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Úbeda F, Fyon F, Bürger R. The Recombination Hotspot Paradox: Co-evolution between PRDM9 and its target sites. Theor Popul Biol 2023; 153:69-90. [PMID: 37451508 DOI: 10.1016/j.tpb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
Recombination often concentrates in small regions called recombination hotspots where recombination is much higher than the genome's average. In many vertebrates, including humans, gene PRDM9 specifies which DNA motifs will be the target for breaks that initiate recombination, ultimately determining the location of recombination hotspots. Because the sequence that breaks (allowing recombination) is converted into the sequence that does not break (preventing recombination), the latter sequence is over-transmitted to future generations and recombination hotspots are self-destructive. Given their self-destructive nature, recombination hotspots should eventually become extinct in genomes where they are found. While empirical evidence shows that individual hotspots do become inactive over time (die), hotspots are abundant in many vertebrates: a contradiction called the Recombination Hotspot Paradox. What saves recombination hotspots from their foretold extinction? Here we formulate a co-evolutionary model of the interaction among sequence-specific gene conversion, fertility selection, and recurrent mutation. We find that allelic frequencies oscillate leading to stable limit cycles. From a biological perspective this means that when fertility selection is weaker than gene conversion, it cannot stop individual hotspots from dying but can save them from extinction by driving their re-activation (resuscitation). In our model, mutation balances death and resuscitation of hotspots, thus maintaining their number over evolutionary time. Interestingly, we find that multiple alleles result in oscillations that are chaotic and multiple targets in oscillations that are asynchronous between targets thus helping to maintain the average genomic recombination probability constant. Furthermore, we find that the level of expression of PRDM9 should control for the fraction of targets that are hotspots and the overall temperature of the genome. Therefore, our co-evolutionary model improves our understanding of how hotspots may be replaced, thus contributing to solve the Recombination Hotspot Paradox. From a more applied perspective our work provides testable predictions regarding the relation between mutation probability and fertility selection with life expectancy of hotspots.
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Affiliation(s)
- Francisco Úbeda
- Department of Biology, Royal Holloway University of London, Egham TW20 0EX, UK.
| | - Frédéric Fyon
- Department of Biology, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Reinhard Bürger
- Faculty of Mathematics, University of Vienna, 1090 Vienna, Austria
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Tebar AB, Perez ESM, Nam-Cha SH, Valls AJS, Singh ND, de la Casa-Esperon E. Diet effects on mouse meiotic recombination: a warning for recombination studies. Genetics 2021; 220:6428542. [PMID: 34791205 DOI: 10.1093/genetics/iyab190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Meiotic recombination is a critical process for sexually reproducing organisms. This exchange of genetic information between homologous chromosomes during meiosis is important not only because it generates genetic diversity, but also because it is often required for proper chromosome segregation. Consequently, the frequency and distribution of crossovers are tightly controlled to ensure fertility and offspring viability. However, in many systems it has been shown that environmental factors can alter the frequency of crossover events. Two studies in flies and yeast point to nutritional status affecting the frequency of crossing over. However, this question remains unexplored in mammals. Here we test how crossover frequency varies in response to diet in Mus musculus males. We use immunohistochemistry to estimate crossover frequency in multiple genotypes under two diet treatments. Our results indicate that while crossover frequency was unaffected by diet in some strains, other strains were sensitive even to small composition changes between two common laboratory chows. Therefore, recombination is both resistant and sensitive to certain dietary changes in a strain-dependent manner and, hence, this response is genetically determined. Our study is the first to report a nutrition effect on genome-wide levels of recombination. Moreover, our work highlights the importance of controlling diet in recombination studies and may point to diet as a potential source of variability among studies, which is relevant for reproducibility.
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Affiliation(s)
- Angela Belmonte Tebar
- Regional Center for Biomedical Research (C.R.I.B.). University of Castilla-La Mancha. Albacete, 02008, Spain
| | - Estefania San Martin Perez
- Regional Center for Biomedical Research (C.R.I.B.). University of Castilla-La Mancha. Albacete, 02008, Spain
| | - Syong Hyun Nam-Cha
- Pathology Department and Biobank of Albacete. University Hospital Complex of Albacete. Albacete, 02006, Spain
| | | | - Nadia D Singh
- Department of Biology, Institute of Ecology and Evolution, University of Oregon. Eugene, Oregon 97403, USA
| | - Elena de la Casa-Esperon
- Regional Center for Biomedical Research (C.R.I.B.). University of Castilla-La Mancha. Albacete, 02008, Spain.,School of Pharmacy. University of Castilla-La Mancha. Albacete, 02071, Spain
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Dong M, Li H, Zhang X, Tan J. Weighted Correlation Gene Network Analysis Reveals New Potential Mechanisms and Biomarkers in Non-obstructive Azoospermia. Front Genet 2021; 12:617133. [PMID: 33868362 PMCID: PMC8044582 DOI: 10.3389/fgene.2021.617133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Non-obstructive azoospermia (NOA) denotes a severe form of male infertility, whose etiology is still poorly understood. This is mainly due to limited knowledge on the molecular mechanisms that lead to spermatogenesis failure. In this study, we acquired microarray data from GEO DataSets and identified differentially expressed genes using the limma package in R. We identified 1,261 differentially expressed genes between non-obstructive and obstructive azoospermia. Analysis of their possible biological functions and related signaling pathways using the cluster profiler package revealed an enrichment of genes involved in germ cell development, cilium organization, and oocyte meiosis. Immune infiltration analysis indicated that macrophages were the most significant immune component of NOA, cooperating with mast cells and natural killer cells. The weighted gene coexpression network analysis algorithm generated three related functional modules, which correlated closely with clinical parameters derived from histopathological subtypes of NOA. The resulting data enabled the construction of a protein–protein interaction network of these three modules, with CDK1, CDC20, CCNB1, CCNB2, and MAD2L1 identified as hub genes. This study provides the basis for further investigation of the molecular mechanism underlying NOA, as well as indications about potential biomarkers and therapeutic targets of NOA. Finally, using tissues containing different tissue types for differential expression analysis can reflect the expression differences in different tissues to a certain extent. But this difference in expression is only related and not causal. The specific causality needs to be verified later.
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Affiliation(s)
- Meng Dong
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China.,School of Life Sciences, China Medical University, Shenyang, China
| | - Hao Li
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xue Zhang
- School of Life Sciences, China Medical University, Shenyang, China
| | - Jichun Tan
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China
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Neto FTL, Flannigan R, Goldstein M. Regulation of Human Spermatogenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1288:255-286. [PMID: 34453741 DOI: 10.1007/978-3-030-77779-1_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human spermatogenesis (HS) is an intricate network of sequential processes responsible for the production of the male gamete, the spermatozoon. These processes take place in the seminiferous tubules (ST) of the testis, which are small tubular structures considered the functional units of the testes. Each human testicle contains approximately 600-1200 STs [1], and are capable of producing up to 275 million spermatozoa per day [2].
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Affiliation(s)
| | - Ryan Flannigan
- Department of Urology, Weill Cornell Medicine, New York, NY, USA.,University of British Columbia, Vancouver, BC, Canada
| | - Marc Goldstein
- Department of Urology, Weill Cornell Medicine, New York, NY, USA.
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Lopes AC, Oliveira PF, Sousa M. Shedding light into the relevance of telomeres in human reproduction and male factor infertility†. Biol Reprod 2018; 100:318-330. [DOI: 10.1093/biolre/ioy215] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/05/2018] [Accepted: 10/01/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Ana Catarina Lopes
- Laboratory of Cell Biology, Department of Microscopy, and Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, New University of Lisbon (FCT-UNL), Campus Caparica, Caparica, Portugal
| | - Pedro F Oliveira
- Laboratory of Cell Biology, Department of Microscopy, and Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal
- i3S- Institute of Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Mário Sousa
- Laboratory of Cell Biology, Department of Microscopy, and Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Centre for Reproductive Genetics Professor Alberto Barros, Porto, Portugal
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Saito TT, Colaiácovo MP. Regulation of Crossover Frequency and Distribution during Meiotic Recombination. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:223-234. [PMID: 29222342 DOI: 10.1101/sqb.2017.82.034132] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Crossover recombination is essential for generating genetic diversity and promoting accurate chromosome segregation during meiosis. The process of crossover recombination is tightly regulated and is initiated by the formation of programmed meiotic DNA double-strand breaks (DSBs). The number of DSBs is around 10-fold higher than the number of crossovers in most species, because only a limited number of DSBs are repaired as crossovers during meiosis. Moreover, crossovers are not randomly distributed. Most crossovers are located on chromosomal arm regions and both centromeres and telomeres are usually devoid of crossovers. Either loss or mislocalization of crossovers frequently results in chromosome nondisjunction and subsequent aneuploidy, leading to infertility, miscarriages, and birth defects such as Down syndrome. Here, we will review aspects of crossover regulation observed in most species and then focus on crossover regulation in the nematode Caenorhabditis elegans in which both the frequency and distribution of crossovers are tightly controlled. In this system, only a single crossover is formed, usually at an off-centered position, between each pair of homologous chromosomes. We have identified C. elegans mutants with deregulated crossover distribution, and we are analyzing crossover control by using an inducible single DSB system with which a single crossover can be produced at specific genomic positions. These combined studies are revealing novel insights into how crossover position is linked to accurate chromosome segregation.
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Affiliation(s)
- Takamune T Saito
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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Embryonic exposure to the widely-used herbicide atrazine disrupts meiosis and normal follicle formation in female mice. Sci Rep 2017; 7:3526. [PMID: 28615648 PMCID: PMC5471253 DOI: 10.1038/s41598-017-03738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/03/2017] [Indexed: 01/28/2023] Open
Abstract
The widely-used herbicide atrazine (ATZ) is detected in ground and surface water in many countries. Several studies in animals have demonstrated that ATZ has endocrine-disrupting effects on male and female reproduction in many vertebrate species. In this study, we investigated the effects of ATZ exposure on meiosis, a key step in gametogenesis in mammals. The treatment was initiated before oocyte entry into meiosis, which occurs during the embryonic period in females. We found that embryonic exposure to ATZ increases the level of 8-oxo-guanine in the nucleus of meiotic cells, reflecting oxidative stress and affecting meiotic double-strand break repair, chromosome synapsis and crossover numbers. Finally, embryonic exposure to ATZ reduces the number of primordial follicles and increases the incidence of multi-oocyte follicles in adult mice. Our data demonstrate that embryonic exposure to ATZ disrupts prophase I of meiosis and affects normal follicle formation in female mice.
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Coppedè F. Risk factors for Down syndrome. Arch Toxicol 2016; 90:2917-2929. [DOI: 10.1007/s00204-016-1843-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 08/29/2016] [Indexed: 12/21/2022]
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