considerable amount of information becomes unavailable. Therefore, in this study intact meiocyte columns were studied by volume microscopy in wild-type rye for the most relevant presentation of 3-D structure of rye meiocytes throughout meiosis. METHODS We used two types of volume light microscopy: confocal laser scanning microscopy and non-confocal bright-field scanning microscopy combined with alcohol and aldehyde fixation, as well as serial block-face scanning electron microscopy. KEY RESULTS Unusual structures, called nuclear protuberances, were detected. At certain meiotic stages, nuclei formed protuberances that crossed the cell wall through intercellular channels and extended into the cytoplasm of neighbouring cells, while all other aspects of cell structure appeared to be normal. This phenomenon of intercellular nuclear migration (INM) was detected in most meiocytes at leptotene/zygotene. No cases of micronucleus formation or appearance of binucleated meiocytes were noticed. There were instances of direct contact between two nuclei during INM. No influence of fixation or of mechanical impact on the induction of INM was detected. CONCLUSIONS Intercellular nuclear migration in rye may be a programmed process (a normal part of rye male meiosis) or a tricky artefact that cannot be avoided in any way no matter which approach to meiocyte imaging is used. In both cases, INM seems to be an obligatory phenomenon that has previously been hidden by limitations of common microscopic techniques and by 2-D perception of plant male meiocytes. Intercellular nuclear migration cannot be ignored in any studies involving manipulations of rye anthers.
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Affiliation(s)
- Sergey Mursalimov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Institute of Postharvest and Food Sciences, Agricultural Research Organization (ARO)-Volcani Institute, Rishon LeZion, 7505101, Israel
| | - Mami Matsumoto
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
- Department of Developmental and Regenerative Neurobiology, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601, Japan
| | - Hidetoshi Urakubo
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
- Department of Biomedical Data Science, School of Medicine, Fujita Health University, Toyoake, 470-1192, Japan
| | - Elena Deineko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, Shimotsuke, 329-0431, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, Okazaki, 444-8585, Japan
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Dereli I, Telychko V, Papanikos F, Raveendran K, Xu J, Boekhout M, Stanzione M, Neuditschko B, Imjeti NS, Selezneva E, Erbasi HT, Demir S, Giannattasio T, Gentzel M, Bondarieva A, Stevense M, Barchi M, Schnittger A, Weir JR, Herzog F, Keeney S, Tóth A. Seeding the meiotic DNA break machinery and initiating recombination on chromosome axes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568863. [PMID: 38077023 PMCID: PMC10705248 DOI: 10.1101/2023.11.27.568863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Programmed DNA double-strand break (DSB) formation is a unique meiotic feature that initiates recombination-mediated linking of homologous chromosomes, thereby enabling chromosome number halving in meiosis. DSBs are generated on chromosome axes by heterooligomeric focal clusters of DSB-factors. Whereas DNA-driven protein condensation is thought to assemble the DSB-machinery, its targeting to chromosome axes is poorly understood. We discovered in mice that efficient biogenesis of DSB-machinery clusters requires seeding by axial IHO1 platforms, which are based on a DBF4-dependent kinase (DDK)-modulated interaction between IHO1 and the chromosomal axis component HORMAD1. IHO1-HORMAD1-mediated seeding of the DSB-machinery on axes ensures sufficiency of DSBs for efficient pairing of homologous chromosomes. Without IHO1-HORMAD1 interaction, residual DSBs depend on ANKRD31, which enhances both the seeding and the growth of DSB-machinery clusters. Thus, recombination initiation is ensured by complementary pathways that differentially support seeding and growth of DSB-machinery clusters, thereby synergistically enabling DSB-machinery condensation on chromosomal axes.
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Rafiei N, Ronceret A. Crossover interference mechanism: New lessons from plants. Front Cell Dev Biol 2023; 11:1156766. [PMID: 37274744 PMCID: PMC10236007 DOI: 10.3389/fcell.2023.1156766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Plants are the source of our understanding of several fundamental biological principles. It is well known that Gregor Mendel discovered the laws of Genetics in peas and that maize was used for the discovery of transposons by Barbara McClintock. Plant models are still useful for the understanding of general key biological concepts. In this article, we will focus on discussing the recent plant studies that have shed new light on the mysterious mechanisms of meiotic crossover (CO) interference, heterochiasmy, obligatory CO, and CO homeostasis. Obligatory CO is necessary for the equilibrated segregation of homologous chromosomes during meiosis. The tight control of the different male and female CO rates (heterochiasmy) enables both the maximization and minimization of genome shuffling. An integrative model can now predict these observed aspects of CO patterning in plants. The mechanism proposed considers the Synaptonemal Complex as a canalizing structure that allows the diffusion of a class I CO limiting factor linearly on synapsed bivalents. The coarsening of this limiting factor along the SC explains the interfering spacing between COs. The model explains the observed coordinated processes between synapsis, CO interference, CO insurance, and CO homeostasis. It also easily explains heterochiasmy just considering the different male and female SC lengths. This mechanism is expected to be conserved in other species.
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Fozard JA, Morgan C, Howard M. Coarsening dynamics can explain meiotic crossover patterning in both the presence and absence of the synaptonemal complex. eLife 2023; 12:e79408. [PMID: 36847348 PMCID: PMC10036115 DOI: 10.7554/elife.79408] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 02/24/2023] [Indexed: 03/01/2023] Open
Abstract
The shuffling of genetic material facilitated by meiotic crossovers is a critical driver of genetic variation. Therefore, the number and positions of crossover events must be carefully controlled. In Arabidopsis, an obligate crossover and repression of nearby crossovers on each chromosome pair are abolished in mutants that lack the synaptonemal complex (SC), a conserved protein scaffold. We use mathematical modelling and quantitative super-resolution microscopy to explore and mechanistically explain meiotic crossover pattering in Arabidopsis lines with full, incomplete, or abolished synapsis. For zyp1 mutants, which lack an SC, we develop a coarsening model in which crossover precursors globally compete for a limited pool of the pro-crossover factor HEI10, with dynamic HEI10 exchange mediated through the nucleoplasm. We demonstrate that this model is capable of quantitatively reproducing and predicting zyp1 experimental crossover patterning and HEI10 foci intensity data. Additionally, we find that a model combining both SC- and nucleoplasm-mediated coarsening can explain crossover patterning in wild-type Arabidopsis and in pch2 mutants, which display partial synapsis. Together, our results reveal that regulation of crossover patterning in wild-type Arabidopsis and SC-defective mutants likely acts through the same underlying coarsening mechanism, differing only in the spatial compartments through which the pro-crossover factor diffuses.
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Affiliation(s)
- John A Fozard
- Computational and Systems Biology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Chris Morgan
- Cell and Developmental Biology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
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