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Genestier A, Duret L, Lartillot N. Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis: A model based exploration of the PRDM9 intra-genomic Red Queen. PLoS Genet 2024; 20:e1011274. [PMID: 38768268 PMCID: PMC11142677 DOI: 10.1371/journal.pgen.1011274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/31/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Molecular dissection of meiotic recombination in mammals, combined with population-genetic and comparative studies, have revealed a complex evolutionary dynamic characterized by short-lived recombination hotspots. Hotspots are chromosome positions containing DNA sequences where the protein PRDM9 can bind and cause crossing-over. To explain these fast evolutionary dynamic, a so-called intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hotspot extinction (the hotspot conversion paradox), followed by positive selection favoring mutant PRDM9 alleles recognizing new sequence motifs. Although this model predicts many empirical observations, the exact causes of the positive selection acting on new PRDM9 alleles is still not well understood. In this direction, experiment on mouse hybrids have suggested that, in addition to targeting double strand breaks, PRDM9 has another role during meiosis. Specifically, PRDM9 symmetric binding (simultaneous binding at the same site on both homologues) would facilitate homology search and, as a result, the pairing of the homologues. Although discovered in hybrids, this second function of PRDM9 could also be involved in the evolutionary dynamic observed within populations. To address this point, here, we present a theoretical model of the evolutionary dynamic of meiotic recombination integrating current knowledge about the molecular function of PRDM9. Our modeling work gives important insights into the selective forces driving the turnover of recombination hotspots. Specifically, the reduced symmetrical binding of PRDM9 caused by the loss of high affinity binding sites induces a net positive selection eliciting new PRDM9 alleles recognizing new targets. The model also offers new insights about the influence of the gene dosage of PRDM9, which can paradoxically result in negative selection on new PRDM9 alleles entering the population, driving their eviction and thus reducing standing variation at this locus.
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Affiliation(s)
- Alice Genestier
- Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, France
| | - Laurent Duret
- Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, France
| | - Nicolas Lartillot
- Universite Claude Bernard Lyon 1, LBBE, UMR 5558, CNRS, VAS, Villeurbanne, France
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2
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Marín-García C, Álvarez-González L, Marín-Gual L, Casillas S, Picón J, Yam K, Garcias-Ramis MM, Vara C, Ventura J, Ruiz-Herrera A. Multiple Genomic Landscapes of Recombination and Genomic Divergence in Wild Populations of House Mice-The Role of Chromosomal Fusions and Prdm9. Mol Biol Evol 2024; 41:msae063. [PMID: 38513632 PMCID: PMC10991077 DOI: 10.1093/molbev/msae063] [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: 11/06/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Chromosomal fusions represent one of the most common types of chromosomal rearrangements found in nature. Yet, their role in shaping the genomic landscape of recombination and hence genome evolution remains largely unexplored. Here, we take advantage of wild mice populations with chromosomal fusions to evaluate the effect of this type of structural variant on genomic landscapes of recombination and divergence. To this aim, we combined cytological analysis of meiotic crossovers in primary spermatocytes with inferred analysis of recombination rates based on linkage disequilibrium using single nucleotide polymorphisms. Our results suggest the presence of a combined effect of Robertsonian fusions and Prdm9 allelic background, a gene involved in the formation of meiotic double strand breaks and postzygotic reproductive isolation, in reshaping genomic landscapes of recombination. We detected a chromosomal redistribution of meiotic recombination toward telomeric regions in metacentric chromosomes in mice with Robertsonian fusions when compared to nonfused mice. This repatterning was accompanied by increased levels of crossover interference and reduced levels of estimated recombination rates between populations, together with high levels of genomic divergence. Interestingly, we detected that Prdm9 allelic background was a major determinant of recombination rates at the population level, whereas Robertsonian fusions showed limited effects, restricted to centromeric regions of fused chromosomes. Altogether, our results provide new insights into the effect of Robertsonian fusions and Prdm9 background on meiotic recombination.
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Affiliation(s)
- Cristina Marín-García
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Lucía Álvarez-González
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Sònia Casillas
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Judith Picón
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Keren Yam
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - María Magdalena Garcias-Ramis
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Covadonga Vara
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Small Mammals Research Unit, Granollers Museum of Natural Sciences, Granollers 08402, Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Barcelona, Spain
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Ding X, Gong X, Fan Y, Cao J, Zhao J, Zhang Y, Wang X, Meng K. DNA double-strand break genetic variants in patients with premature ovarian insufficiency. J Ovarian Res 2023; 16:135. [PMID: 37430352 DOI: 10.1186/s13048-023-01221-2] [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: 09/10/2022] [Accepted: 06/20/2023] [Indexed: 07/12/2023] Open
Abstract
Premature ovarian insufficiency (POI) is a clinically heterogeneous disease that may seriously affect the physical and mental health of women of reproductive age. POI primarily manifests as ovarian function decline and endocrine disorders in women prior to age 40 and is an established cause of female infertility. It is crucial to elucidate the causative factors of POI, not only to expand the understanding of ovarian physiology, but also to provide genetic counselling and fertility guidance to affected patients. Factors leading to POI are multifaceted with genetic factors accounting for 7% to 30%. In recent years, an increasing number of DNA damage-repair-related genes have been linked with the occurrence of POI. Among them, DNA double-strand breaks (DSBs), one of the most damaging to DNA, and its main repair methods including homologous recombination (HR) and non-homologous end joining (NHEJ) are of particular interest. Numerous genes are known to be involved in the regulation of programmed DSB formation and damage repair. The abnormal expression of several genes have been shown to trigger defects in the overall repair pathway and induce POI and other diseases. This review summarises the DSB-related genes that may contribute to the development of POI and their potential regulatory mechanisms, which will help to further establish role of DSB in the pathogenesis of POI and provide theoretical guidance for the study of the pathogenesis and clinical treatment of this disease.
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Affiliation(s)
- Xuechun Ding
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Xiaowei Gong
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Yingying Fan
- Affiliated Hospital of Jining Medical University, Jining, China
| | - Jinghe Cao
- Affiliated Hospital of Jining Medical University, Jining, China
| | - Jingyu Zhao
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Yixin Zhang
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
- College of Second Clinical Medical, Jining Medical University, Jining, China
| | - Xiaomei Wang
- College of Basic Medicine, Jining Medical University, Jining, China.
| | - Kai Meng
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China.
- Lin He's Academician Workstation of New Medicine and Clinical Translation, Jining Medical University, Jining, China.
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Giannattasio T, Testa E, Palombo R, Chellini L, Franceschini F, Crevenna Á, Petkov PM, Paronetto MP, Barchi M. The RNA-binding protein FUS/TLS interacts with SPO11 and PRDM9 and localize at meiotic recombination hotspots. Cell Mol Life Sci 2023; 80:107. [PMID: 36967403 PMCID: PMC10040399 DOI: 10.1007/s00018-023-04744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
In mammals, meiotic recombination is initiated by the introduction of DNA double strand breaks (DSBs) into narrow segments of the genome, defined as hotspots, which is carried out by the SPO11/TOPOVIBL complex. A major player in the specification of hotspots is PRDM9, a histone methyltransferase that, following sequence-specific DNA binding, generates trimethylation on lysine 4 (H3K4me3) and lysine 36 (H3K36me3) of histone H3, thus defining the hotspots. PRDM9 activity is key to successful meiosis, since in its absence DSBs are redirected to functional sites and synapsis between homologous chromosomes fails. One protein factor recently implicated in guiding PRDM9 activity at hotspots is EWS, a member of the FET family of proteins that also includes TAF15 and FUS/TLS. Here, we demonstrate that FUS/TLS partially colocalizes with PRDM9 on the meiotic chromosome axes, marked by the synaptonemal complex component SYCP3, and physically interacts with PRDM9. Furthermore, we show that FUS/TLS also interacts with REC114, one of the axis-bound SPO11-auxiliary factors essential for DSB formation. This finding suggests that FUS/TLS is a component of the protein complex that promotes the initiation of meiotic recombination. Accordingly, we document that FUS/TLS coimmunoprecipitates with SPO11 in vitro and in vivo. The interaction occurs with both SPO11β and SPO11α splice isoforms, which are believed to play distinct functions in the formation of DSBs in autosomes and male sex chromosomes, respectively. Finally, using chromatin immunoprecipitation experiments, we show that FUS/TLS is localized at H3K4me3-marked hotspots in autosomes and in the pseudo-autosomal region, the site of genetic exchange between the XY chromosomes.
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Affiliation(s)
- Teresa Giannattasio
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Erika Testa
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Ramona Palombo
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy
| | - Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy
| | - Flavia Franceschini
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy
| | - Álvaro Crevenna
- European Molecular Biology Laboratory, Neurobiology and Epigenetics Unit, Monterotondo, Italy
| | | | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, CERC, 00143, Rome, Italy.
- Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 6, 00135, Rome, Italy.
| | - Marco Barchi
- University of Rome "Tor Vergata", Section of Anatomy, Via Montpellier, 1, 00133, Rome, Italy.
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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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Billiard S, Castric V, Llaurens V. The integrative biology of genetic dominance. Biol Rev Camb Philos Soc 2021; 96:2925-2942. [PMID: 34382317 PMCID: PMC9292577 DOI: 10.1111/brv.12786] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022]
Abstract
Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype‐to‐phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross‐talk among research fields in the integrative study of dominance evolution.
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Affiliation(s)
- Sylvain Billiard
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Vincent Castric
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | - Violaine Llaurens
- Institut de Systématique, Evolution et Biodiversité, CNRS/MNHN/Sorbonne Université/EPHE, Museum National d'Histoire Naturelle, CP50, 57 rue Cuvier, 75005, Paris, France
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Wang Y, Guo T, Ke H, Zhang Q, Li S, Luo W, Qin Y. Pathogenic variants of meiotic double strand break (DSB) formation genes PRDM9 and ANKRD31 in premature ovarian insufficiency. Genet Med 2021; 23:2309-2315. [PMID: 34257419 PMCID: PMC8629753 DOI: 10.1038/s41436-021-01266-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose The etiology of premature ovarian insufficiency (POI) is heterogeneous, and genetic factors account for 20–25% of the patients. The primordial follicle pool is determined by the meiosis process, which is initiated by programmed DNA double strand breaks (DSB) and homologous recombination. The objective of the study is to explore the role of DSB formation genes in POI pathogenesis. Methods Variants in DSB formation genes were analyzed from a database of exome sequencing in 1,030 patients with POI. The pathogenic effects of the potentially causative variants were verified by further functional studies. Results Three pathogenic heterozygous variants in PRDM9 and two in ANKRD31 were identified in seven patients. Functional studies showed the variants in PRDM9 impaired its methyltransferase activity, and the ANKRD31 variations disturbed its interaction with another DSB formation factor REC114 by haploinsufficiency effect, indicating the pathogenic effects of the two genes on ovarian function were dosage dependent. Conclusion Our study identified pathogenic variants of PRDM9 and ANKRD31 in POI patients, shedding new light on the contribution of meiotic DSB formation genes in ovarian development, further expanding the genetic architecture of POI.
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Affiliation(s)
- Yiyang Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Ting Guo
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Hanni Ke
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Qian Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Shan Li
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Wei Luo
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China.,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China
| | - Yingying Qin
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, Shandong, China. .,Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China. .,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, Shandong, China.
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Mihola O, Landa V, Pratto F, Brick K, Kobets T, Kusari F, Gasic S, Smagulova F, Grey C, Flachs P, Gergelits V, Tresnak K, Silhavy J, Mlejnek P, Camerini-Otero RD, Pravenec M, Petukhova GV, Trachtulec Z. Rat PRDM9 shapes recombination landscapes, duration of meiosis, gametogenesis, and age of fertility. BMC Biol 2021; 19:86. [PMID: 33910563 PMCID: PMC8082845 DOI: 10.1186/s12915-021-01017-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 04/01/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Vertebrate meiotic recombination events are concentrated in regions (hotspots) that display open chromatin marks, such as trimethylation of lysines 4 and 36 of histone 3 (H3K4me3 and H3K36me3). Mouse and human PRDM9 proteins catalyze H3K4me3 and H3K36me3 and determine hotspot positions, whereas other vertebrates lacking PRDM9 recombine in regions with chromatin already opened for another function, such as gene promoters. While these other vertebrate species lacking PRDM9 remain fertile, inactivation of the mouse Prdm9 gene, which shifts the hotspots to the functional regions (including promoters), typically causes gross fertility reduction; and the reasons for these species differences are not clear. RESULTS We introduced Prdm9 deletions into the Rattus norvegicus genome and generated the first rat genome-wide maps of recombination-initiating double-strand break hotspots. Rat strains carrying the same wild-type Prdm9 allele shared 88% hotspots but strains with different Prdm9 alleles only 3%. After Prdm9 deletion, rat hotspots relocated to functional regions, about 40% to positions corresponding to Prdm9-independent mouse hotspots, including promoters. Despite the hotspot relocation and decreased fertility, Prdm9-deficient rats of the SHR/OlaIpcv strain produced healthy offspring. The percentage of normal pachytene spermatocytes in SHR-Prdm9 mutants was almost double than in the PWD male mouse oligospermic sterile mutants. We previously found a correlation between the crossover rate and sperm presence in mouse Prdm9 mutants. The crossover rate of SHR is more similar to sperm-carrying mutant mice, but it did not fully explain the fertility of the SHR mutants. Besides mild meiotic arrests at rat tubular stages IV (mid-pachytene) and XIV (metaphase), we also detected postmeiotic apoptosis of round spermatids. We found delayed meiosis and age-dependent fertility in both sexes of the SHR mutants. CONCLUSIONS We hypothesize that the relative increased fertility of rat versus mouse Prdm9 mutants could be ascribed to extended duration of meiotic prophase I. While rat PRDM9 shapes meiotic recombination landscapes, it is unnecessary for recombination. We suggest that PRDM9 has additional roles in spermatogenesis and speciation-spermatid development and reproductive age-that may help to explain male-specific hybrid sterility.
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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
| | - Vladimir Landa
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Florencia Pratto
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kevin Brick
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tatyana Kobets
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Fitore Kusari
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Srdjan Gasic
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Fatima Smagulova
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, 20814, USA
- Present address: Inserm U1085 IRSET, 35042, Rennes, France
| | - Corinne Grey
- Institut de Génétique Humaine, CNRS UMR 9002, 34396, Montpellier, France
| | - Petr Flachs
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
- Present address: Division BIOCEV, Laboratory of Epigenetics of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Vaclav Gergelits
- Laboratory of Mouse Molecular Genetics, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Karel Tresnak
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220, Prague, Czech Republic
| | - Jan Silhavy
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - R Daniel Camerini-Otero
- National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michal Pravenec
- Laboratory of Genetics of Model Diseases, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Galina V Petukhova
- Department of Biochemistry and Molecular Biology, Uniformed Services University of Health Sciences, Bethesda, MD, 20814, 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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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: 10] [Impact Index Per Article: 3.3] [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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10
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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: 32] [Impact Index Per Article: 8.0] [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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11
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Shen Z, Huang L, Jin S, Zheng Y. Cloning and Expression Analysis of Two Kdm Lysine Demethylases in the Testes of Mature Yaks and Their Sterile Hybrids. Animals (Basel) 2020; 10:ani10030521. [PMID: 32244964 PMCID: PMC7142534 DOI: 10.3390/ani10030521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/08/2020] [Accepted: 03/10/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The hybrid of male cattle (Bos taurus) with female yaks (Bos grunniens) is called the cattle–yak. All female cattle–yaks are fertile, but all males are sterile. To date, there is no clear conclusion on the mechanism leading to cattle–yak male sterility. The domain conservation and expression profiles of lysine histone demethylases (KDMs) suggest that they might play important roles during gametogenesis. The objective of this study was to explore the molecular mechanism for male sterility of yak hybrids based on two demethylases, KDM1A and KDM4B. The mRNA and protein expression of KDM1A and KDM4B were dramatically decreased in the testes of adult cattle–yaks compared with adult yaks. In addition, the level of H3K36me3 in the testes of cattle–yaks was significantly lower than in yaks. These results suggest that the male sterility of cattle–yaks might be associated with reduced histone methylation modifications. These results provide valuable epigenetic information regarding the molecular mechanism resulting in male sterility of cattle–yaks. Abstract The objective of this study was to explore the molecular mechanism for male sterility of yak hybrids based on two demethylases. Total RNA was extracted from the testes of adult yaks (n = 10) and yak hybrids (cattle–yaks, n = 10). The coding sequences (CDS) of two lysine demethylases (KDMs), KDM1A and KDM4B, were cloned by RT-PCR. The levels of KDM1A and KDM4B in yaks and cattle–yaks testes were detected using Real-time PCR and Western blotting for mRNA and protein, respectively. In addition, the histone methylation modifications of H3K36me3 and H3K27me3 were compared between testes of yaks and cattle–yaks using ELISA. The CDS of KDM1A and KDM4B were obtained from yak testes. The results showed that the CDS of KDM1A exhibited two variants: variant 1 has a CDS of 2622 bp, encoding 873 amino acids, while variant 2 has a CDS of 2562 bp, encoding 853 amino acids. The CDS of the KDM4B gene was 3351 bp in length, encoding 1116 amino acids. The mRNA and protein expression of KDM1A and KDM4B, as well as the level of H3K36me3, were dramatically decreased in the testes of cattle–yaks compared with yaks. The present results suggest that the male sterility of cattle–yaks might be associated with reduced histone methylation modifications.
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Affiliation(s)
| | | | | | - Yucai Zheng
- Correspondence: ; Tel.: +86-02885522400; Fax: +86-28-85528039
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12
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Spruce C, Dlamini S, Ananda G, Bronkema N, Tian H, Paigen K, Carter GW, Baker CL. HELLS and PRDM9 form a pioneer complex to open chromatin at meiotic recombination hot spots. Genes Dev 2020; 34:398-412. [PMID: 32001511 PMCID: PMC7050486 DOI: 10.1101/gad.333542.119] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
Abstract
Chromatin barriers prevent spurious interactions between regulatory elements and DNA-binding proteins. One such barrier, whose mechanism for overcoming is poorly understood, is access to recombination hot spots during meiosis. Here we show that the chromatin remodeler HELLS and DNA-binding protein PRDM9 function together to open chromatin at hot spots and provide access for the DNA double-strand break (DSB) machinery. Recombination hot spots are decorated by a unique combination of histone modifications not found at other regulatory elements. HELLS is recruited to hot spots by PRDM9 and is necessary for both histone modifications and DNA accessibility at hot spots. In male mice lacking HELLS, DSBs are retargeted to other sites of open chromatin, leading to germ cell death and sterility. Together, these data provide a model for hot spot activation in which HELLS and PRDM9 form a pioneer complex to create a unique epigenomic environment of open chromatin, permitting correct placement and repair of DSBs.
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Affiliation(s)
| | | | | | | | - Hui Tian
- The Jackson Laboratory, Bar Harbor, Maine 04660, USA
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13
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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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14
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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: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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15
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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: 27] [Impact Index Per Article: 5.4] [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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16
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Kang R, Zelazowski MJ, Cole F. Missing the Mark: PRDM9-Dependent Methylation Is Required for Meiotic DSB Targeting. Mol Cell 2018; 69:725-727. [PMID: 29499130 DOI: 10.1016/j.molcel.2018.02.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
PRDM9 determines the localization of meiotic recombination hotspots, which are associated with histone H3 methylation. It is not known whether PRDM9's methyltransferase activity is required or how some PRDM9 alleles can dominate the distribution of hotspots over other alleles. Diagouraga, Clément, and colleagues (2018) show that methyltransferase activity is required for hotspot localization and that this activity is additive in combination, suggesting that the dominance of particular alleles is simply proportional to the frequency of targeted sites.
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Affiliation(s)
- Rhea Kang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Science Park, Smithville, TX 78957, USA
| | - Maciej J Zelazowski
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA
| | - Francesca Cole
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Science Park, Smithville, TX 78957, USA.
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17
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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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18
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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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19
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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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20
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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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21
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Forsdyke DR. The chromosomal basis of species initiation: Prdm9 as an anti-speciation gene. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON, Canada
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22
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Gregorova S, Gergelits V, Chvatalova I, Bhattacharyya T, Valiskova B, Fotopulosova V, Jansa P, Wiatrowska D, Forejt J. Modulation of Prdm9-controlled meiotic chromosome asynapsis overrides hybrid sterility in mice. eLife 2018. [PMID: 29537370 PMCID: PMC5902161 DOI: 10.7554/elife.34282] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Hybrid sterility is one of the reproductive isolation mechanisms leading to speciation. Prdm9, the only known vertebrate hybrid-sterility gene, causes failure of meiotic chromosome synapsis and infertility in male hybrids that are the offspring of two mouse subspecies. Within species, Prdm9 determines the sites of programmed DNA double-strand breaks (DSBs) and meiotic recombination hotspots. To investigate the relation between Prdm9-controlled meiotic arrest and asynapsis, we inserted random stretches of consubspecific homology on several autosomal pairs in sterile hybrids, and analyzed their ability to form synaptonemal complexes and to rescue male fertility. Twenty-seven or more megabases of consubspecific (belonging to the same subspecies) homology fully restored synapsis in a given autosomal pair, and we predicted that two or more DSBs within symmetric hotspots per chromosome are necessary for successful meiosis. We hypothesize that impaired recombination between evolutionarily diverged chromosomes could function as one of the mechanisms of hybrid sterility occurring in various sexually reproducing species.
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Affiliation(s)
- Sona Gregorova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Vaclav Gergelits
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Irena Chvatalova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Tanmoy Bhattacharyya
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Barbora Valiskova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladana Fotopulosova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Petr Jansa
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Diana Wiatrowska
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
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23
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Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F. PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites. Mol Cell 2018; 69:853-865.e6. [PMID: 29478809 DOI: 10.1016/j.molcel.2018.01.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/09/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.
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Affiliation(s)
| | | | - Laurent Duret
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Jan Kadlec
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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24
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Paigen K, Petkov PM. PRDM9 and Its Role in Genetic Recombination. Trends Genet 2018; 34:291-300. [PMID: 29366606 DOI: 10.1016/j.tig.2017.12.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/14/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022]
Abstract
PRDM9 is a zinc finger protein that binds DNA at specific locations in the genome where it trimethylates histone H3 at lysines 4 and 36 at surrounding nucleosomes. During meiosis in many species, including humans and mice where PRDM9 has been most intensely studied, these actions determine the location of recombination hotspots, where genetic recombination occurs. In addition, PRDM9 facilitates the association of hotspots with the chromosome axis, the site of the programmed DNA double-strand breaks (DSBs) that give rise to genetic exchange between chromosomes. In the absence of PRDM9 DSBs are not properly repaired. Collectively, these actions determine patterns of genetic linkage and the possibilities for chromosome reorganization over successive generations.
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25
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Alves I, Houle AA, Hussin JG, Awadalla P. The impact of recombination on human mutation load and disease. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160465. [PMID: 29109227 PMCID: PMC5698626 DOI: 10.1098/rstb.2016.0465] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Recombination promotes genomic integrity among cells and tissues through double-strand break repair, and is critical for gamete formation and fertility through a strict regulation of the molecular mechanisms associated with proper chromosomal disjunction. In humans, congenital defects and recurrent structural abnormalities can be attributed to aberrant meiotic recombination. Moreover, mutations affecting genes involved in recombination pathways are directly linked to pathologies including infertility and cancer. Recombination is among the most prominent mechanism shaping genome variation, and is associated with not only the structuring of genomic variability, but is also tightly linked with the purging of deleterious mutations from populations. Together, these observations highlight the multiple roles of recombination in human genetics: its ability to act as a major force of evolution, its molecular potential to maintain genome repair and integrity in cell division and its mutagenic cost impacting disease evolution.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)
- Isabel Alves
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
| | - Armande Ang Houle
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
- Department of Molecular Genetics, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Julie G Hussin
- Montreal Heart Institute, Department of Medicine, University of Montreal, 5000 Rue Bélanger, Montréal, Quebec, Canada H1T 1C8
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Philip Awadalla
- Ontario Institute of Cancer Research, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3
- Department of Molecular Genetics, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
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26
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Altemose N, Noor N, Bitoun E, Tumian A, Imbeault M, Chapman JR, Aricescu AR, Myers SR. A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis. eLife 2017; 6:e28383. [PMID: 29072575 PMCID: PMC5705219 DOI: 10.7554/elife.28383] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
PRDM9 binding localizes almost all meiotic recombination sites in humans and mice. However, most PRDM9-bound loci do not become recombination hotspots. To explore factors that affect binding and subsequent recombination outcomes, we mapped human PRDM9 binding sites in a transfected human cell line and measured PRDM9-induced histone modifications. These data reveal varied DNA-binding modalities of PRDM9. We also find that human PRDM9 frequently binds promoters, despite their low recombination rates, and it can activate expression of a small number of genes including CTCFL and VCX. Furthermore, we identify specific sequence motifs that predict consistent, localized meiotic recombination suppression around a subset of PRDM9 binding sites. These motifs strongly associate with KRAB-ZNF protein binding, TRIM28 recruitment, and specific histone modifications. Finally, we demonstrate that, in addition to binding DNA, PRDM9's zinc fingers also mediate its multimerization, and we show that a pair of highly diverged alleles preferentially form homo-multimers.
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Affiliation(s)
- Nicolas Altemose
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Nudrat Noor
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Afidalina Tumian
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Michael Imbeault
- Global Health InstituteÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - J Ross Chapman
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - A Radu Aricescu
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
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27
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Imai Y, Baudat F, Taillepierre M, Stanzione M, Toth A, de Massy B. The PRDM9 KRAB domain is required for meiosis and involved in protein interactions. Chromosoma 2017; 126:681-695. [PMID: 28527011 PMCID: PMC5688218 DOI: 10.1007/s00412-017-0631-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. Here, we show that truncation of the KRAB domain of mouse PRDM9 leads to loss of PRDM9 function and altered meiotic prophase and gametogenesis. In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. We also show that CXXC1 interacts with IHO1, an essential component of the meiotic double-strand break (DSB) machinery. As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis.
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Affiliation(s)
- Yukiko Imai
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France
| | - Frédéric Baudat
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France
| | | | - Marcello Stanzione
- Faculty of Medicine at the TU Dresden, Institute of Physiological Chemistry, Fetscherstraße 74, 01307, Dresden, Germany
| | - Attila Toth
- Faculty of Medicine at the TU Dresden, Institute of Physiological Chemistry, Fetscherstraße 74, 01307, Dresden, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France.
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28
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Striedner Y, Schwarz T, Welte T, Futschik A, Rant U, Tiemann-Boege I. The long zinc finger domain of PRDM9 forms a highly stable and long-lived complex with its DNA recognition sequence. Chromosome Res 2017; 25:155-172. [PMID: 28155083 PMCID: PMC5440498 DOI: 10.1007/s10577-017-9552-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/09/2017] [Accepted: 01/18/2017] [Indexed: 01/23/2023]
Abstract
PR domain containing protein 9 (PRDM9) is a meiosis-specific, multi-domain protein that regulates the location of recombination hotspots by targeting its DNA recognition sequence for double-strand breaks (DSBs). PRDM9 specifically recognizes DNA via its tandem array of zinc fingers (ZnFs), epigenetically marks the local chromatin by its histone methyltransferase activity, and is an important tether that brings the DNA into contact with the recombination initiation machinery. A strong correlation between PRDM9-ZnF variants and specific DNA motifs at recombination hotspots has been reported; however, the binding specificity and kinetics of the ZnF domain are still obscure. Using two in vitro methods, gel mobility shift assays and switchSENSE, a quantitative biophysical approach that measures binding rates in real time, we determined that the PRDM9-ZnF domain forms a highly stable and long-lived complex with its recognition sequence, with a dissociation halftime of many hours. The ZnF domain exhibits an equilibrium dissociation constant (K D) in the nanomolar (nM) range, with polymorphisms in the recognition sequence directly affecting the binding affinity. We also determined that alternative sequences (15-16 nucleotides in length) can be specifically bound by different subsets of the ZnF domain, explaining the binding plasticity of PRDM9 for different sequences. Finally, longer binding targets are preferred than predicted from the numbers of ZnFs contacting the DNA. Functionally, a long-lived complex translates into an enzymatically active PRDM9 at specific DNA-binding sites throughout meiotic prophase I that might be relevant in stabilizing the components of the recombination machinery to a specific DNA target until DSBs are initiated by Spo11.
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Affiliation(s)
- Yasmin Striedner
- 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
| | - Thomas Welte
- Dynamic Biosensors GmbH, 82152, Planegg, Germany
| | - Andreas Futschik
- Department of Applied Statistics, Johannes Kepler University, 4040, Linz, Austria
| | - Ulrich Rant
- Dynamic Biosensors GmbH, 82152, Planegg, Germany
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020, Linz, Austria.
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29
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Parvanov ED, Tian H, Billings T, Saxl RL, Spruce C, Aithal R, Krejci L, Paigen K, Petkov PM. PRDM9 interactions with other proteins provide a link between recombination hotspots and the chromosomal axis in meiosis. Mol Biol Cell 2016; 28:488-499. [PMID: 27932493 PMCID: PMC5341731 DOI: 10.1091/mbc.e16-09-0686] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/28/2016] [Accepted: 11/30/2016] [Indexed: 11/11/2022] Open
Abstract
In mammals, meiotic recombination occurs at 1- to 2-kb genomic regions termed hotspots, whose positions and activities are determined by PRDM9, a DNA-binding histone methyltransferase. We show that the KRAB domain of PRDM9 forms complexes with additional proteins to allow hotspots to proceed into the next phase of recombination. By a combination of yeast-two hybrid assay, in vitro binding, and coimmunoprecipitation from mouse spermatocytes, we identified four proteins that directly interact with PRDM9's KRAB domain, namely CXXC1, EWSR1, EHMT2, and CDYL. These proteins are coexpressed in spermatocytes at the early stages of meiotic prophase I, the limited period when PRDM9 is expressed. We also detected association of PRDM9-bound complexes with the meiotic cohesin REC8 and the synaptonemal complex proteins SYCP3 and SYCP1. Our results suggest a model in which PRDM9-bound hotspot DNA is brought to the chromosomal axis by the action of these proteins, ensuring the proper chromatin and spatial environment for subsequent recombination events.
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Affiliation(s)
- Emil D Parvanov
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609.,Department of Biology, Masaryk University, Brno, Czech Republic 625 00
| | - Hui Tian
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Timothy Billings
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Ruth L Saxl
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Catrina Spruce
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Rakesh Aithal
- Department of Biology, Masaryk University, Brno, Czech Republic 625 00
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno, Czech Republic 625 00 .,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic 625 00
| | - Kenneth Paigen
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
| | - Petko M Petkov
- Center for Genome Dynamics, Jackson Laboratory, Bar Harbor, ME 04609
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30
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Ahlawat S, De S, Sharma P, Sharma R, Arora R, Kataria RS, Datta TK, Singh RK. Evolutionary dynamics of meiotic recombination hotspots regulator PRDM9 in bovids. Mol Genet Genomics 2016; 292:117-131. [DOI: 10.1007/s00438-016-1260-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/11/2016] [Indexed: 12/15/2022]
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31
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The pioneering role of PRDM9 indel mutations in tarsier evolution. Sci Rep 2016; 6:34618. [PMID: 27698394 PMCID: PMC5048142 DOI: 10.1038/srep34618] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/09/2016] [Indexed: 01/01/2023] Open
Abstract
PRDM9 is currently the sole speciation gene found in vertebrates causing hybrid sterility probably due to incompatible alleles. Its role in defining the double strand break loci during the meiotic prophase I is crucial for proper chromosome segregation. Therefore, the rapid turnover of the loci determining zinc finger array seems to be causative for incompatibilities. We here investigated the zinc finger domain-containing exon of PRDM9 in 23 tarsiers. Tarsiers, the most basal extant haplorhine primates, exhibit two frameshifting indels at the 5'-end of the array. The first mutation event interrupts the reading frame and function while the second compensates both. The fixation of this allele variant in tarsiers led to hypothesize that de- and reactivation of the zinc finger domain drove the speciation in early haplorhine or tarsiiform primates. Moreover, the high allelic diversity within Tarsius points to multiple effects of genetic drift reflecting their phylogeographic history since the Miocene.
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32
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Ahlawat S, Sharma P, Sharma R, Arora R, Verma NK, Brahma B, Mishra P, De S. Evidence of positive selection and concerted evolution in the rapidly evolving PRDM9 zinc finger domain in goats and sheep. Anim Genet 2016; 47:740-751. [PMID: 27621101 DOI: 10.1111/age.12487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2016] [Indexed: 01/20/2023]
Abstract
Meiotic recombination contributes to augmentation of genetic diversity, exclusion of deleterious alleles and proper segregation of chromatids. PRDM9 has been identified as the gene responsible for specifying the location of recombination hotspots during meiosis and is also the only known vertebrate gene associated with reproductive isolation between species. PRDM9 encodes a protein with a highly variable zinc finger (ZF) domain that varies between as well as within species. In the present study, the ZF domain of PRDM9 on chromosome 1 was characterized for the first time in 15 goat breeds and 25 sheep breeds of India. A remarkable variation in the number and sequence of ZF domains was observed. The number of ZF repeats in the ZF array varied from eight to 12 yielding five homozygous and 10 heterozygous genotypes. The number of different ZF domains was 84 and 52 producing 36 and 26 unique alleles in goats and sheep respectively. The posterior mean of dN/dS or omega values were calculated using the codeml tool of pamlx to identify amino acids that are evolving positively in goats and sheep, as positions -1, +3 and +6 in the ZF domain have been reported to experience strong positive selection across different lineages. Our study identified sites -5, -1, +3, +4 and +6 to be experiencing positive selection. Small ruminant zinc fingers were also found to be evolving under concerted evolution. Our results demonstrate the existence of a vast diversity of PRDM9 in goats and sheep, which is in concert with reports in many metazoans.
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Affiliation(s)
- S Ahlawat
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - P Sharma
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R Sharma
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - R Arora
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - N K Verma
- National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India
| | - B Brahma
- National Dairy Research Institute, Karnal 132001, Haryana, India
| | - P Mishra
- National Dairy Research Institute, Karnal 132001, Haryana, India
| | - S De
- National Dairy Research Institute, Karnal 132001, Haryana, India
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33
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Zelazowski MJ, Cole F. X marks the spot: PRDM9 rescues hybrid sterility by finding hidden treasure in the genome. Nat Struct Mol Biol 2016; 23:267-9. [PMID: 27045445 DOI: 10.1038/nsmb.3201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Maciej J Zelazowski
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Francesca Cole
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
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34
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Luense LJ, Wang X, Schon SB, Weller AH, Lin Shiao E, Bryant JM, Bartolomei MS, Coutifaris C, Garcia BA, Berger SL. Comprehensive analysis of histone post-translational modifications in mouse and human male germ cells. Epigenetics Chromatin 2016; 9:24. [PMID: 27330565 PMCID: PMC4915177 DOI: 10.1186/s13072-016-0072-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023] Open
Abstract
Background During the process of spermatogenesis, male germ cells undergo dramatic chromatin reorganization, whereby most histones are replaced by protamines, as part of the pathway to compact the genome into the small nuclear volume of the sperm head. Remarkably, approximately 90 % (human) to 95 % (mouse) of histones are evicted during the process. An intriguing hypothesis is that post-translational modifications (PTMs) decorating histones play a critical role in epigenetic regulation of spermatogenesis and embryonic development following fertilization. Although a number of specific histone PTMs have been individually studied during spermatogenesis and in mature mouse and human sperm, to date, there is a paucity of comprehensive identification of histone PTMs and their dynamics during this process. Results Here we report systematic investigation of sperm histone PTMs and their dynamics during spermatogenesis. We utilized “bottom-up” nanoliquid chromatography–tandem mass spectrometry (nano-LC–MS/MS) to identify histone PTMs and to determine their relative abundance in distinct stages of mouse spermatogenesis (meiotic, round spermatids, elongating/condensing spermatids, and mature sperm) and in human sperm. We detected peptides and histone PTMs from all four canonical histones (H2A, H2B, H3, and H4), the linker histone H1, and multiple histone isoforms of H1, H2A, H2B, and H3 in cells from all stages of mouse spermatogenesis and in mouse sperm. We found strong conservation of histone PTMs for histone H3 and H4 between mouse and human sperm; however, little conservation was observed between H1, H2A, and H2B. Importantly, across eight individual normozoospermic human semen samples, little variation was observed in the relative abundance of nearly all histone PTMs. Conclusion In summary, we report the first comprehensive and unbiased analysis of histone PTMs at multiple time points during mouse spermatogenesis and in mature mouse and human sperm. Furthermore, our results suggest a largely uniform histone PTM signature in sperm from individual humans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0072-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lacey J Luense
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Xiaoshi Wang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Samantha B Schon
- Department of Reproductive Endocrinology and Infertility, Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Angela H Weller
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Enrique Lin Shiao
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA.,Biomedical Sciences Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jessica M Bryant
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA.,Biomedical Sciences Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA.,Institute Pasteur, 75724 Paris, France
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Christos Coutifaris
- Department of Reproductive Endocrinology and Infertility, Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104 USA.,Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104 USA
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35
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Patel A, Horton JR, Wilson GG, Zhang X, Cheng X. Structural basis for human PRDM9 action at recombination hot spots. Genes Dev 2016; 30:257-65. [PMID: 26833727 PMCID: PMC4743056 DOI: 10.1101/gad.274928.115] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The multidomain zinc finger (ZnF) protein PRDM9 (PRD1-BF1-RIZ1 homologous domain-containing 9) is thought to influence the locations of recombination hot spots during meiosis by sequence-specific DNA binding and trimethylation of histone H3 Lys4. The most common variant of human PRDM9, allele A (hPRDM9A), recognizes the consensus sequence 5'-NCCNCCNTNNCCNCN-3'. We cocrystallized ZnF8-12 of hPRDM9A with an oligonucleotide representing a known hot spot sequence and report the structure here. ZnF12 was not visible, but ZnF8-11, like other ZnF arrays, follows the right-handed twist of the DNA, with the α helices occupying the major groove. Each α helix makes hydrogen-bond (H-bond) contacts with up to four adjacent bases, most of which are purines of the complementary DNA strand. The consensus C:G base pairs H-bond with conserved His or Arg residues in ZnF8, ZnF9, and ZnF11, and the consensus T:A base pair H-bonds with an Asn that replaces His in ZnF10. Most of the variable base pairs (N) also engage in H bonds with the protein. These interactions appear to compensate to some extent for changes from the consensus sequence, implying an adaptability of PRDM9 to sequence variations. We investigated the binding of various alleles of hPRDM9 to different hot spot sequences. Allele C was found to bind a C-specific hot spot with higher affinity than allele A bound A-specific hot spots, perhaps explaining why the former is dominant in A/C heterozygotes. Allele L13 displayed higher affinity for several A-specific sequences, allele L9/L24 displayed lower affinity, and allele L20 displayed an altered sequence preference. These differences can be rationalized structurally and might contribute to the variation observed in the locations and activities of meiotic recombination hot spots.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - John R Horton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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36
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Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ, Barnes MR, Barnett AH, Bates C, Bellary S, Bockett NA, Giorda K, Griffiths CJ, Hemingway H, Jia Z, Kelly MA, Khawaja HA, Lek M, McCarthy S, McEachan R, O'Donnell-Luria A, Paigen K, Parisinos CA, Sheridan E, Southgate L, Tee L, Thomas M, Xue Y, Schnall-Levin M, Petkov PM, Tyler-Smith C, Maher ER, Trembath RC, MacArthur DG, Wright J, Durbin R, van Heel DA. Health and population effects of rare gene knockouts in adult humans with related parents. Science 2016; 352:474-7. [PMID: 26940866 DOI: 10.1126/science.aac8624] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/18/2016] [Indexed: 12/13/2022]
Abstract
Examining complete gene knockouts within a viable organism can inform on gene function. We sequenced the exomes of 3222 British adults of Pakistani heritage with high parental relatedness, discovering 1111 rare-variant homozygous genotypes with predicted loss of function (knockouts) in 781 genes. We observed 13.7% fewer homozygous knockout genotypes than we expected, implying an average load of 1.6 recessive-lethal-equivalent loss-of-function (LOF) variants per adult. When genetic data were linked to the individuals' lifelong health records, we observed no significant relationship between gene knockouts and clinical consultation or prescription rate. In this data set, we identified a healthy PRDM9-knockout mother and performed phased genome sequencing on her, her child, and control individuals. Our results show that meiotic recombination sites are localized away from PRDM9-dependent hotspots. Thus, natural LOF variants inform on essential genetic loci and demonstrate PRDM9 redundancy in humans.
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Affiliation(s)
| | - Karen A Hunt
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Dan Mason
- Bradford Institute for Health Research, Bradford Teaching Hospitals National Health Service (NHS) Foundation Trust, Bradford BD9 6RJ, UK
| | - Christopher L Baker
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael R Barnes
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Anthony H Barnett
- Diabetes and Endocrine Centre, Heart of England NHS Foundation Trust and University of Birmingham, Birmingham B9 5SS, UK
| | - Chris Bates
- TPP, Mill House, Troy Road, Leeds LS18 5TN, UK
| | - Srikanth Bellary
- Aston Research Centre for Healthy Ageing, Aston University, Birmingham B4 7ET, UK
| | - Nicholas A Bockett
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Kristina Giorda
- 10X Genomics, 7068 Koll Center Parkway, Suite 415, Pleasanton, CA 94566, USA
| | - Christopher J Griffiths
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Harry Hemingway
- Farr Institute of Health Informatics Research, London NW1 2DA, UK. Institute of Health Informatics, University College London, London NW1 2DA, UK
| | - Zhilong Jia
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - M Ann Kelly
- School of Clinical and Experimental Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Hajrah A Khawaja
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shane McCarthy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Rosie McEachan
- Bradford Institute for Health Research, Bradford Teaching Hospitals National Health Service (NHS) Foundation Trust, Bradford BD9 6RJ, UK
| | - Anne O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kenneth Paigen
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Constantinos A Parisinos
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Eamonn Sheridan
- Bradford Institute for Health Research, Bradford Teaching Hospitals National Health Service (NHS) Foundation Trust, Bradford BD9 6RJ, UK
| | - Laura Southgate
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Louise Tee
- School of Clinical and Experimental Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark Thomas
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Petko M Petkov
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | | | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and National Institute for Health Research (NIHR) Cambridge Biomedical Research Centre, Box 238, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK. Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Richard C Trembath
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK. Faculty of Life Sciences and Medicine, King's College London, London SE1 1UL, UK
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals National Health Service (NHS) Foundation Trust, Bradford BD9 6RJ, UK
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - David A van Heel
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
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37
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Hillmer M, Wagner D, Summerer A, Daiber M, Mautner VF, Messiaen L, Cooper DN, Kehrer-Sawatzki H. Fine mapping of meiotic NAHR-associated crossovers causing large NF1 deletions. Hum Mol Genet 2015; 25:484-96. [PMID: 26614388 DOI: 10.1093/hmg/ddv487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023] Open
Abstract
Large deletions encompassing the NF1 gene and its flanking regions belong to the group of genomic disorders caused by copy number changes that are mediated by the local genomic architecture. Although nonallelic homologous recombination (NAHR) is known to be a major mutational mechanism underlying such genomic copy number changes, the sequence determinants of NAHR location and frequency are still poorly understood since few high-resolution mapping studies of NAHR hotspots have been performed to date. Here, we have characterized two NAHR hotspots, PRS1 and PRS2, separated by 20 kb and located within the low-copy repeats NF1-REPa and NF1-REPc, which flank the human NF1 gene region. High-resolution mapping of the crossover sites identified in 78 type 1 NF1 deletions mediated by NAHR indicated that PRS2 is a much stronger NAHR hotspot than PRS1 since 80% of these deletions exhibited crossovers within PRS2, whereas 20% had crossovers within PRS1. The identification of the most common strand exchange regions of these 78 deletions served to demarcate the cores of the PRS1 and PRS2 hotspots encompassing 1026 and 1976 bp, respectively. Several sequence features were identified that may influence hotspot intensity and direct the positional preference of NAHR to the hotspot cores. These features include regions of perfect sequence identity encompassing 700 bp at the hotspot core, the presence of PRDM9 binding sites perfectly matching the consensus motif for the most common PRDM9 variant, specific pre-existing patterns of histone modification and open chromatin conformations that are likely to facilitate PRDM9 binding.
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Affiliation(s)
- Morten Hillmer
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - David Wagner
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Anna Summerer
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Michaela Daiber
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Victor-Felix Mautner
- Department of Neurology, University Hospital Hamburg Eppendorf, 20246 Hamburg, Germany
| | - Ludwine Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35242, USA and
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
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