1
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Biot M, Toth A, Brun C, Guichard L, de Massy B, Grey C. Principles of chromosome organization for meiotic recombination. Mol Cell 2024; 84:1826-1841.e5. [PMID: 38657614 DOI: 10.1016/j.molcel.2024.04.001] [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: 11/15/2023] [Revised: 03/01/2024] [Accepted: 04/02/2024] [Indexed: 04/26/2024]
Abstract
In meiotic cells, chromosomes are organized as chromatin loop arrays anchored to a protein axis. This organization is essential to regulate meiotic recombination, from DNA double-strand break (DSB) formation to their repair. In mammals, it is unknown how chromatin loops are organized along the genome and how proteins participating in DSB formation are tethered to the chromosome axes. Here, we identify three categories of axis-associated genomic sites: PRDM9 binding sites, where DSBs form; binding sites of the insulator protein CTCF; and H3K4me3-enriched sites. We demonstrate that PRDM9 promotes the recruitment of MEI4 and IHO1, two proteins essential for DSB formation. In turn, IHO1 anchors DSB sites to the axis components HORMAD1 and SYCP3. We discovered that IHO1, HORMAD1, and SYCP3 are associated at the DSB ends during DSB repair. Our results highlight how interactions of proteins with specific genomic elements shape the meiotic chromosome organization for recombination.
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Affiliation(s)
- Mathilde Biot
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Attila Toth
- Institute of Physiological Chemistry, Faculty of Medicine at the TU Dresden, Dresden, Germany
| | - Christine Brun
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Leon Guichard
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Bernard de Massy
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
| | - Corinne Grey
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France.
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2
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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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3
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AbuAlia KFN, Damm E, Ullrich KK, Mukaj A, Parvanov E, Forejt J, Odenthal-Hesse L. Natural variation in the zinc-finger-encoding exon of Prdm9 affects hybrid sterility phenotypes in mice. Genetics 2024; 226:iyae004. [PMID: 38217871 PMCID: PMC10917509 DOI: 10.1093/genetics/iyae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/15/2024] Open
Abstract
PRDM9-mediated reproductive isolation was first described in the progeny of Mus musculus musculus (MUS) PWD/Ph and Mus musculus domesticus (DOM) C57BL/6J inbred strains. These male F1 hybrids fail to complete chromosome synapsis and arrest meiosis at prophase I, due to incompatibilities between the Prdm9 gene and hybrid sterility locus Hstx2. We identified 14 alleles of Prdm9 in exon 12, encoding the DNA-binding domain of the PRDM9 protein in outcrossed wild mouse populations from Europe, Asia, and the Middle East, 8 of which are novel. The same allele was found in all mice bearing introgressed t-haplotypes encompassing Prdm9. We asked whether 7 novel Prdm9 alleles in MUS populations and the t-haplotype allele in 1 MUS and 3 DOM populations induce Prdm9-mediated reproductive isolation. The results show that only combinations of the dom2 allele of DOM origin and the MUS msc1 allele ensure complete infertility of intersubspecific hybrids in outcrossed wild populations and inbred mouse strains examined so far. The results further indicate that MUS mice may share the erasure of PRDM9msc1 binding motifs in populations with different Prdm9 alleles, which implies that erased PRDM9 binding motifs may be uncoupled from their corresponding Prdm9 alleles at the population level. Our data corroborate the model of Prdm9-mediated hybrid sterility beyond inbred strains of mice and suggest that sterility alleles of Prdm9 may be rare.
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Affiliation(s)
- Khawla F N AbuAlia
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Elena Damm
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Kristian K Ullrich
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
| | - Amisa Mukaj
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Emil Parvanov
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, 9002 Varna, Bulgaria
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, 1090 Vienna, Austria
| | - Jiri Forejt
- Laboratory of Mouse Molecular Genetics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec CZ-25250, Czech Republic
| | - Linda Odenthal-Hesse
- Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön D-24306, Germany
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4
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Hoge C, de Manuel M, Mahgoub M, Okami N, Fuller Z, Banerjee S, Baker Z, McNulty M, Andolfatto P, Macfarlan TS, Schumer M, Tzika AC, Przeworski M. Patterns of recombination in snakes reveal a tug-of-war between PRDM9 and promoter-like features. Science 2024; 383:eadj7026. [PMID: 38386752 DOI: 10.1126/science.adj7026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/04/2024] [Indexed: 02/24/2024]
Abstract
In some mammals, notably humans, recombination occurs almost exclusively where the protein PRDM9 binds, whereas in vertebrates lacking an intact PRDM9, such as birds and canids, recombination rates are elevated near promoter-like features. To determine whether PRDM9 directs recombination in nonmammalian vertebrates, we focused on an exemplar species with a single, intact PRDM9 ortholog, the corn snake (Pantherophis guttatus). Analyzing historical recombination rates along the genome and crossovers in pedigrees, we found evidence that PRDM9 specifies the location of recombination events, but we also detected a separable effect of promoter-like features. These findings reveal that the uses of PRDM9 and promoter-like features need not be mutually exclusive and instead reflect a tug-of-war that is more even in some species than others.
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Affiliation(s)
- Carla Hoge
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Marc de Manuel
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Naima Okami
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Zachary Fuller
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Shreya Banerjee
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Zachary Baker
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Morgan McNulty
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - Athanasia C Tzika
- Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
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5
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Rosspopoff O, Trono D. Take a walk on the KRAB side. Trends Genet 2023; 39:844-857. [PMID: 37716846 DOI: 10.1016/j.tig.2023.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged some 420 million years ago in the last common ancestor of coelacanth, lungfish, and tetrapods, and dramatically expanded to give rise to lineage-specific repertoires in contemporary species paralleling their TE load and turnover. However, the KRAB domain displays sequence and function variations that reveal repeated diversions from a linear TE-KZFP trajectory. This Review summarizes current knowledge on the evolution of KZFPs and discusses how ancestral noncanonical KZFPs endowed with variant KRAB, SCAN or DUF3669 domains have been utilized to achieve KAP1-independent functions.
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Affiliation(s)
- Olga Rosspopoff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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6
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Baker Z, Przeworski M, Sella G. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence. eLife 2023; 12:e83769. [PMID: 37830496 DOI: 10.7554/elife.83769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/12/2023] [Indexed: 10/14/2023] Open
Abstract
In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. This assumption, however, does not align with current evidence. Recent experimental work indicates that PRDM9 binding on both homologs facilitates DSB repair, and that the absence of sufficient symmetric binding disrupts meiosis. We therefore consider an alternative hypothesis: that rapid PRDM9 evolution is driven by the need to restore symmetric binding because of its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population genetic processes that govern the evolution of the zinc finger array and its binding sites. We show that the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease, in turn, drives rapid PRDM9 evolutionary turnover. Our results therefore suggest that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
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Affiliation(s)
- Zachary Baker
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
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7
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Ito M, Shinohara A. Chromosome architecture and homologous recombination in meiosis. Front Cell Dev Biol 2023; 10:1097446. [PMID: 36684419 PMCID: PMC9853400 DOI: 10.3389/fcell.2022.1097446] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Meiocytes organize higher-order chromosome structures comprising arrays of chromatin loops organized at their bases by linear axes. As meiotic prophase progresses, the axes of homologous chromosomes align and synapse along their lengths to form ladder-like structures called synaptonemal complexes (SCs). The entire process of meiotic recombination, from initiation via programmed DNA double-strand breaks (DSBs) to completion of DSB repair with crossover or non-crossover outcomes, occurs in the context of chromosome axes and SCs. These meiosis-specific chromosome structures provide specialized environments for the regulation of DSB formation and crossing over. In this review, we summarize insights into the importance of chromosome architecture in the regulation of meiotic recombination, focusing on cohesin-mediated axis formation, DSB regulation via tethered loop-axis complexes, inter-homolog template bias facilitated by axial proteins, and crossover regulation in the context of the SCs. We also discuss emerging evidence that the SUMO and the ubiquitin-proteasome system function in the organization of chromosome structure and regulation of meiotic recombination.
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Affiliation(s)
- Masaru Ito
- *Correspondence: Masaru Ito, ; Akira Shinohara,
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8
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Huang Y, Roig I. Genetic control of meiosis surveillance mechanisms in mammals. Front Cell Dev Biol 2023; 11:1127440. [PMID: 36910159 PMCID: PMC9996228 DOI: 10.3389/fcell.2023.1127440] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Meiosis is a specialized cell division that generates haploid gametes and is critical for successful sexual reproduction. During the extended meiotic prophase I, homologous chromosomes progressively pair, synapse and desynapse. These chromosomal dynamics are tightly integrated with meiotic recombination (MR), during which programmed DNA double-strand breaks (DSBs) are formed and subsequently repaired. Consequently, parental chromosome arms reciprocally exchange, ultimately ensuring accurate homolog segregation and genetic diversity in the offspring. Surveillance mechanisms carefully monitor the MR and homologous chromosome synapsis during meiotic prophase I to avoid producing aberrant chromosomes and defective gametes. Errors in these critical processes would lead to aneuploidy and/or genetic instability. Studies of mutation in mouse models, coupled with advances in genomic technologies, lead us to more clearly understand how meiosis is controlled and how meiotic errors are linked to mammalian infertility. Here, we review the genetic regulations of these major meiotic events in mice and highlight our current understanding of their surveillance mechanisms. Furthermore, we summarize meiotic prophase genes, the mutations that activate the surveillance system leading to meiotic prophase arrest in mouse models, and their corresponding genetic variants identified in human infertile patients. Finally, we discuss their value for the diagnosis of causes of meiosis-based infertility in humans.
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Affiliation(s)
- Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Histology Unit, Department of Cell Biology, Physiology, and Immunology, Cytology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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9
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Wang Y, Li SY, Wang YZ, He Y. ZmASY1 interacts with ZmPRD3 and is crucial for meiotic double-strand break formation in maize. THE NEW PHYTOLOGIST 2023; 237:454-470. [PMID: 36221195 DOI: 10.1111/nph.18528] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
During meiosis, recombination-mediated pairing and synapsis of homologous chromosomes begin with programmed DNA double-strand breaks (DSBs). In yeast and mice, DSBs form in a tethered loop-axis complex, in which DSB sites are located within chromatin loops and tethered to the proteinaceous axial element (AE) by DSB-forming factors. In plants, the molecular connection between DSB sites and chromosome axes is poorly understood. By integrating genetic analysis, immunostaining technology, and protein-protein interaction studies, the putative factors linking DSB formation to chromosome axis were explored in maize meiosis. Here, we report that the AE protein ZmASY1 directly interacts with the DSB-forming protein ZmPRD3 in maize (Zea mays) and mediates DSB formation, synaptonemal complex assembly, and homologous recombination. ZmPRD3 also interacts with ZmPRD1, which plays a central role in organizing the DSB-forming complex. These results suggest that ZmASY1 and ZmPRD3 may work as a key module linking DSB sites to chromosome axes during DSB formation in maize. This mechanism is similar to that described in yeast and recently Arabidopsis involving the homologs Mer2/ZmPRD3 and HOP1/ZmASY1, thus indicating that the process of tethering DSBs in chromatin loops to the chromosome axes may be evolutionarily conserved in diverse taxa.
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Affiliation(s)
- Yan Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Shu-Yue Li
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Ya-Zhong Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
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10
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Damm E, Odenthal-Hesse L. Orchestrating recombination initiation in mice and men. Curr Top Dev Biol 2022; 151:27-42. [PMID: 36681473 DOI: 10.1016/bs.ctdb.2022.05.001] [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] [Indexed: 01/25/2023]
Abstract
Recent discoveries have advanced our understanding of recombination initiation beyond the placement of double-stranded DNA breaks (DSBs) from germline replication timing to the dynamic reorganization of chromatin, and defined critical players of recombination initiation. This article focuses on recombination initiation in mammals utilizing the PRDM9 protein to orchestrate crucial stages of meiotic recombination initiation by interacting with the local DNA environment and several protein complexes. The Pioneer Complex with the SNF2-type chromatin remodeling enzyme HELLS, exposes PRDM9-bound DNA. At the same time, a Compass-Complex containing EWSR1, CXXC1, CDYL, EHMT2 and PRDM9 facilitates the association of putative hotspot sites in DNA loops with the chromosomal axis where DSB-promoting complexes are located, and DSBs are catalyzed by the SPO11/TOPOVIBL complex. Finally, homology search is facilitated at PRDM9-directed sites by ANKRD31. The Reader-Writer system consists of PRDM9 writing characteristic histone methylation signatures, which are read by ZCWPW1, promoting efficient homology engagement.
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Affiliation(s)
- Elena Damm
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany.
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11
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Ki BS, Shim SH, Park C, Yoo H, La H, Lee OH, Kwon Y, Skalnik DG, Okada Y, Yoon HG, Kim JH, Hong K, Choi Y. Epigenetic regulator Cfp1 safeguards male meiotic progression by regulating meiotic gene expression. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1098-1108. [PMID: 35918532 PMCID: PMC9440128 DOI: 10.1038/s12276-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Meiosis occurs specifically in germ cells to produce sperm and oocytes that are competent for sexual reproduction. Multiple factors are required for successful meiotic entry, progression, and termination. Among them, trimethylation of histone H3 on lysine 4 (H3K4me3), a mark of active transcription, has been implicated in spermatogenesis by forming double-strand breaks (DSBs). However, the role of H3K4me in transcriptional regulation during meiosis remains poorly understood. Here, we reveal that mouse CXXC finger protein 1 (Cfp1), a component of the H3K4 methyltransferase Setd1a/b, is dynamically expressed in differentiating male germ cells and safeguards meiosis by controlling gene expression. Genetic ablation of mouse CFP1 in male germ cells caused complete infertility with failure in prophase I of the 1st meiosis. Mechanistically, CFP1 binds to genes essential for spermatogenesis, and its loss leads to a reduction in H3K4me3 levels and gene expression. Importantly, CFP1 is highly enriched within the promoter/TSS of target genes to elevate H3K4me3 levels and gene expression at the pachytene stage of meiotic prophase I. The most enriched genes were associated with meiosis and homologous recombination during the differentiation of spermatocytes to round spermatids. Therefore, our study establishes a mechanistic link between CFP1-mediated transcriptional control and meiotic progression and might provide an unprecedented genetic basis for understanding human sterility. Details of the role of a protein in the development of sperm cells in mice could lead to new understanding of sterility in men. An international research team led by Youngsok Choi and Kwonho Hong at Konkuk University, Seoul, South Korea, investigated the role of protein Cfp1, which they found to be required for sperm formation in mice. The protein is a component of an enzyme complex that transfers methyl groups (CH3) onto other proteins involved in controlling gene activity. The researchers identified key aspects of the mechanism by which Cfp1 controls the activity of genes essential for sperm formation to proceed normally. Absence of Cfp1 specifically interferes with the process of meiosis, which generates sperm cells containing only one copy of each chromosome instead of the two copies found in other cells.
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Affiliation(s)
- Byeong Seong Ki
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ok-Hee Lee
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - David G Skalnik
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, 113-0032, Japan
| | - Ho-Geun Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea.
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12
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Damm E, Ullrich KK, Amos WB, Odenthal-Hesse L. Evolution of the recombination regulator PRDM9 in minke whales. BMC Genomics 2022; 23:212. [PMID: 35296233 PMCID: PMC8925151 DOI: 10.1186/s12864-022-08305-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Background PRDM9 is a key regulator of meiotic recombination in most metazoans, responsible for reshuffling parental genomes. During meiosis, the PRDM9 protein recognizes and binds specific target motifs via its array of C2H2 zinc-fingers encoded by a rapidly evolving minisatellite. The gene coding for PRDM9 is the only speciation gene identified in vertebrates to date and shows high variation, particularly in the DNA-recognizing positions of the zinc-finger array, within and between species. Across all vertebrate genomes studied for PRDM9 evolution, only one genome lacks variability between repeat types – that of the North Pacific minke whale. This study aims to understand the evolution and diversity of Prdm9 in minke whales, which display the most unusual genome reference allele of Prdm9 so far discovered in mammals. Results Minke whales possess all the features characteristic of PRDM9-directed recombination, including complete KRAB, SSXRD and SET domains and a rapidly evolving array of C2H2-type-Zincfingers (ZnF) with evidence of rapid evolution, particularly at DNA-recognizing positions that evolve under positive diversifying selection. Seventeen novel PRDM9 variants were identified within the Antarctic minke whale species, plus a single distinct PRDM9 variant in Common minke whales – shared across North Atlantic and North Pacific minke whale subspecies boundaries. Conclusion The PRDM9 ZnF array evolves rapidly, in minke whales, with at least one DNA-recognizing position under positive selection. Extensive PRDM9 diversity is observed, particularly in the Antarctic in minke whales. Common minke whales shared a specific Prdm9 allele across subspecies boundaries, suggesting incomplete speciation by the mechanisms associated with PRDM9 hybrid sterility. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08305-1.
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Affiliation(s)
- Elena Damm
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany
| | - Kristian K Ullrich
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany
| | - William B Amos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, August-Thienemann Str. 2, D-24306, Plön, Germany.
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13
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PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2. Proc Natl Acad Sci U S A 2022; 119:2114401119. [PMID: 35217607 PMCID: PMC8892340 DOI: 10.1073/pnas.2114401119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2022] [Indexed: 01/12/2023] Open
Abstract
We take a phylogenetic approach to search for molecular partners of PRDM9, a key meiotic recombination gene, by leveraging the fact that the complete PRDM9 gene has been lost at least 13 times independently in vertebrates. We identify two genes, ZCWPW1 and its paralog ZCWPW2, whose presence or absence across vertebrates is coupled to that of PRDM9. ZCWPW1 was recently shown to be recruited to sites of PRDM9 binding and to aid in the repair of double strand breaks. ZCWPW2 is likely recruited to sites of PRDM9 binding as well; its tight coevolution with PRDM9 across vertebrates suggests that it too plays an important role in mammals and beyond, either in double strand break formation or repair. In most mammals and likely throughout vertebrates, the gene PRDM9 specifies the locations of meiotic double strand breaks; in mice and humans at least, it also aids in their repair. For both roles, many of the molecular partners remain unknown. Here, we take a phylogenetic approach to identify genes that may be interacting with PRDM9 by leveraging the fact that PRDM9 arose before the origin of vertebrates but was lost many times, either partially or entirely—and with it, its role in recombination. As a first step, we characterize PRDM9 domain composition across 446 vertebrate species, inferring at least 13 independent losses. We then use the interdigitation of PRDM9 orthologs across vertebrates to test whether it coevolved with any of 241 candidate genes coexpressed with PRDM9 in mice or associated with recombination phenotypes in mammals. Accounting for the phylogenetic relationship among a subsample of 189 species, we find two genes whose presence and absence is unexpectedly coincident with that of PRDM9: ZCWPW1, which was recently shown to facilitate double strand break repair, and its paralog ZCWPW2, as well as, more tentatively, TEX15 and FBXO47. ZCWPW2 is expected to be recruited to sites of PRDM9 binding; its tight coevolution with PRDM9 across vertebrates suggests that it is a key interactor within mammals and beyond, with a role either in recruiting the recombination machinery or in double strand break repair.
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14
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:ijms23031072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Correspondence: ; Tel.: +49-(0)381-494-5879; Fax: +49-(0)381-494-5882
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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15
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Xie C, Wang W, Tu C, Meng L, Lu G, Lin G, Lu LY, Tan YQ. OUP accepted manuscript. Hum Reprod Update 2022; 28:763-797. [PMID: 35613017 DOI: 10.1093/humupd/dmac024] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/18/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chunbo Xie
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Weili Wang
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
| | - Chaofeng Tu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lanlan Meng
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Guangxiu Lu
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ge Lin
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lin-Yu Lu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Women's Reproductive Health Laboratory of Zhejiang Province, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yue-Qiu Tan
- Institute of Reproduction and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, Central South University, Changsha, China
- College of Life Sciences, Hunan Normal University, Changsha, China
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16
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Alleva B, Brick K, Pratto F, Huang M, Camerini-Otero RD. Cataloging Human PRDM9 Allelic Variation Using Long-Read Sequencing Reveals PRDM9 Population Specificity and Two Distinct Groupings of Related Alleles. Front Cell Dev Biol 2021; 9:675286. [PMID: 34805134 PMCID: PMC8600002 DOI: 10.3389/fcell.2021.675286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
The PRDM9 protein determines sites of meiotic recombination in humans by directing meiotic DNA double-strand breaks to specific loci. Targeting specificity is encoded by a long array of C2H2 zinc fingers that bind to DNA. This zinc finger array is hypervariable, and the resulting alleles each have a potentially different DNA binding preference. The assessment of PRDM9 diversity is important for understanding the complexity of human population genetics, inheritance linkage patterns, and predisposition to genetic disease. Due to the repetitive nature of the PRDM9 zinc finger array, the large-scale sequencing of human PRDM9 is challenging. We, therefore, developed a long-read sequencing strategy to infer the diploid PRDM9 zinc finger array genotype in a high-throughput manner. From an unbiased study of PRDM9 allelic diversity in 720 individuals from seven human populations, we detected 69 PRDM9 alleles. Several alleles differ in frequency among human populations, and 32 alleles had not been identified by previous studies, which were heavily biased to European populations. PRDM9 alleles are distinguished by their DNA binding site preferences and fall into two major categories related to the most common PRDM9-A and PRDM9-C alleles. We also found that it is likely that inter-conversion between allele types is rare. By mapping meiotic double-strand breaks (DSBs) in the testis, we found that small variations in PRDM9 can substantially alter the meiotic recombination landscape, demonstrating that minor PRDM9 variants may play an under-appreciated role in shaping patterns of human recombination. In summary, our data greatly expands knowledge of PRDM9 diversity in humans.
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Affiliation(s)
- Benjamin Alleva
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kevin Brick
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Florencia Pratto
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Mini Huang
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rafael Daniel Camerini-Otero
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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17
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Qu W, Liu C, Xu YT, Xu YM, Luo MC. The formation and repair of DNA double-strand breaks in mammalian meiosis. Asian J Androl 2021; 23:572-579. [PMID: 34708719 PMCID: PMC8577251 DOI: 10.4103/aja202191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) are necessary for meiosis in mammals. A sufficient number of DSBs ensure the normal pairing/synapsis of homologous chromosomes. Abnormal DSB repair undermines meiosis, leading to sterility in mammals. The DSBs that initiate recombination are repaired as crossovers and noncrossovers, and crossovers are required for correct chromosome separation. Thus, the placement, timing, and frequency of crossover formation must be tightly controlled. Importantly, mutations in many genes related to the formation and repair of DSB result in infertility in humans. These mutations cause nonobstructive azoospermia in men, premature ovarian insufficiency and ovarian dysgenesis in women. Here, we have illustrated the formation and repair of DSB in mammals, summarized major factors influencing the formation of DSB and the theories of crossover regulation.
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Affiliation(s)
- Wei Qu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Cong Liu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ting Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Min Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Meng-Cheng Luo
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
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18
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Powers NR, Billings T, Paigen K, Petkov PM. Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudomodularity. Genetics 2021; 219:6385243. [PMID: 34747456 DOI: 10.1093/genetics/iyab172] [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: 09/02/2021] [Accepted: 09/30/2021] [Indexed: 11/14/2022] Open
Abstract
PRDM9 is a DNA-binding histone methyltransferase that designates and activates recombination hotspots in mammals by locally trimethylating lysines 4 and 36 of histone H3. In mice, we recently reported two independently produced point mutations at the same residue, Glu360Pro (Prdm9EP) and Glu360Lys (Prdm9EK), which severely reduce its H3K4 and H3K36 methyltransferase activities in vivo. Prdm9EP is slightly less hypomorphic than Prdm9EK, but both mutations reduce both the number and amplitude of PRDM9-dependent H3K4me3 and H3K36me3 peaks in spermatocytes. While both mutations cause infertility with complete meiotic arrest in males, Prdm9EP, but not Prdm9EK, is compatible with some female fertility. When we tested the effects of these mutations in vitro, both Prdm9EP and Prdm9EK abolished H3K4 and H3K36 methyltransferase activity in full-length PRDM9. However, in the isolated PRDM9 PR/SET domain, these mutations selectively compromised H3K36 methyltransferase activity, while leaving H3K4 methyltransferase activity intact. The difference in these effects on the PR/SET domain vs the full-length protein shows that PRDM9 is not an intrinsically modular enzyme; its catalytic domain is influenced by its tertiary structure and possibly by its interactions with DNA and other proteins in vivo. These two informative mutations illuminate the enzymatic chemistry of PRDM9, and potentially of PR/SET domains in general, reveal the minimal threshold of PRDM9-dependent catalytic activity for female fertility, and potentially have some practical utility for genetic mapping and genomics.
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19
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Yang Y, Yang Y, Chan K, Couture JF. Analyzing the impact of CFP1 mutational landscape on epigenetic signaling. FASEB J 2021; 35:e21790. [PMID: 34320252 DOI: 10.1096/fj.202100427r] [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: 03/11/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/11/2022]
Abstract
CXXC Zinc finger protein 1 (CFP1) is a multitasking protein playing essential roles during various developmental processes. Its ability to interact with several proteins contribute to several epigenetic events. Here, we review CFP1's functions and its impact on DNA methylation and the post-translational modification of histone proteins such as lysine acetylation and methylation. We will also discuss the potential role of CFP1 in carcinogenesis and the impact of the mutations identified in patients suffering from various cancers.
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Affiliation(s)
- Yidai Yang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Yaqing Yang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kin Chan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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20
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Schield DR, Pasquesi GIM, Perry BW, Adams RH, Nikolakis ZL, Westfall AK, Orton RW, Meik JM, Mackessy SP, Castoe TA. Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9. Mol Biol Evol 2021; 37:1272-1294. [PMID: 31926008 DOI: 10.1093/molbev/msaa003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions-a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions-a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | | | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX.,Department of Computer & Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
| | | | | | - Richard W Orton
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
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21
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Tian H, Billings T, Petkov PM. EWSR1 affects PRDM9-dependent histone 3 methylation and provides a link between recombination hotspots and the chromosome axis protein REC8. Mol Biol Cell 2021; 32:1-14. [PMID: 33175657 PMCID: PMC8098819 DOI: 10.1091/mbc.e20-09-0604] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022] Open
Abstract
Meiotic recombination in most mammals requires recombination hotspot activation through the action of the histone 3 Lys-4 and Lys-36 methyltransferase PRDM9 to ensure successful double-strand-break initiation and repair. Here we show that EWSR1, a protein whose role in meiosis was not previously clarified in detail, binds to both PRDM9 and pREC8, a phosphorylated meiosis-specific cohesin, in male meiotic cells. We created a Ewsr1 conditional knockout mouse model to deplete EWSR1 before the onset of meiosis and found that absence of EWSR1 causes meiotic arrest with decreased histone trimethylation at meiotic hotspots, impaired DNA double-strand-break repair, and reduced crossover number. Our results demonstrate that EWSR1 is essential for promoting PRDM9-dependent histone methylation and normal meiotic progress, possibly by facilitating the linking between PRDM9-bound hotspots and the nascent chromosome axis through its component cohesin pREC8.
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Affiliation(s)
- Hui Tian
- The Jackson Laboratory, Bar Harbor, ME 04609
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22
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Wang JJ, Ge W, Zhai QY, Liu JC, Sun XW, Liu WX, Li L, Lei CZ, Dyce PW, De Felici M, Shen W. Single-cell transcriptome landscape of ovarian cells during primordial follicle assembly in mice. PLoS Biol 2020; 18:e3001025. [PMID: 33351795 PMCID: PMC7787681 DOI: 10.1371/journal.pbio.3001025] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/06/2021] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
Primordial follicle assembly in the mouse occurs during perinatal ages and largely determines the ovarian reserve that will be available to support the reproductive life span. The development of primordial follicles is controlled by a complex network of interactions between oocytes and ovarian somatic cells that remain poorly understood. In the present research, using single-cell RNA sequencing performed over a time series on murine ovaries, coupled with several bioinformatics analyses, the complete dynamic genetic programs of germ and granulosa cells from E16.5 to postnatal day (PD) 3 were reported. Along with confirming the previously reported expression of genes by germ cells and granulosa cells, our analyses identified 5 distinct cell clusters associated with germ cells and 6 with granulosa cells. Consequently, several new genes expressed at significant levels at each investigated stage were assigned. By building single-cell pseudotemporal trajectories, 3 states and 1 branch point of fate transition for the germ cells were revealed, as well as for the granulosa cells. Moreover, Gene Ontology (GO) term enrichment enabled identification of the biological process most represented in germ cells and granulosa cells or common to both cell types at each specific stage, and the interactions of germ cells and granulosa cells basing on known and novel pathway were presented. Finally, by using single-cell regulatory network inference and clustering (SCENIC) algorithm, we were able to establish a network of regulons that can be postulated as likely candidates for sustaining germ cell-specific transcription programs throughout the period of investigation. Above all, this study provides the whole transcriptome landscape of ovarian cells and unearths new insights during primordial follicle assembly in mice.
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Affiliation(s)
- Jun-Jie Wang
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Ge
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Qiu-Yue Zhai
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jing-Cai Liu
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Wen Sun
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wen-Xiang Liu
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lan Li
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chu-Zhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Paul W. Dyce
- Department of Animal Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Massimo De Felici
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Wei Shen
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, China
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23
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Imai Y, Biot M, Clément JA, Teragaki M, Urbach S, Robert T, Baudat F, Grey C, de Massy B. PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment. eLife 2020; 9:57117. [PMID: 33047671 PMCID: PMC7599071 DOI: 10.7554/elife.57117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) at specific genomic locations that correspond to PRDM9-binding sites. The molecular steps occurring from PRDM9 binding to DSB formation are unknown. Using proteomic approaches to find PRDM9 partners, we identified HELLS, a member of the SNF2-like family of chromatin remodelers. Upon functional analyses during mouse male meiosis, we demonstrated that HELLS is required for PRDM9 binding and DSB activity at PRDM9 sites. However, HELLS is not required for DSB activity at PRDM9-independent sites. HELLS is also essential for 5-hydroxymethylcytosine (5hmC) enrichment at PRDM9 sites. Analyses of 5hmC in mice deficient for SPO11, which catalyzes DSB formation, and in PRDM9 methyltransferase deficient mice reveal that 5hmC is triggered at DSB-prone sites upon PRDM9 binding and histone modification, but independent of DSB activity. These findings highlight the complex regulation of the chromatin and epigenetic environments at PRDM9-specified hotspots.
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Affiliation(s)
- Yukiko Imai
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Mathilde Biot
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Julie Aj Clément
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Mariko Teragaki
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Thomas Robert
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Corinne Grey
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique, Univ Montpellier, Montpellier, France
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24
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Fujiwara Y, Horisawa-Takada Y, Inoue E, Tani N, Shibuya H, Fujimura S, Kariyazono R, Sakata T, Ohta K, Araki K, Okada Y, Ishiguro KI. Meiotic cohesins mediate initial loading of HORMAD1 to the chromosomes and coordinate SC formation during meiotic prophase. PLoS Genet 2020; 16:e1009048. [PMID: 32931493 PMCID: PMC7518614 DOI: 10.1371/journal.pgen.1009048] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 09/25/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022] Open
Abstract
During meiotic prophase, sister chromatids are organized into axial element (AE), which underlies the structural framework for the meiotic events such as meiotic recombination and homolog synapsis. HORMA domain-containing proteins (HORMADs) localize along AE and play critical roles in the regulation of those meiotic events. Organization of AE is attributed to two groups of proteins: meiotic cohesins REC8 and RAD21L; and AE components SYCP2 and SYCP3. It has been elusive how these chromosome structural proteins contribute to the chromatin loading of HORMADs prior to AE formation. Here we newly generated Sycp2 null mice and showed that initial chromatin loading of HORMAD1 was mediated by meiotic cohesins prior to AE formation. HORMAD1 interacted not only with the AE components SYCP2 and SYCP3 but also with meiotic cohesins. Notably, HORMAD1 interacted with meiotic cohesins even in Sycp2-KO, and localized along cohesin axial cores independently of the AE components SYCP2 and SYCP3. Hormad1/Rad21L-double knockout (dKO) showed more severe defects in the formation of synaptonemal complex (SC) compared to Hormad1-KO or Rad21L-KO. Intriguingly, Hormad1/Rec8-dKO but not Hormad1/Rad21L-dKO showed precocious separation of sister chromatid axis. These findings suggest that meiotic cohesins REC8 and RAD21L mediate chromatin loading and the mode of action of HORMAD1 for synapsis during early meiotic prophase.
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Affiliation(s)
- Yasuhiro Fujiwara
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuki Horisawa-Takada
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Erina Inoue
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Naoki Tani
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Hiroki Shibuya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Sayoko Fujimura
- Liaison Laboratory Research Promotion Center, IMEG, Kumamoto University, Kumamoto, Japan
| | - Ryo Kariyazono
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Toyonori Sakata
- Laboratory of Genome Structure and Function, the Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis & Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Yuki Okada
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kei-ichiro Ishiguro
- Department of Chromosome Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Chuo-ku, Kumamoto, Japan
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25
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Mahgoub M, Paiano J, Bruno M, Wu W, Pathuri S, Zhang X, Ralls S, Cheng X, Nussenzweig A, Macfarlan TS. Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice. eLife 2020; 9:e53360. [PMID: 32352380 PMCID: PMC7237205 DOI: 10.7554/elife.53360] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/29/2020] [Indexed: 12/14/2022] Open
Abstract
Meiotic crossovers result from homology-directed repair of DNA double-strand breaks (DSBs). Unlike yeast and plants, where DSBs are generated near gene promoters, in many vertebrates DSBs are enriched at hotspots determined by the DNA binding activity of the rapidly evolving zinc finger array of PRDM9 (PR domain zinc finger protein 9). PRDM9 subsequently catalyzes tri-methylation of lysine 4 and lysine 36 of Histone H3 in nearby nucleosomes. Here, we identify the dual histone methylation reader ZCWPW1, which is tightly co-expressed during spermatogenesis with Prdm9, as an essential meiotic recombination factor required for efficient repair of PRDM9-dependent DSBs and for pairing of homologous chromosomes in male mice. In sum, our results indicate that the evolution of a dual histone methylation writer/reader (PRDM9/ZCWPW1) system in vertebrates remodeled genetic recombination hotspot selection from an ancestral static pattern near genes towards a flexible pattern controlled by the rapidly evolving DNA binding activity of PRDM9.
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Affiliation(s)
- Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIHBethesdaUnited States
- Immunology Graduate Group, University of PennsylvaniaPhiladelphiaUnited States
| | - Melania Bruno
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIHBethesdaUnited States
| | - Sarath Pathuri
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Sherry Ralls
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIHBethesdaUnited States
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
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26
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Jiang Y, Zhang HY, Lin Z, Zhu YZ, Yu C, Sha QQ, Tong MH, Shen L, Fan HY. CXXC finger protein 1-mediated histone H3 lysine-4 trimethylation is essential for proper meiotic crossover formation in mice. Development 2020; 147:dev183764. [PMID: 32094118 DOI: 10.1242/dev.183764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/14/2020] [Indexed: 12/20/2022]
Abstract
The most significant feature of meiosis is the recombination process during prophase I. CXXC finger protein 1 (CXXC1) binds to CpG islands and mediates the deposition of H3K4me3 by the SETD1 complex. CXXC1 is also predicted to recruit H3K4me3-marked regions to the chromosome axis for the generation of double-strand breaks (DSBs) in the prophase of meiosis. Therefore, we deleted Cxxc1 before the onset of meiosis with Stra8-Cre The conditional knockout mice were completely sterile with spermatogenesis arrested at MII. Knockout of Cxxc1 led to a decrease in the H3K4me3 level from the pachytene to the MII stage and caused transcriptional disorder. Many spermatogenesis pathway genes were expressed early leading to abnormal acrosome formation in arrested MII cells. In meiotic prophase, deletion of Cxxc1 caused delayed DSB repair and improper crossover formation in cells at the pachytene stage, and more than half of the diplotene cells exhibited precocious homologous chromosome segregation in both male and female meiosis. Cxxc1 deletion also led to a significant decrease of H3K4me3 enrichment at DMC1-binding sites, which might compromise DSB generation. Taken together, our results show that CXXC1 is essential for proper meiotic crossover formation in mice and suggest that CXXC1-mediated H3K4me3 plays an essential role in meiotic prophase of spermatogenesis and oogenesis.
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Affiliation(s)
- Yu Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hui-Ying Zhang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Zhen Lin
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chao Yu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qian-Qian Sha
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ming-Han Tong
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
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27
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Yang Y, Joshi M, Takahashi YH, Ning Z, Qu Q, Brunzelle JS, Skiniotis G, Figeys D, Shilatifard A, Couture JF. A non-canonical monovalent zinc finger stabilizes the integration of Cfp1 into the H3K4 methyltransferase complex COMPASS. Nucleic Acids Res 2020; 48:421-431. [PMID: 31724694 PMCID: PMC7145517 DOI: 10.1093/nar/gkz1037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/16/2019] [Accepted: 10/24/2019] [Indexed: 12/28/2022] Open
Abstract
COMPlex ASsociating with SET1 (COMPASS) is a histone H3 Lys-4 methyltransferase that typically marks the promoter region of actively transcribed genes. COMPASS is a multi-subunit complex in which the catalytic unit, SET1, is required for H3K4 methylation. An important subunit known to regulate SET1 methyltransferase activity is the CxxC zinc finger protein 1 (Cfp1). Cfp1 binds to COMPASS and is critical to maintain high level of H3K4me3 in cells but the mechanisms underlying its stimulatory activity is poorly understood. In this study, we show that Cfp1 only modestly activates COMPASS methyltransferase activity in vitro. Binding of Cfp1 to COMPASS is in part mediated by a new type of monovalent zinc finger (ZnF). This ZnF interacts with the COMPASS's subunits RbBP5 and disruption of this interaction blunts its methyltransferase activity in cells and in vivo. Collectively, our studies reveal that a novel form of ZnF on Cfp1 enables its integration into COMPASS and contributes to epigenetic signaling.
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Affiliation(s)
- Yidai Yang
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Monika Joshi
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Yoh-hei Takahashi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Zhibin Ning
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Qianhui Qu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph S Brunzelle
- Northwestern Synchrotron Research Centers, Life Science Collaborative Access Team, Northwestern University, Evanston, IL, USA
| | - Georgios Skiniotis
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Figeys
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jean-François Couture
- Shanghai Institute of Materia Medica-University of Ottawa Joint Research Centre on Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology , University of Ottawa, Ottawa , ON K1H 8M5 , Canada
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28
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Al Chiblak M, Steinbeck F, Thiesen HJ, Lorenz P. DUF3669, a "domain of unknown function" within ZNF746 and ZNF777, oligomerizes and contributes to transcriptional repression. BMC Mol Cell Biol 2019; 20:60. [PMID: 31856708 PMCID: PMC6923878 DOI: 10.1186/s12860-019-0243-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
Background ZNF746 and ZNF777 belong to a subset of the large Krüppel-associated box (KRAB) zinc finger (ZNF) transcription factor family. They contain, like four other members in human, an additional conserved domain, the “domain of unknown function 3669” (DUF3669). Previous work on members of this subfamily suggested involvement in transcriptional regulation and aberrant ZNF746 overexpression leads to neuronal cell death in Parkinson’s disease. Results Here we demonstrate that N-terminal protein segments of the ZNF746a major isoform and ZNF777 act in concert to exert moderate transcriptional repression activities. Full potency depended on the intact configuration consisting of DUF3669, a variant KRAB domain and adjacent sequences. While DUF3669 contributes an intrinsic weak inhibitory activity, the isolated KRAB-AB domains did not repress. Importantly, DUF3669 provides a novel protein-protein interaction interface and mediates direct physical interaction between the members of the subfamily in oligomers. The ZNF746 protein segment encoded by exons 5 and 6 boosted repressor potency, potentially due to the presence of an acceptor lysine for sumoylation at K189. Repressor activity of the potent canonical ZNF10 KRAB domain was not augmented by heterologous transfer of DUF3669, pointing to the importance of context for DUF3669’s impact on transcription. Neither ZNF746a nor ZNF777 protein segments stably associated with TRIM28 within cells. Isoform ZNF746b that contains, unlike the major isoform, a full-length KRAB-A subdomain, displayed substantially increased repressor potency. This increase is due to canonical mechanisms known for KRAB domains since it did not take place in HAP1 knockout models of TRIM28 and SETDB1. A glycine to glutamic acid replacement that complies with a bona fide conserved “MLE” sequence within KRAB-A led to a further strong gain in repressor potency to levels comparable to those of the canonical ZNF10 KRAB domain. Each gain of repressive activity was accompanied by an enhanced interaction with TRIM28 protein. Conclusion DUF3669 adds a protein-protein interaction surface to a subgroup of KRAB-ZNF proteins within an N-terminal configuration with variant KRAB and adjacent sequences likely regulated by sumoylation. DUF3669 contributes to transcriptional repression strength and its homo- and hetero-oligomerization characteristics probably extended the regulatory repertoire of KRAB-ZNF transcription factors during amniote evolution.
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Affiliation(s)
- Mohannad Al Chiblak
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Felix Steinbeck
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Hans-Jürgen Thiesen
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Peter Lorenz
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany.
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29
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Allali-Hassani A, Szewczyk MM, Ivanochko D, Organ SL, Bok J, Ho JSY, Gay FPH, Li F, Blazer L, Eram MS, Halabelian L, Dilworth D, Luciani GM, Lima-Fernandes E, Wu Q, Loppnau P, Palmer N, Talib SZA, Brown PJ, Schapira M, Kaldis P, O'Hagan RC, Guccione E, Barsyte-Lovejoy D, Arrowsmith CH, Sanders JM, Kattar SD, Bennett DJ, Nicholson B, Vedadi M. Discovery of a chemical probe for PRDM9. Nat Commun 2019; 10:5759. [PMID: 31848333 PMCID: PMC6917776 DOI: 10.1038/s41467-019-13652-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC50: 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.
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Affiliation(s)
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Shawna L Organ
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence P H Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Qin Wu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore (NUS), Department of Biochemistry, 117597, Singapore, Singapore
| | - Ronan C O'Hagan
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Nature Research Center, Vilnius, Akademijos, 2, Lithuania
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - John M Sanders
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Solomon D Kattar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | | | - Benjamin Nicholson
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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30
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Bruno M, Mahgoub M, Macfarlan TS. The Arms Race Between KRAB–Zinc Finger Proteins and Endogenous Retroelements and Its Impact on Mammals. Annu Rev Genet 2019; 53:393-416. [DOI: 10.1146/annurev-genet-112618-043717] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nearly half of the human genome consists of endogenous retroelements (EREs) and their genetic remnants, a small fraction of which carry the potential to propagate in the host genome, posing a threat to genome integrity and cell/organismal survival. The largest family of transcription factors in tetrapods, the Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs), binds to specific EREs and represses their transcription. Since their first appearance over 400 million years ago, KRAB-ZFPs have undergone dramatic expansion and diversification in mammals, correlating with the invasions of new EREs. In this article we review our current understanding of the structure, function, and evolution of KRAB-ZFPs and discuss growing evidence that the arms race between KRAB-ZFPs and the EREs they target is a major driving force for the evolution of new traits in mammals, often accompanied by domestication of EREs themselves.
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Affiliation(s)
- Melania Bruno
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mohamed Mahgoub
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Todd S. Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland 20892, USA
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31
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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32
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Advances Towards How Meiotic Recombination Is Initiated: A Comparative View and Perspectives for Plant Meiosis Research. Int J Mol Sci 2019; 20:ijms20194718. [PMID: 31547623 PMCID: PMC6801837 DOI: 10.3390/ijms20194718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Meiosis is an essential cell-division process for ensuring genetic diversity across generations. Meiotic recombination ensures the accuracy of genetic interchange between homolous chromosomes and segregation of parental alleles. Programmed DNA double-strand breaks (DSBs), catalyzed by the evolutionarily conserved topoisomerase VIA (a subunit of the archaeal type II DNA topoisomerase)-like enzyme Spo11 and several other factors, is a distinctive feature of meiotic recombination initiation. The meiotic DSB formation and its regulatory mechanisms are similar among species, but certain aspects are distinct. In this review, we introduced the cumulative knowledge of the plant proteins crucial for meiotic DSB formation and technical advances in DSB detection. We also summarized the genome-wide DSB hotspot profiles for different model organisms. Moreover, we highlighted the classical views and recent advances in our knowledge of the regulatory mechanisms that ensure the fidelity of DSB formation, such as multifaceted kinase-mediated phosphorylation and the consequent high-dimensional changes in chromosome structure. We provided an overview of recent findings concerning DSB formation, distribution and regulation, all of which will help us to determine whether meiotic DSB formation is evolutionarily conserved or varies between plants and other organisms.
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Helleboid P, Heusel M, Duc J, Piot C, Thorball CW, Coluccio A, Pontis J, Imbeault M, Turelli P, Aebersold R, Trono D. The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification. EMBO J 2019; 38:e101220. [PMID: 31403225 PMCID: PMC6745500 DOI: 10.15252/embj.2018101220] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 01/24/2023] Open
Abstract
Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) are encoded in the hundreds by the genomes of higher vertebrates, and many act with the heterochromatin-inducing KAP1 as repressors of transposable elements (TEs) during early embryogenesis. Yet, their widespread expression in adult tissues and enrichment at other genetic loci indicate additional roles. Here, we characterized the protein interactome of 101 of the ~350 human KZFPs. Consistent with their targeting of TEs, most KZFPs conserved up to placental mammals essentially recruit KAP1 and associated effectors. In contrast, a subset of more ancient KZFPs rather interacts with factors related to functions such as genome architecture or RNA processing. Nevertheless, KZFPs from coelacanth, our most distant KZFP-encoding relative, bind the cognate KAP1. These results support a hypothetical model whereby KZFPs first emerged as TE-controlling repressors, were continuously renewed by turnover of their hosts' TE loads, and occasionally produced derivatives that escaped this evolutionary flushing by development and exaptation of novel functions.
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Affiliation(s)
| | - Moritz Heusel
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Julien Duc
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Cécile Piot
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Christian W Thorball
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Coluccio
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Julien Pontis
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Michaël Imbeault
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Priscilla Turelli
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Didier Trono
- School of Life SciencesEcole Polytechnique Fédérale de LausanneLausanneSwitzerland
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Bolcun-Filas E, Handel MA. Meiosis: the chromosomal foundation of reproduction. Biol Reprod 2019; 99:112-126. [PMID: 29385397 DOI: 10.1093/biolre/ioy021] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/23/2018] [Indexed: 12/14/2022] Open
Abstract
Meiosis is the chromosomal foundation of reproduction, with errors in this important process leading to aneuploidy and/or infertility. In this review celebrating the 50th anniversary of the founding of the Society for the Study of Reproduction, the important chromosomal structures and dynamics contributing to genomic integrity across generations are highlighted. Critical unsolved biological problems are identified, and the advances that will lead to their ultimate resolution are predicted.
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Schwarz T, Striedner Y, Horner A, Haase K, Kemptner J, Zeppezauer N, Hermann P, Tiemann-Boege I. PRDM9 forms a trimer by interactions within the zinc finger array. Life Sci Alliance 2019; 2:2/4/e201800291. [PMID: 31308055 PMCID: PMC6643046 DOI: 10.26508/lsa.201800291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 11/24/2022] Open
Abstract
PRDM9 forms a trimer as a soluble protein and in complex with DNA mediated by the ZnF domain. Five ZnFs are already sufficient for multimerization and only one DNA molecule is complexed in the trimer. PRDM9 is a trans-acting factor directing meiotic recombination to specific DNA-binding sites by its zinc finger (ZnF) array. It was suggested that PRDM9 is a multimer; however, we do not know the stoichiometry or the components inducing PRDM9 multimerization. In this work, we used in vitro binding studies and characterized with electrophoretic mobility shift assays, mass spectrometry, and fluorescence correlation spectroscopy the stoichiometry of the PRDM9 multimer of two different murine PRDM9 alleles carrying different tags and domains produced with different expression systems. Based on the migration distance of the PRDM9–DNA complex, we show that PRDM9 forms a trimer. Moreover, this stoichiometry is adapted already by the free, soluble protein with little exchange between protein monomers. The variable ZnF array of PRDM9 is sufficient for multimerization, and at least five ZnFs form already a functional trimer. Finally, we also show that only one ZnF array within the PRDM9 oligomer binds to the DNA, whereas the remaining two ZnF arrays likely maintain the trimer by ZnF–ZnF interactions.
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Affiliation(s)
- Theresa Schwarz
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Karin Haase
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Jasmin Kemptner
- Red Cross Blood Transfusion Center Upper Austria, MedCampus II, Johannes Kepler University, Linz, Austria
| | | | - Philipp Hermann
- Institute of Applied Statistics, Johannes Kepler University, Linz, Austria
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36
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Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1. Biochem J 2019; 476:1957-1973. [PMID: 31253666 DOI: 10.1042/bcj20190091] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023]
Abstract
Saccharomyces cerevisiae Spp1, a plant homeodomain (PHD) finger containing protein, is a critical subunit of the histone H3K4 methyltransferase complex of proteins associated with Set1 (COMPASS). The chromatin binding affinity of the PHD finger of Spp1 has been proposed to modulate COMPASS activity. During meiosis, Spp1 plays another role in promoting programmed double-strand break (DSB) formation by binding H3K4me3 via its PHD finger and interacting with a DSB protein, Mer2. However, how the Spp1 PHD finger performs site-specific readout of H3K4me3 is still not fully understood. In the present study, we determined the crystal structure of the highly conserved Spp1 N-terminal domain (Sc_Spp1NTD) in complex with the H3K4me3 peptide. The structure shows that Sc_Spp1NTD comprises a PHD finger responsible for methylated H3K4 recognition and a C3H-type zinc finger necessary to ensure the overall structural stability. Our isothermal titration calorimetry results show that binding of H3K4me3 to Sc_Spp1NTD is mildly inhibited by H3R2 methylation, weakened by H3T6 phosphorylation, and abrogated by H3T3 phosphorylation. This histone modification cross-talk, which is conserved in the Saccharomyces pombe and mammalian orthologs of Sc_Spp1 in vitro, can be rationalized structurally and might contribute to the roles of Spp1 in COMPASS activity regulation and meiotic recombination.
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Jung M, Wells D, Rusch J, Ahmad S, Marchini J, Myers SR, Conrad DF. Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. eLife 2019; 8:e43966. [PMID: 31237565 PMCID: PMC6615865 DOI: 10.7554/elife.43966] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.
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Affiliation(s)
- Min Jung
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Daniel Wells
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Jannette Rusch
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Suhaira Ahmad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Jonathan Marchini
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Donald F Conrad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
- Division of Genetics, Oregon National Primate Research CenterOregon Health & Science UniversityPortlandUnited States
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38
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Mihola O, Pratto F, Brick K, Linhartova E, Kobets T, Flachs P, Baker CL, Sedlacek R, Paigen K, Petkov PM, Camerini-Otero RD, Trachtulec Z. Histone methyltransferase PRDM9 is not essential for meiosis in male mice. Genome Res 2019; 29:1078-1086. [PMID: 31186301 PMCID: PMC6633264 DOI: 10.1101/gr.244426.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 06/07/2019] [Indexed: 01/03/2023]
Abstract
A hallmark of meiosis is the rearrangement of parental alleles to ensure genetic diversity in the gametes. These chromosome rearrangements are mediated by the repair of programmed DNA double-strand breaks (DSBs) as genetic crossovers between parental homologs. In mice, humans, and many other mammals, meiotic DSBs occur primarily at hotspots, determined by sequence-specific binding of the PRDM9 protein. Without PRDM9, meiotic DSBs occur near gene promoters and other functional sites. Studies in a limited number of mouse strains showed that functional PRDM9 is required to complete meiosis, but despite its apparent importance, Prdm9 has been repeatedly lost across many animal lineages. Both the reason for mouse sterility in the absence of PRDM9 and the mechanism by which Prdm9 can be lost remain unclear. Here, we explore whether mice can tolerate the loss of Prdm9. By generating Prdm9 functional knockouts in an array of genetic backgrounds, we observe a wide range of fertility phenotypes and ultimately demonstrate that PRDM9 is not required for completion of male meiosis. Although DSBs still form at a common subset of functional sites in all mice lacking PRDM9, meiotic outcomes differ substantially. We speculate that DSBs at functional sites are difficult to repair as a crossover and that by increasing the efficiency of crossover formation at these sites, genetic modifiers of recombination rates can allow for meiotic progression. This model implies that species with a sufficiently high recombination rate may lose Prdm9 yet remain fertile.
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Affiliation(s)
- Ondrej Mihola
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Florencia Pratto
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kevin Brick
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Eliska Linhartova
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Tatyana Kobets
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Flachs
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Christopher L Baker
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Kenneth Paigen
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Petko M Petkov
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - R Daniel Camerini-Otero
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Zdenek Trachtulec
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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40
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Hinch AG, Zhang G, Becker PW, Moralli D, Hinch R, Davies B, Bowden R, Donnelly P. Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm. Science 2019; 363:eaau8861. [PMID: 30898902 PMCID: PMC6445350 DOI: 10.1126/science.aau8861] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023]
Abstract
Recombination is critical to meiosis and evolution, yet many aspects of the physical exchange of DNA via crossovers remain poorly understood. We report an approach for single-cell whole-genome DNA sequencing by which we sequenced 217 individual hybrid mouse sperm, providing a kilobase-resolution genome-wide map of crossovers. Combining this map with molecular assays measuring stages of recombination, we identified factors that affect crossover probability, including PRDM9 binding on the non-initiating template homolog and telomere proximity. These factors also influence the time for sites of recombination-initiating DNA double-strand breaks to find and engage their homologs, with rapidly engaging sites more likely to form crossovers. We show that chromatin environment on the template homolog affects positioning of crossover breakpoints. Our results also offer insights into recombination in the pseudoautosomal region.
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Affiliation(s)
| | - Gang Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Philipp W Becker
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daniela Moralli
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Robert Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Big Data Institute, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Department of Statistics, University of Oxford, Oxford, UK
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Bhattacharyya T, Walker M, Powers NR, Brunton C, Fine AD, Petkov PM, Handel MA. Prdm9 and Meiotic Cohesin Proteins Cooperatively Promote DNA Double-Strand Break Formation in Mammalian Spermatocytes. Curr Biol 2019; 29:1002-1018.e7. [PMID: 30853435 PMCID: PMC6544150 DOI: 10.1016/j.cub.2019.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/20/2018] [Accepted: 02/01/2019] [Indexed: 11/19/2022]
Abstract
Meiotic recombination is required for correct segregation of chromosomes to gametes and to generate genetic diversity. In mice and humans, DNA double-strand breaks (DSBs) are initiated by SPO11 at recombination hotspots activated by PRDM9-catalyzed histone modifications on open chromatin. However, the DSB-initiating and repair proteins are associated with a linear proteinaceous scaffold called the chromosome axis, the core of which is composed of cohesin proteins. STAG3 is a stromalin subunit common to all meiosis-specific cohesin complexes. Mutations of meiotic cohesin proteins, especially STAG3, perturb both axis formation and recombination in the mouse, prompting determination of how the processes are mechanistically related. Protein interaction and genetic analyses revealed that PRDM9 interacts with STAG3 and REC8 in cooperative relationships that promote normal levels of meiotic DSBs at recombination hotspots in spermatocytes. The efficacy of the Prdm9-Stag3 genetic interaction in promoting DSB formation depends on PRDM9-mediated histone methyltransferase activity. Moreover, STAG3 deficiency has a major effect on DSB number even in the absence of PRDM9, showing that its role is not restricted to canonical PRDM9-activated hotspots. STAG3 and REC8 promote axis localization of the DSB-promoting proteins HORMAD1, IHO1, and MEI4, as well as SPO11 activity. These results establish that PRDM9 and axis-associated cohesin complexes together coordinate and facilitate meiotic recombination by recruiting key proteins for initiation of DSBs, thereby associating activated hotspots with DSB-initiating complexes on the axis.
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Affiliation(s)
| | | | | | | | - Alexander D Fine
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | | | - Mary Ann Handel
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
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42
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Marand AP, Zhao H, Zhang W, Zeng Z, Fang C, Jiang J. Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice. THE PLANT CELL 2019; 31:645-662. [PMID: 30705136 PMCID: PMC6482639 DOI: 10.1105/tpc.18.00750] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/28/2019] [Indexed: 05/15/2023]
Abstract
Recombination plays an integral role in the creation of novel genetic variation in sexually reproducing species. Despite this important role, the determinants and evolution of crossover hotspots have remained poorly understood in plants. Here, we present a comparative analysis of two rice (Oryza sativa) historical recombination maps from two subspecies (indica and japonica) using 150 resequenced genomes. Fine-scale recombination rates and crossover hotspots were validated by comparison with a consensus genetic map and empirically derived crossovers, respectively. Strikingly, nearly 80% of crossover hotspots were unique to each subspecies, despite their relatively recent divergence and broad-scale correlated recombination rates. Crossover hotspots were enriched with Stowaway and P instability factor (PIF)/Harbinger transposons and overlapped accessible chromatin regions. Increased nucleotide diversity and signatures of population differentiation augmented by Stowaway and PIF/Harbinger transposons were prevalent at subspecies-specific crossover hotspots. Motifs derived from lineage-specific indica and japonica crossover hotspots were nearly identical in the two subspecies, implicating a core set of crossover motifs in rice. Finally, Stowaway and PIF/Harbinger transposons were associated with stabilized G/C bias within highly active hotspots, suggesting that hotspot activity can be fueled by de novo variation. These results provide evolutionary insight into historical crossover hotspots as potentially powerful drivers of sequence and subspecies evolution in plants.
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Affiliation(s)
- Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Chao Fang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
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43
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Chen CP, Chang SY, Lin CJ, Chern SR, Wu PS, Chen SW, Lai ST, Chuang TY, Chen WL, Yang CW, Wang W. Prenatal diagnosis of a familial 5p14.3-p14.1 deletion encompassing CDH18, CDH12, PMCHL1, PRDM9 and CDH10 in a fetus with congenital heart disease on prenatal ultrasound. Taiwan J Obstet Gynecol 2019; 57:734-738. [PMID: 30342662 DOI: 10.1016/j.tjog.2018.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2018] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of a familial 5p14.3-p14.1 deletion in a fetus with congenital heart disease on prenatal ultrasound. CASE REPORT A 33-year-old woman underwent amniocentesis at 18 weeks of gestation because of fetal ventricular septal defect (VSD) and echogenic bowel on prenatal ultrasound. Amniocentesis revealed a karyotype of 46,XX,del (5) (p14p14). Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed a 5.589-Mb 5p14.3-p14.1 deletion or arr 5p14.3p14.1 (19, 497, 649-25,086,268) × 1.0 [GRCh37 (hg19)] encompassing CDH18, CDH12, PMCHL1, PRDM9 and CDH10. Cytogenetic and aCGH analyses of the parents showed that the phenotypically normal mother carried the 5p14.3-p14.1 deletion. The father did not have such a deletion. The parents elected to continue the pregnancy, and a 3426-g female baby was delivered at 38 weeks of gestation with no gross abnormalities. The infant postnatally manifested VSD, atrial septal defect and patent ductus areriosus, and underwent cardiac surgery to treat the congenital heart disease. When follow-up at age 1 year and 4 months, she had a body weight of 8.8 Kg (50th-75th centile), a body height of 75.6 cm (85th-95th centile) and normal psychomotor development. CONCLUSION Fetuses with a 5p14.3-p14.1 deletion may present congenital heart disease on prenatal ultrasound, and aCGH is helpful for prenatal diagnosis under such a circumstance.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Shu-Yuan Chang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chen-Ju Lin
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wen-Lin Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chien-Wen Yang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Interhomolog polymorphism shapes meiotic crossover within the Arabidopsis RAC1 and RPP13 disease resistance genes. PLoS Genet 2018; 14:e1007843. [PMID: 30543623 PMCID: PMC6307820 DOI: 10.1371/journal.pgen.1007843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 12/27/2018] [Accepted: 11/20/2018] [Indexed: 12/11/2022] Open
Abstract
During meiosis, chromosomes undergo DNA double-strand breaks (DSBs), which can be repaired using a homologous chromosome to produce crossovers. Meiotic recombination frequency is variable along chromosomes and tends to concentrate in narrow hotspots. We mapped crossover hotspots located in the Arabidopsis thaliana RAC1 and RPP13 disease resistance genes, using varying haplotypic combinations. We observed a negative non-linear relationship between interhomolog divergence and crossover frequency within the hotspots, consistent with polymorphism locally suppressing crossover repair of DSBs. The fancm, recq4a recq4b, figl1 and msh2 mutants, or lines with increased HEI10 dosage, are known to show increased crossovers throughout the genome. Surprisingly, RAC1 crossovers were either unchanged or decreased in these genetic backgrounds, showing that chromosome location and local chromatin environment are important for regulation of crossover activity. We employed deep sequencing of crossovers to examine recombination topology within RAC1, in wild type, fancm, recq4a recq4b and fancm recq4a recq4b backgrounds. The RAC1 recombination landscape was broadly conserved in the anti-crossover mutants and showed a negative relationship with interhomolog divergence. However, crossovers at the RAC1 5'-end were relatively suppressed in recq4a recq4b backgrounds, further indicating that local context may influence recombination outcomes. Our results demonstrate the importance of interhomolog divergence in shaping recombination within plant disease resistance genes and crossover hotspots.
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45
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Tian H, Billings T, Petkov PM. CXXC1 is not essential for normal DNA double-strand break formation and meiotic recombination in mouse. PLoS Genet 2018; 14:e1007657. [PMID: 30365547 PMCID: PMC6221362 DOI: 10.1371/journal.pgen.1007657] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/07/2018] [Accepted: 08/24/2018] [Indexed: 12/28/2022] Open
Abstract
In most mammals, including mice and humans, meiotic recombination is determined by the meiosis specific histone methytransferase PRDM9, which binds to specific DNA sequences and trimethylates histone 3 at lysine-4 and lysine-36 at the adjacent nucleosomes. These actions ensure successful DNA double strand break formation and repair that occur on the proteinaceous structure forming the chromosome axis. The process of hotspot association with the axis after their activation by PRDM9 is poorly understood. Previously, we and others have identified CXXC1, an ortholog of S. cerevisiae Spp1 in mammals, as a PRDM9 interactor. In yeast, Spp1 is a histone methyl reader that links H3K4me3 sites with the recombination machinery, promoting DSB formation. Here, we investigated whether CXXC1 has a similar function in mouse meiosis. We created two Cxxc1 conditional knockout mouse models to deplete CXXC1 generally in germ cells, and before the onset of meiosis. Surprisingly, male knockout mice were fertile, and the loss of CXXC1 in spermatocytes had no effect on PRDM9 hotspot trimethylation, double strand break formation or repair. Our results demonstrate that CXXC1 is not an essential link between PRDM9-activated recombination hotspot sites and DSB machinery and that the hotspot recognition pathway in mouse is independent of CXXC1. Meiotic recombination increases genetic diversity by ensuring novel combination of alleles passing correctly to the next generation. In most mammals, the meiotic recombination sites are determined by histone methyltransferase PRDM9. These sites are proposed to become associated with the chromosome axis with the participation of additional proteins and undergo double strand breaks, which are repaired by homologous recombination. In budding yeast, Spp1 (ortholog of CXXC1) binds to methylated H3K4 and connects these sites with the chromosome axis promoting DSB formation. However, our data suggest that even though CXXC1 interacts with PRDM9 in male germ cells, it does not play a crucial role in mouse meiotic recombination. These results indicate that, unlike in yeast, a recombination initiation pathway that includes CXXC1 could only serve as a non-essential pathway in mouse meiosis.
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Affiliation(s)
- Hui Tian
- The Jackson Laboratory, Bar Harbor, ME 04609, United States of America
| | - Timothy Billings
- The Jackson Laboratory, Bar Harbor, ME 04609, United States of America
| | - Petko M. Petkov
- The Jackson Laboratory, Bar Harbor, ME 04609, United States of America
- * E-mail:
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46
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Houle AA, Gibling H, Lamaze FC, Edgington HA, Soave D, Fave MJ, Agbessi M, Bruat V, Stein LD, Awadalla P. Aberrant PRDM9 expression impacts the pan-cancer genomic landscape. Genome Res 2018; 28:1611-1620. [PMID: 30341163 PMCID: PMC6211651 DOI: 10.1101/gr.231696.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/04/2018] [Indexed: 12/15/2022]
Abstract
The binding of PRDM9 to chromatin is a key step in the induction of DNA double-strand breaks associated with meiotic recombination hotspots; it is normally expressed solely in germ cells. We interrogated 1879 cancer samples in 39 different cancer types and found that PRDM9 is unexpectedly expressed in 20% of these tumors even after stringent gene homology correction. The expression levels of PRDM9 in tumors are significantly higher than those found in healthy neighboring tissues and in healthy nongerm tissue databases. Recurrently mutated regions located within 5 Mb of the PRDM9 loci, as well as differentially expressed genes in meiotic pathways, correlate with PRDM9 expression. In samples with aberrant PRDM9 expression, structural variant breakpoints frequently neighbor the DNA motif recognized by PRDM9, and there is an enrichment of structural variants at sites of known meiotic PRDM9 activity. This study is the first to provide evidence of an association between aberrant expression of the meiosis-specific gene PRDM9 with genomic instability in cancer.
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Affiliation(s)
- Armande Ang Houle
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Heather Gibling
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Fabien C Lamaze
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Hilary A Edgington
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Marie-Julie Fave
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Mawusse Agbessi
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Vanessa Bruat
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
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47
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Abstract
During meiosis, maternal and paternal chromosomes undergo exchanges by homologous recombination. This is essential for fertility and contributes to genome evolution. In many eukaryotes, sites of meiotic recombination, also called hotspots, are regions of accessible chromatin, but in many vertebrates, their location follows a distinct pattern and is specified by PR domain-containing protein 9 (PRDM9). The specification of meiotic recombination hotspots is achieved by the different activities of PRDM9: DNA binding, histone methyltransferase, and interaction with other proteins. Remarkably, PRDM9 activity leads to the erosion of its own binding sites and the rapid evolution of its DNA-binding domain. PRDM9 may also contribute to reproductive isolation, as it is involved in hybrid sterility potentially due to a reduction of its activity in specific heterozygous contexts.
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Affiliation(s)
- Corinne Grey
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Frédéric Baudat
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Bernard de Massy
- Institut de Génétique Humaine, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
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48
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Lukaszewicz A, Lange J, Keeney S, Jasin M. Control of meiotic double-strand-break formation by ATM: local and global views. Cell Cycle 2018; 17:1155-1172. [PMID: 29963942 PMCID: PMC6110601 DOI: 10.1080/15384101.2018.1464847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/19/2018] [Accepted: 04/08/2018] [Indexed: 10/28/2022] Open
Abstract
DNA double-strand breaks (DSBs) generated by the SPO11 protein initiate meiotic recombination, an essential process for successful chromosome segregation during gametogenesis. The activity of SPO11 is controlled by multiple factors and regulatory mechanisms, such that the number of DSBs is limited and DSBs form at distinct positions in the genome and at the right time. Loss of this control can affect genome integrity or cause meiotic arrest by mechanisms that are not fully understood. Here we focus on the DSB-responsive kinase ATM and its functions in regulating meiotic DSB numbers and distribution. We review the recently discovered roles of ATM in this context, discuss their evolutionary conservation, and examine future research perspectives.
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Affiliation(s)
- Agnieszka Lukaszewicz
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Tiemann-Boege I, Schwarz T, Striedner Y, Heissl A. The consequences of sequence erosion in the evolution of recombination hotspots. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0462. [PMID: 29109225 PMCID: PMC5698624 DOI: 10.1098/rstb.2016.0462] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
Meiosis is initiated by a double-strand break (DSB) introduced in the DNA by a highly controlled process that is repaired by recombination. In many organisms, recombination occurs at specific and narrow regions of the genome, known as recombination hotspots, which overlap with regions enriched for DSBs. In recent years, it has been demonstrated that conversions and mutations resulting from the repair of DSBs lead to a rapid sequence evolution at recombination hotspots eroding target sites for DSBs. We still do not fully understand the effect of this erosion in the recombination activity, but evidence has shown that the binding of trans-acting factors like PRDM9 is affected. PRDM9 is a meiosis-specific, multi-domain protein that recognizes DNA target motifs by its zinc finger domain and directs DSBs to these target sites. Here we discuss the changes in affinity of PRDM9 to eroded recognition sequences, and explain how these changes in affinity of PRDM9 can affect recombination, leading sometimes to sterility in the context of hybrid crosses. We also present experimental data showing that DNA methylation reduces PRDM9 binding in vitro. Finally, we discuss PRDM9-independent hotspots, posing the question how these hotspots evolve and change with sequence erosion. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.
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Affiliation(s)
- Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Theresa Schwarz
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Yasmin Striedner
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
| | - Angelika Heissl
- Institute of Biophysics, Johannes Kepler University, Linz, Gruberstraße 40, 4020 Linz, Austria
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50
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Abstract
Homologous recombination is required for proper segregation of homologous chromosomes during meiosis. It occurs predominantly at recombination hotspots that are defined by the DNA binding specificity of the PRDM9 protein. PRDM9 contains three conserved domains typically involved in regulation of transcription; yet, the role of PRDM9 in gene expression control is not clear. Here, we analyze the germline transcriptome of Prdm9−/− male mice in comparison to Prdm9+/+ males and find no apparent differences in the mRNA and miRNA profiles. We further explore the role of PRDM9 in meiosis by analyzing the effect of the KRAB, SSXRD, and post-SET zinc finger deletions in a cell culture expression system and the KRAB domain deletion in mice. We found that although the post-SET zinc finger and the KRAB domains are not essential for the methyltransferase activity of PRDM9 in cell culture, the KRAB domain mutant mice show only residual PRDM9 methyltransferase activity and undergo meiotic arrest. In aggregate, our data indicate that domains typically involved in regulation of gene expression do not serve that role in PRDM9, but are likely involved in setting the proper chromatin environment for initiation and completion of homologous recombination.
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