1
|
Baker Z, Przeworski M, Sella G. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence. eLife 2023; 12:e83769. [PMID: 37830496 DOI: 10.7554/elife.83769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/12/2023] [Indexed: 10/14/2023] Open
Abstract
In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. This assumption, however, does not align with current evidence. Recent experimental work indicates that PRDM9 binding on both homologs facilitates DSB repair, and that the absence of sufficient symmetric binding disrupts meiosis. We therefore consider an alternative hypothesis: that rapid PRDM9 evolution is driven by the need to restore symmetric binding because of its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population genetic processes that govern the evolution of the zinc finger array and its binding sites. We show that the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease, in turn, drives rapid PRDM9 evolutionary turnover. Our results therefore suggest that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
Collapse
Affiliation(s)
- Zachary Baker
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| |
Collapse
|
2
|
Llano E, Pendás AM. Synaptonemal Complex in Human Biology and Disease. Cells 2023; 12:1718. [PMID: 37443752 PMCID: PMC10341275 DOI: 10.3390/cells12131718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/18/2023] [Indexed: 07/15/2023] Open
Abstract
The synaptonemal complex (SC) is a meiosis-specific multiprotein complex that forms between homologous chromosomes during prophase of meiosis I. Upon assembly, the SC mediates the synapses of the homologous chromosomes, leading to the formation of bivalents, and physically supports the formation of programmed double-strand breaks (DSBs) and their subsequent repair and maturation into crossovers (COs), which are essential for genome haploidization. Defects in the assembly of the SC or in the function of the associated meiotic recombination machinery can lead to meiotic arrest and human infertility. The majority of proteins and complexes involved in these processes are exclusively expressed during meiosis or harbor meiosis-specific subunits, although some have dual functions in somatic DNA repair and meiosis. Consistent with their functions, aberrant expression and malfunctioning of these genes have been associated with cancer development. In this review, we focus on the significance of the SC and their meiotic-associated proteins in human fertility, as well as how human genetic variants encoding for these proteins affect the meiotic process and contribute to infertility and cancer development.
Collapse
Affiliation(s)
- Elena Llano
- Departamento Fisiología y Farmacología, Universidad de Salamanca, 37007 Salamanca, Spain
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biologıía Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Alberto M. Pendás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer, Instituto de Biologıía Molecular y Celular del Cáncer, CSIC-Universidad de Salamanca, 37007 Salamanca, Spain;
| |
Collapse
|
3
|
Soleymani Moud S, Kamal Seraji K, Ramezani M, Piravar Z. Association of Single Nucleotide Polymorphisms in the PYGO2 and PRDM9 Genes with Idiopathic Azoospermia in Iranian Infertile Male Patients. IRANIAN JOURNAL OF MEDICAL SCIENCES 2023; 48:77-84. [PMID: 36688188 PMCID: PMC9843457 DOI: 10.30476/ijms.2022.93009.2433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 01/24/2023]
Abstract
Background Azoospermia is a risk factor for infertility affecting approximately 1% of the male population. Genetic factors are associated with non-obstructive azoospermia (NOA). Pygo2 and PRDM9 genes are involved in the spermatogenesis process. The present study aimed to assess the association of single nucleotide polymorphism (SNP) in the Pygo2 (rs61758740 and rs61758741) and PRDM9 (rs2973631 and rs1874165) genes with idiopathic azoospermia (IA). Methods A cross-sectional study was conducted from October 2018 to August 2019 at Rooya Infertility Centre (Qom, Iran). A total of 100 infertile patients with NOA and 100 men with normal fertility were enrolled in the study. Tetra-primer amplification refractory mutation system-PCR method was used to detect SNPs rs61758740, rs61758741, and rs2973631. The restriction fragment length polymorphism method was used for SNP rs1874165. In addition, luteinizing, follicle-stimulating, and testosterone hormone levels were measured. Results The results showed a significant increase in luteinizing and follicle-stimulating hormone levels in the patient group (P<0.001), but a non-significant difference in testosterone levels in both groups. SNP rs61758740 (T>C) was associated with the increased risk of azoospermia (OR: 2.359, 95% Cl: 1.192-4.666, P=0.012). SNP rs2973631 showed a significant difference in genotype frequency between the patient and control groups in the dominant, recessive, and codominant models. However, in the case of SNP rs1874165, the difference was significant in the dominant, codominant, and overdominant models. Conclusion There is an association between azoospermia and SNPs in Pygo2 and PRDM9 genes in Iranian infertile male patients with IA. SNPs can be considered a risk factor for male infertility. It should be noted that this article was published in preprint form on the website of europepmc (https://europepmc.org/article/ppr/ppr416800).
Collapse
Affiliation(s)
- Sanaz Soleymani Moud
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Katayun Kamal Seraji
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mina Ramezani
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Zeynab Piravar
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| |
Collapse
|
4
|
Qu W, Liu C, Xu YT, Xu YM, Luo MC. The formation and repair of DNA double-strand breaks in mammalian meiosis. Asian J Androl 2021; 23:572-579. [PMID: 34708719 PMCID: PMC8577251 DOI: 10.4103/aja202191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) are necessary for meiosis in mammals. A sufficient number of DSBs ensure the normal pairing/synapsis of homologous chromosomes. Abnormal DSB repair undermines meiosis, leading to sterility in mammals. The DSBs that initiate recombination are repaired as crossovers and noncrossovers, and crossovers are required for correct chromosome separation. Thus, the placement, timing, and frequency of crossover formation must be tightly controlled. Importantly, mutations in many genes related to the formation and repair of DSB result in infertility in humans. These mutations cause nonobstructive azoospermia in men, premature ovarian insufficiency and ovarian dysgenesis in women. Here, we have illustrated the formation and repair of DSB in mammals, summarized major factors influencing the formation of DSB and the theories of crossover regulation.
Collapse
Affiliation(s)
- Wei Qu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Cong Liu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Ya-Ting Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Min Xu
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Meng-Cheng Luo
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
5
|
Powers NR, Billings T, Paigen K, Petkov PM. Differential effects of two catalytic mutations on full-length PRDM9 and its isolated PR/SET domain reveal a case of pseudomodularity. Genetics 2021; 219:6385243. [PMID: 34747456 DOI: 10.1093/genetics/iyab172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/30/2021] [Indexed: 11/14/2022] Open
Abstract
PRDM9 is a DNA-binding histone methyltransferase that designates and activates recombination hotspots in mammals by locally trimethylating lysines 4 and 36 of histone H3. In mice, we recently reported two independently produced point mutations at the same residue, Glu360Pro (Prdm9EP) and Glu360Lys (Prdm9EK), which severely reduce its H3K4 and H3K36 methyltransferase activities in vivo. Prdm9EP is slightly less hypomorphic than Prdm9EK, but both mutations reduce both the number and amplitude of PRDM9-dependent H3K4me3 and H3K36me3 peaks in spermatocytes. While both mutations cause infertility with complete meiotic arrest in males, Prdm9EP, but not Prdm9EK, is compatible with some female fertility. When we tested the effects of these mutations in vitro, both Prdm9EP and Prdm9EK abolished H3K4 and H3K36 methyltransferase activity in full-length PRDM9. However, in the isolated PRDM9 PR/SET domain, these mutations selectively compromised H3K36 methyltransferase activity, while leaving H3K4 methyltransferase activity intact. The difference in these effects on the PR/SET domain vs the full-length protein shows that PRDM9 is not an intrinsically modular enzyme; its catalytic domain is influenced by its tertiary structure and possibly by its interactions with DNA and other proteins in vivo. These two informative mutations illuminate the enzymatic chemistry of PRDM9, and potentially of PR/SET domains in general, reveal the minimal threshold of PRDM9-dependent catalytic activity for female fertility, and potentially have some practical utility for genetic mapping and genomics.
Collapse
|
6
|
Tan GX, Jiang L, Li GQ, Bai K. Evaluation of association between methylenetetrahydrofolate reductase and azoospermia: A meta-analysis. Medicine (Baltimore) 2021; 100:e24523. [PMID: 33847607 PMCID: PMC8051989 DOI: 10.1097/md.0000000000024523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 11/19/2020] [Accepted: 01/08/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Infertility affects childbearing age couples all over the world. One of the important reasons for infertility is genetic factors. Our study evaluated the association between methylenetetrahydrofolate reductase (MTHFR) and azoospermia. METHODS Multiple databases like MEDLINE, EMBASE, Cochrane library, and China journal full-text database were used to search for relevant studies, and full-text articles involved in the evaluation of MTHFR and azoospermia. The results were evaluated using STATA 12.0. Heterogeneity analysis, sensitivity analysis, and bias analysis were also performed on the data. RESULTS Thirteen related studies eventually met the inclusion criteria. Significant association between C677T polymorphism and azoospermia (relative risk [RR] = 0.94 [0.90, 0.99], I2 = 60.9%, P = .002), and between A1298C polymorphism and azoospermia (RR = 0.98 [0.94, 1.02], I2 = 56.3%, P = .011) was observed. Meanwhile, in subgroup analysis, Caucasians had higher risk than Mongolians in association between MTHFR and azoospermia. CONCLUSION There was association between MTHFR polymorphism and azoospermia. Caucasian populations had higher risk than Mongolian populations in association between MTHFR and azoospermia.
Collapse
|
7
|
Powers NR, Dumont BL, Emori C, Lawal RA, Brunton C, Paigen K, Handel MA, Bolcun-Filas E, Petkov PM, Bhattacharyya T. Sexual dimorphism in the meiotic requirement for PRDM9: A mammalian evolutionary safeguard. SCIENCE ADVANCES 2020; 6:6/43/eabb6606. [PMID: 33097538 PMCID: PMC7608834 DOI: 10.1126/sciadv.abb6606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 09/03/2020] [Indexed: 05/14/2023]
Abstract
In many mammals, genomic sites for recombination are determined by the histone methyltransferase PRMD9. Some mouse strains lacking PRDM9 are infertile, but instances of fertility or semifertility in the absence of PRDM9 have been reported in mice, canines, and a human female. Such findings raise the question of how the loss of PRDM9 is circumvented to maintain fertility. We show that genetic background and sex-specific modifiers can obviate the requirement for PRDM9 in mice. Specifically, the meiotic DNA damage checkpoint protein CHK2 acts as a modifier allowing female-specific fertility in the absence of PRDM9. We also report that, in the absence of PRDM9, a PRDM9-independent recombination system is compatible with female meiosis and fertility, suggesting sex-specific regulation of meiotic recombination, a finding with implications for speciation.
Collapse
Affiliation(s)
- Natalie R Powers
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Chihiro Emori
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | | | - Kenneth Paigen
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Mary Ann Handel
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Petko M Petkov
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | |
Collapse
|
8
|
Robertson MJ, Kent K, Tharp N, Nozawa K, Dean L, Mathew M, Grimm SL, Yu Z, Légaré C, Fujihara Y, Ikawa M, Sullivan R, Coarfa C, Matzuk MM, Garcia TX. Large-scale discovery of male reproductive tract-specific genes through analysis of RNA-seq datasets. BMC Biol 2020; 18:103. [PMID: 32814578 PMCID: PMC7436996 DOI: 10.1186/s12915-020-00826-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022] Open
Abstract
Background The development of a safe, effective, reversible, non-hormonal contraceptive method for men has been an ongoing effort for the past few decades. However, despite significant progress on elucidating the function of key proteins involved in reproduction, understanding male reproductive physiology is limited by incomplete information on the genes expressed in reproductive tissues, and no contraceptive targets have so far reached clinical trials. To advance product development, further identification of novel reproductive tract-specific genes leading to potentially druggable protein targets is imperative. Results In this study, we expand on previous single tissue, single species studies by integrating analysis of publicly available human and mouse RNA-seq datasets whose initial published purpose was not focused on identifying male reproductive tract-specific targets. We also incorporate analysis of additional newly acquired human and mouse testis and epididymis samples to increase the number of targets identified. We detected a combined total of 1178 genes for which no previous evidence of male reproductive tract-specific expression was annotated, many of which are potentially druggable targets. Through RT-PCR, we confirmed the reproductive tract-specific expression of 51 novel orthologous human and mouse genes without a reported mouse model. Of these, we ablated four epididymis-specific genes (Spint3, Spint4, Spint5, and Ces5a) and two testis-specific genes (Pp2d1 and Saxo1) in individual or double knockout mice generated through the CRISPR/Cas9 system. Our results validate a functional requirement for Spint4/5 and Ces5a in male mouse fertility, while demonstrating that Spint3, Pp2d1, and Saxo1 are each individually dispensable for male mouse fertility. Conclusions Our work provides a plethora of novel testis- and epididymis-specific genes and elucidates the functional requirement of several of these genes, which is essential towards understanding the etiology of male infertility and the development of male contraceptives.
Collapse
Affiliation(s)
- Matthew J Robertson
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Center for Precision Environmental Health, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Katarzyna Kent
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Biology and Biotechnology, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, TX, 77058, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Nathan Tharp
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Biology and Biotechnology, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, TX, 77058, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Kaori Nozawa
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Laura Dean
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Biology and Biotechnology, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, TX, 77058, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Michelle Mathew
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Biology and Biotechnology, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, TX, 77058, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Sandra L Grimm
- Center for Precision Environmental Health, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Zhifeng Yu
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Christine Légaré
- Department Obstetrics, Gynecology and Reproduction, Faculty Medicine, Université Laval, Quebec, QC, Canada.,Reproduction, Mother and Youth Health Division, Centre de recherche du CHU de Québec-Université Laval, 2705 boul Laurier, Quebec, QC, G1V 4G2, Canada
| | - Yoshitaka Fujihara
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Experimental Genome Research, Research Institute for Microbial Diseases, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, 6-1 Kishibeshinmachi, Suita, Osaka, 564-8565, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Robert Sullivan
- Department Obstetrics, Gynecology and Reproduction, Faculty Medicine, Université Laval, Quebec, QC, Canada.,Reproduction, Mother and Youth Health Division, Centre de recherche du CHU de Québec-Université Laval, 2705 boul Laurier, Quebec, QC, G1V 4G2, Canada
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Center for Precision Environmental Health, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Martin M Matzuk
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Thomas X Garcia
- Department of Pathology and Immunology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Department of Biology and Biotechnology, University of Houston-Clear Lake, 2700 Bay Area Blvd., Houston, TX, 77058, USA. .,Center for Drug Discovery, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| |
Collapse
|
9
|
Mahgoub M, Paiano J, Bruno M, Wu W, Pathuri S, Zhang X, Ralls S, Cheng X, Nussenzweig A, Macfarlan TS. Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice. eLife 2020; 9:e53360. [PMID: 32352380 PMCID: PMC7237205 DOI: 10.7554/elife.53360] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/29/2020] [Indexed: 12/14/2022] Open
Abstract
Meiotic crossovers result from homology-directed repair of DNA double-strand breaks (DSBs). Unlike yeast and plants, where DSBs are generated near gene promoters, in many vertebrates DSBs are enriched at hotspots determined by the DNA binding activity of the rapidly evolving zinc finger array of PRDM9 (PR domain zinc finger protein 9). PRDM9 subsequently catalyzes tri-methylation of lysine 4 and lysine 36 of Histone H3 in nearby nucleosomes. Here, we identify the dual histone methylation reader ZCWPW1, which is tightly co-expressed during spermatogenesis with Prdm9, as an essential meiotic recombination factor required for efficient repair of PRDM9-dependent DSBs and for pairing of homologous chromosomes in male mice. In sum, our results indicate that the evolution of a dual histone methylation writer/reader (PRDM9/ZCWPW1) system in vertebrates remodeled genetic recombination hotspot selection from an ancestral static pattern near genes towards a flexible pattern controlled by the rapidly evolving DNA binding activity of PRDM9.
Collapse
Affiliation(s)
- Mohamed Mahgoub
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIHBethesdaUnited States
- Immunology Graduate Group, University of PennsylvaniaPhiladelphiaUnited States
| | - Melania Bruno
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIHBethesdaUnited States
| | - Sarath Pathuri
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Sherry Ralls
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIHBethesdaUnited States
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIHBethesdaUnited States
| |
Collapse
|
10
|
Allali-Hassani A, Szewczyk MM, Ivanochko D, Organ SL, Bok J, Ho JSY, Gay FPH, Li F, Blazer L, Eram MS, Halabelian L, Dilworth D, Luciani GM, Lima-Fernandes E, Wu Q, Loppnau P, Palmer N, Talib SZA, Brown PJ, Schapira M, Kaldis P, O'Hagan RC, Guccione E, Barsyte-Lovejoy D, Arrowsmith CH, Sanders JM, Kattar SD, Bennett DJ, Nicholson B, Vedadi M. Discovery of a chemical probe for PRDM9. Nat Commun 2019; 10:5759. [PMID: 31848333 PMCID: PMC6917776 DOI: 10.1038/s41467-019-13652-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC50: 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.
Collapse
Affiliation(s)
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Shawna L Organ
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence P H Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Qin Wu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore (NUS), Department of Biochemistry, 117597, Singapore, Singapore
| | - Ronan C O'Hagan
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Nature Research Center, Vilnius, Akademijos, 2, Lithuania
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - John M Sanders
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Solomon D Kattar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | | | - Benjamin Nicholson
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
11
|
Tanaka H, Miyagawa Y, Tsujimura A, Wada M. Genetic Polymorphisms within The Intronless ACTL7A and ACTL7B Genes Encoding Spermatogenesis-Specific Actin-Like Proteins in Japanese Males. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2019; 13:245-249. [PMID: 31310081 PMCID: PMC6642428 DOI: 10.22074/ijfs.2019.5702] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 02/16/2019] [Indexed: 11/18/2022]
Abstract
Actins play essential roles in cellular morphogenesis. In mice, the T-actin1 and 2 genes, which encode actin-like
proteins, are specifically expressed in haploid germ cells. Both T-ACTIN1/ACTLB and T-ACTIN2/ACTL7A have also
been cloned and studied. The orthologous genes in humans are present on chromosome 9q31.3 as intronless genes.
Defects of germ cell-specific genes can introduce infertility without somatic function impairment. We determined T-
ACTIN1 and 2, specifically expressed in the testis using reverse-transcription polymerase chain reaction (RT-PCR).
To examine whether genetic polymorphisms of the T-ACTIN1 and 2 genes are associated with male infertility, we
screened for T-ACTIN1 and 2 polymorphisms by direct sequencing of DNA from 282 sterile and 89 fertile Japanese
men. We identified five and six single nucleotide polymorphisms (SNPs) in the T-ACTIN1 and 2 regions of the sterile
and fertile subjects respectively. Among these genetic polymorphisms was a novel SNP that was not in the National
Center for Biotechnology Information SNP database. Although we could not determine whether these SNPs cause
infertility, the prevalence of these genetic polymorphisms may be useful for analyzing polymorphisms in future large-
scale genetic analyses.
Collapse
Affiliation(s)
- Hiromitsu Tanaka
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Huis Ten Bosch, Sasebo, Nagasaki, Japan.Electronic Address:
| | - Yasushi Miyagawa
- Department of Urology, Graduate School of Medicine, Osaka University, Yamadaoka, Suita, Osaka, Japan
| | - Akira Tsujimura
- Department of Urology, Juntendo University Hospital, Hongo, bunnkyouku, Tokyo, Japan
| | - Morimasa Wada
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Huis Ten Bosch, Sasebo, Nagasaki, Japan
| |
Collapse
|
12
|
Houle AA, Gibling H, Lamaze FC, Edgington HA, Soave D, Fave MJ, Agbessi M, Bruat V, Stein LD, Awadalla P. Aberrant PRDM9 expression impacts the pan-cancer genomic landscape. Genome Res 2018; 28:1611-1620. [PMID: 30341163 PMCID: PMC6211651 DOI: 10.1101/gr.231696.117] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/04/2018] [Indexed: 12/15/2022]
Abstract
The binding of PRDM9 to chromatin is a key step in the induction of DNA double-strand breaks associated with meiotic recombination hotspots; it is normally expressed solely in germ cells. We interrogated 1879 cancer samples in 39 different cancer types and found that PRDM9 is unexpectedly expressed in 20% of these tumors even after stringent gene homology correction. The expression levels of PRDM9 in tumors are significantly higher than those found in healthy neighboring tissues and in healthy nongerm tissue databases. Recurrently mutated regions located within 5 Mb of the PRDM9 loci, as well as differentially expressed genes in meiotic pathways, correlate with PRDM9 expression. In samples with aberrant PRDM9 expression, structural variant breakpoints frequently neighbor the DNA motif recognized by PRDM9, and there is an enrichment of structural variants at sites of known meiotic PRDM9 activity. This study is the first to provide evidence of an association between aberrant expression of the meiosis-specific gene PRDM9 with genomic instability in cancer.
Collapse
Affiliation(s)
- Armande Ang Houle
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Heather Gibling
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Fabien C Lamaze
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Hilary A Edgington
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Marie-Julie Fave
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Mawusse Agbessi
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Vanessa Bruat
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Department of Computational Biology, Toronto, Ontario M5G 0A3, Canada.,University of Toronto, Department of Molecular Genetics, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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
| |
Collapse
|
15
|
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: 82] [Impact Index Per Article: 13.7] [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.
Collapse
|
16
|
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'.
Collapse
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
| |
Collapse
|
17
|
Nagamatsu G, Hayashi K. Stem cells, in vitro gametogenesis and male fertility. Reproduction 2017; 154:F79-F91. [PMID: 29133304 DOI: 10.1530/rep-17-0510] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022]
Abstract
Reconstitution in culture of biological processes, such as differentiation and organization, is a key challenge in regenerative medicine, and one in which stem cell technology plays a central role. Pluripotent stem cells and spermatogonial stem cells are useful materials for reconstitution of germ cell development in vitro, as they are capable of differentiating into gametes. Reconstitution of germ cell development, termed in vitro gametogenesis, will provide an experimental platform for a better understanding of germ cell development, as well as an alternative source of gametes for reproduction, with the potential to cure infertility. Since germ cells are the cells for 'the next generation', both the culture system and its products must be carefully evaluated. In this issue, we summarize the progress in in vitro gametogenesis, most of which has been made using mouse models, as well as the future challenges in this field.
Collapse
Affiliation(s)
- Go Nagamatsu
- Department of Stem Cell Biology and MedicineGraduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and MedicineGraduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| |
Collapse
|
18
|
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]
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Blazer LL, Lima-Fernandes E, Gibson E, Eram MS, Loppnau P, Arrowsmith CH, Schapira M, Vedadi M. PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase. J Biol Chem 2016; 291:13509-19. [PMID: 27129774 PMCID: PMC4919437 DOI: 10.1074/jbc.m116.721472] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report that PRDM7 is an efficient methyltransferase that selectively catalyzes the trimethylation of H3 lysine 4 (H3K4) both in vitro and in cells. Through selective mutagenesis we have dissected the functional roles of each of the three divergent residues between the PR domains of PRDM7 and PRDM9. These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36.
Collapse
Affiliation(s)
- Levi L Blazer
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Evelyne Lima-Fernandes
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Elisa Gibson
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Mohammad S Eram
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, and
| | - Matthieu Schapira
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masoud Vedadi
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
21
|
Baker CL, Petkova P, Walker M, Flachs P, Mihola O, Trachtulec Z, Petkov PM, Paigen K. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots. PLoS Genet 2015; 11:e1005512. [PMID: 26368021 PMCID: PMC4569383 DOI: 10.1371/journal.pgen.1005512] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/17/2015] [Indexed: 02/04/2023] Open
Abstract
Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. During formation of sperm and eggs chromosomes exchange DNA in a process known as recombination, creating new combinations responsible for much of the enormous diversity in populations. In some mammals, including humans, the locations of recombination are chosen by a DNA-binding protein named PRDM9. Importantly, there are tens to hundreds of different variations of the Prdm9 gene (termed alleles), many of which are predicted to bind a unique DNA sequence. This high frequency of variation results in many individuals having two different copies of Prdm9, and several lines of evidence indicate that alleles compete to initiate recombination. In seeking to understand the mechanism of this competition we found that Prdm9 activity is sensitive to the number of gene copies present, suggesting that availability of this protein is a limiting factor during recombination. Moreover, we found that variant forms of PRDM9 protein can physically interact suggesting that when this happens one variant can influence which hotspots will become activated. Genetic crosses in mice support these observations; the presence of a dominant Prdm9 allele can completely suppress recombination at some locations. We conclude that allele-dominance of PRDM9 is a consequence of protein-protein interaction and competition for DNA binding in a limited pool of molecules, thus shaping the recombination landscape in natural populations.
Collapse
Affiliation(s)
- Christopher L. Baker
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Pavlina Petkova
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Michael Walker
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Petr Flachs
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic
| | - Ondrej Mihola
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic
| | - Zdenek Trachtulec
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic
| | - Petko M. Petkov
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Kenneth Paigen
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail:
| |
Collapse
|
22
|
Primate evolution of the recombination regulator PRDM9. Nat Commun 2014; 5:4370. [PMID: 25001002 PMCID: PMC4110516 DOI: 10.1038/ncomms5370] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 06/11/2014] [Indexed: 11/08/2022] Open
Abstract
The PRDM9 gene encodes a protein with a highly variable tandem-repeat zinc finger (ZF) DNA-binding domain that plays a key role in determining sequence-specific hotspots of meiotic recombination genome wide. Here we survey the diversity of the PRDM9 ZF domain by sequencing this region in 64 primates from 18 species, revealing 68 unique alleles across all groups. We report ubiquitous positive selection at nucleotide positions corresponding to DNA contact residues and the expansion of ZFs within clades, which confirms the rapid evolution of the ZF domain throughout the primate lineage. Alignment of Neandertal and Denisovan sequences suggests that PRDM9 in archaic hominins was closely related to present-day human alleles that are rare and specific to African populations. In the context of its role in reproduction, our results are consistent with variation in PRDM9 contributing to speciation events in primates.
Collapse
|
23
|
Zanders SE, Eickbush MT, Yu JS, Kang JW, Fowler KR, Smith GR, Malik HS. Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. eLife 2014; 3:e02630. [PMID: 24963140 PMCID: PMC4066438 DOI: 10.7554/elife.02630] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Here we identify causes underlying hybrid infertility of two recently diverged fission yeast species Schizosaccharomyces pombe and S. kambucha, which mate to form viable hybrid diploids that efficiently complete meiosis, but generate few viable gametes. We find that chromosomal rearrangements and related recombination defects are major but not sole causes of hybrid infertility. At least three distinct meiotic drive alleles, one on each S. kambucha chromosome, independently contribute to hybrid infertility by causing nonrandom spore death. Two of these driving loci are linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. Our study reveals how quickly multiple barriers to fertility can arise. In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation. DOI:http://dx.doi.org/10.7554/eLife.02630.001 It is widely thought that all of the billions of species on Earth are descended from a common ancestor. New species are created via a process called speciation, and nature employs various ‘barriers’ to keep closely related species distinct from one another. One of these barriers is called hybrid sterility. Horses and donkeys, for example, can mate to produce hybrids called mules, but mules cannot produce offspring of their own because they are infertile. Hybrid sterility can occur for a number of reasons. Mules are infertile because they inherit 32 chromosomes from their horse parent, but only 31 chromosomes from their donkey parent—and so have an odd chromosome that they cannot pair-off when they make sperm or egg cells. However, even if a hybrid inherits the same number of chromosomes from each parent, if the chromosomes from the two parents have different structures, the hybrid may still be infertile. Zanders et al. have now looked at two species of fission yeast—S. pombe and S. kambucha—that share 99.5% of their DNA sequence. Although hybrids of these two species inherit three chromosomes from each parent, the majority of spores (the yeast equivalent of sperm) that these hybrids produce fail to develop into new yeast cells. Zanders et al. identified two causes of this infertility: one of these was chromosomal rearrangement; the other was due to three different sites in the DNA of S. kambucha that interfere with the development of the spores that inherit S. pombe chromosomes. Since these two yeast species are so closely related, the findings of Zanders et al. reveal how quickly multiple barriers to fertility can arise. In addition, these findings provide further support for models in which conflicts between different genes in genomes can drive the process of speciation. DOI:http://dx.doi.org/10.7554/eLife.02630.002
Collapse
Affiliation(s)
- Sarah E Zanders
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Michael T Eickbush
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jonathan S Yu
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Ji-Won Kang
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States University of Washington, Seattle, United States
| | - Kyle R Fowler
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Harmit Singh Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
| |
Collapse
|
24
|
Eram MS, Bustos SP, Lima-Fernandes E, Siarheyeva A, Senisterra G, Hajian T, Chau I, Duan S, Wu H, Dombrovski L, Schapira M, Arrowsmith CH, Vedadi M. Trimethylation of histone H3 lysine 36 by human methyltransferase PRDM9 protein. J Biol Chem 2014; 289:12177-12188. [PMID: 24634223 PMCID: PMC4002121 DOI: 10.1074/jbc.m113.523183] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 03/13/2014] [Indexed: 11/06/2022] Open
Abstract
PRDM9 (PR domain-containing protein 9) is a meiosis-specific protein that trimethylates H3K4 and controls the activation of recombination hot spots. It is an essential enzyme in the progression of early meiotic prophase. Disruption of the PRDM9 gene results in sterility in mice. In human, several PRDM9 SNPs have been implicated in sterility as well. Here we report on kinetic studies of H3K4 methylation by PRDM9 in vitro indicating that PRDM9 is a highly active histone methyltransferase catalyzing mono-, di-, and trimethylation of the H3K4 mark. Screening for other potential histone marks, we identified H3K36 as a second histone residue that could also be mono-, di-, and trimethylated by PRDM9 as efficiently as H3K4. Overexpression of PRDM9 in HEK293 cells also resulted in a significant increase in trimethylated H3K36 and H3K4 further confirming our in vitro observations. Our findings indicate that PRDM9 may play critical roles through H3K36 trimethylation in cells.
Collapse
Affiliation(s)
- Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Susan P Bustos
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | | | - Alena Siarheyeva
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | | | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Shili Duan
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Ludmila Dombrovski
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7; Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8.
| |
Collapse
|
25
|
Alemany-Schmidt A, Navarro-Palou M, Voltes-Cobo A, Rosell J, Heine-Suñer D, Picornell A, Oliver-Bonet M. Geographical genetic variability: a factor to consider when assessing clinical implications of PRDM9. Mol Genet Genomic Med 2014; 2:201-3. [PMID: 24689083 PMCID: PMC3960062 DOI: 10.1002/mgg3.56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alexandra Alemany-Schmidt
- Laboratori de Genòmica de la Salut, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain ; Fundació d'Investigació Sanitària de les Illes Balears (FISIB) Palma de Mallorca, Spain
| | - Maria Navarro-Palou
- Laboratori de Genòmica de la Salut, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain ; Fundació d'Investigació Sanitària de les Illes Balears (FISIB) Palma de Mallorca, Spain
| | - Adrià Voltes-Cobo
- Laboratori de Genòmica de la Salut, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain
| | - Jordi Rosell
- Secció de Genètica, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain ; CIBERER Centro de Investigación Biomédica en Red de Enfermedades Raras Madrid, Spain
| | - Damià Heine-Suñer
- Laboratori de Genòmica de la Salut, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain ; Secció de Genètica, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain ; CIBERER Centro de Investigación Biomédica en Red de Enfermedades Raras Madrid, Spain
| | - Antònia Picornell
- Laboratori de Genètica, Institut Universitari d'Investigació en Ciències de la Salut i Departament Biologia, Universitat de les Illes Balears (UIB) Palma de Mallorca, Spain
| | - Maria Oliver-Bonet
- Laboratori de Genòmica de la Salut, Hospital Universitari Son Espases (HUSE) Palma de Mallorca, Spain ; Fundació d'Investigació Sanitària de les Illes Balears (FISIB) Palma de Mallorca, Spain
| |
Collapse
|
26
|
Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier JC, de Malliard T, Busche S, Spinella JF, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing JR, Mullighan CG, Awadalla P. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res 2012; 23:419-30. [PMID: 23222848 PMCID: PMC3589531 DOI: 10.1101/gr.144188.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis.
Collapse
Affiliation(s)
- Julie Hussin
- Department of Biochemistry, Faculty of Medicine, University of Montreal, Montreal H3C 3J7, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
Background The PRDM9 locus in mammals has increasingly attracted research attention due to its role in mediating chromosomal recombination and possible involvement in hybrid sterility and hence speciation processes. The aim of this study was to characterize sequence variation at the PRDM9 locus in a sample of our closest living relatives, the chimpanzees and bonobos. Methodology/Principal Findings PRDM9 contains a highly variable and repetitive zinc finger array. We amplified this domain using long-range PCR and determined the DNA sequences using conventional Sanger sequencing. From 17 chimpanzees representing three subspecies and five bonobos we obtained a total of 12 alleles differing at the nucleotide level. Based on a data set consisting of our data and recently published Pan PRDM9 sequences, we found that at the subspecies level, diversity levels did not differ among chimpanzee subspecies or between chimpanzee subspecies and bonobos. In contrast, the sample of chimpanzees harbors significantly more diversity at PRDM9 than samples of humans. Pan PRDM9 shows signs of rapid evolution including no alleles or ZnFs in common with humans as well as signals of positive selection in the residues responsible for DNA binding. Conclusions and Significance The high number of alleles specific to the genus Pan, signs of positive selection in the DNA binding residues, and reported lack of conservation of recombination hotspots between chimpanzees and humans suggest that PRDM9 could be active in hotspot recruitment in the genus Pan. Chimpanzees and bonobos are considered separate species and do not have overlapping ranges in the wild, making the presence of shared alleles at the amino acid level between the chimpanzee and bonobo species interesting in view of the hypothesis that PRDM9 plays a universal role in interspecific hybrid sterility.
Collapse
|
28
|
Solomon BD, Hadley DW, Pineda-Alvarez DE, Kamat A, Teer JK, Cherukuri PF, Hansen NF, Cruz P, Young AC, Berkman BE, Chandrasekharappa SC, Mullikin JC, Mullikin JC. Incidental medical information in whole-exome sequencing. Pediatrics 2012; 129:e1605-11. [PMID: 22585771 PMCID: PMC3362899 DOI: 10.1542/peds.2011-0080] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genomic technologies, such as whole-exome sequencing, are a powerful tool in genetic research. Such testing yields a great deal of incidental medical information, or medical information not related to the primary research target. We describe the management of incidental medical information derived from whole-exome sequencing in the research context. We performed whole-exome sequencing on a monozygotic twin pair in which only 1 child was affected with congenital anomalies and applied an institutional review board-approved algorithm to determine what genetic information would be returned. Whole-exome sequencing identified 79525 genetic variants in the twins. Here, we focus on novel variants. After filtering artifacts and excluding known single nucleotide polymorphisms and variants not predicted to be pathogenic, the twins had 32 novel variants in 32 genes that were felt to be likely to be associated with human disease. Eighteen of these novel variants were associated with recessive disease and 18 were associated with dominantly manifesting conditions (variants in some genes were potentially associated with both recessive and dominant conditions), but only 1 variant ultimately met our institutional review board-approved criteria for return of information to the research participants.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Benjamin E. Berkman
- Department of Bioethics, Clinical Center, and Office of the Clinical Director, and
| | - Settara C. Chandrasekharappa
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | | |
Collapse
|
29
|
Massart A, Lissens W, Tournaye H, Stouffs K. Genetic causes of spermatogenic failure. Asian J Androl 2012; 14:40-8. [PMID: 22138898 PMCID: PMC3735159 DOI: 10.1038/aja.2011.67] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 08/01/2011] [Accepted: 08/11/2011] [Indexed: 01/16/2023] Open
Abstract
Approximately 10%-15% of couples are infertile, and a male factor is involved in almost half of these cases. This observation is due in part to defects in spermatogenesis, and the underlying causes, including genetic abnormalities, remain largely unknown. Until recently, the only genetic tests used in the diagnosis of male infertility were aimed at detecting the presence of microdeletions of the long arm of the Y chromosome and/or chromosomal abnormalities. Various other single-gene or polygenic defects have been proposed to be involved in male fertility. However, their causative effects often remain unproven. The recent evolution in the development of whole-genome-based techniques and the large-scale analysis of mouse models might help in this process. Through knockout mouse models, at least 388 genes have been shown to be associated with spermatogenesis in mice. However, problems often arise when translating this information from mice to humans.
Collapse
Affiliation(s)
- Annelien Massart
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | | | | | | |
Collapse
|
30
|
The case of the fickle fingers: how the PRDM9 zinc finger protein specifies meiotic recombination hotspots in humans. PLoS Biol 2011; 9:e1001211. [PMID: 22162947 PMCID: PMC3232208 DOI: 10.1371/journal.pbio.1001211] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recent discoveries have revealed the central role of PRDM9 in mammalian recombination. The precise function of this protein, however, remains poorly understood, as do the causes for its rapid evolution and its role in reproductive isolation. During mammalian meiosis, double-strand breaks are deliberately made throughout the genome and then repaired, leading to the exchange of genetic material between copies of chromosomes. How the locations of breaks are specified was largely unknown until a fortuitous confluence of statistical genetics and molecular biology uncovered the role of PRDM9, a DNA binding protein. Many properties of this protein remain mysterious, however, including how it binds to DNA, how it contributes to male infertility—both in humans, and in hybrid mice—and why, in spite of its fundamental function in meiosis, its binding domain varies extensively among humans and across mammals. We present a brief summary of what has recently been learned about PRDM9 in different fields, focusing on the puzzles yet to be resolved.
Collapse
|
31
|
Ogorevc J, Dovc P, Kunej T. Comparative Genomics Approach to Identify Candidate Genetic Loci for Male Fertility. Reprod Domest Anim 2011; 46:229-39. [DOI: 10.1111/j.1439-0531.2010.01648.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
32
|
What are the genomic drivers of the rapid evolution of PRDM9? Trends Genet 2011; 27:165-71. [PMID: 21388701 DOI: 10.1016/j.tig.2011.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/31/2011] [Accepted: 02/02/2011] [Indexed: 11/23/2022]
Abstract
Mammalian Prdm9 has been proposed to be a key determinant of the positioning of chromosome double-strand breaks during meiosis, a contributor to speciation processes, and the most rapidly evolving gene in human, and other animal, genomes. Prdm9 genes often exhibit substantial variation in their numbers of encoded zinc fingers (ZFs), not only between closely related species but also among individuals of a species. The near-identity of these ZF sequences appears to render them very unstable in copy number. The rare sequence differences, however, cluster within ZF sites that determine the DNA-binding specificity of PRDM9, and these substitutions are frequently positively selected. Here, possible drivers of the rapid evolution of Prdm9 are discussed, including selection for efficient pairing of homologous chromosomes or for recombination of deleterious linked alleles, and selection against depletion of recombination hotspots or against disease-associated genome rearrangement.
Collapse
|
33
|
Carrell DT, Aston KI. The search for SNPs, CNVs, and epigenetic variants associated with the complex disease of male infertility. Syst Biol Reprod Med 2011; 57:17-26. [PMID: 21208142 DOI: 10.3109/19396368.2010.521615] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Understanding the genetic basis of idiopathic male infertility has long been the focus of many researchers. Numerous recent studies have attempted to identify relevant single nucleotide polymorphisms (SNPs) through medical re-sequencing studies in which candidate genes are sequenced in large numbers of cases and controls in the search for risk or causative polymorphisms. Two major characteristics have limited the utility of the re-sequencing studies. First, reported SNPs have only accounted for a small percentage of idiopathic male infertility. Second, SNPs reported to have an association with male infertility based on gene re-sequencing studies often fail validation in follow-up studies. Recent advances in the tools available for genetic studies have enabled interrogation of the entire genome in search of common, and more recently, rare variants. In this review, we discuss the progress of studies on genetic and epigenetic variants of male infertility as well as future directions that we predict will be the most productive in identifying the genetic basis for male factor infertility based on our current state of knowledge in this field as well as lessons learned about the genetic basis for complex diseases from other disease models.
Collapse
Affiliation(s)
- Douglas T Carrell
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA.
| | | |
Collapse
|
34
|
Abstract
Recombination hotspots are small chromosomal regions, where meiotic crossover events happen with high frequency. Recombination is initiated by a double-strand break (DSB) that requires the intervention of the molecular repair mechanism. The DSB repair mechanism may result in the exchange of homologous chromosomes (crossover) and the conversion of the allelic sequence that breaks into the one that does not break (biased gene conversion). Biased gene conversion results in a transmission advantage for the allele that does not break, thus preventing recombination and rendering recombination hotspots transient. How is it possible that recombination hotspots persist over evolutionary time (maintaining the average chromosomal crossover rate) when they are self-destructive? This fundamental question is known as the recombination hotspot paradox and has attracted much attention in recent years. Yet, that attention has not translated into a fully satisfactory answer. No existing model adequately explains all aspects of the recombination hotspot paradox. Here, we formulate an intragenomic conflict model resulting in Red Queen dynamics that fully accounts for all empirical observations regarding the molecular mechanisms of recombination hotspots, the nonrandom targeting of the recombination machinery to hotspots and the evolutionary dynamics of hotspot turnover.
Collapse
Affiliation(s)
- F Ubeda
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.
| | | |
Collapse
|
35
|
Current Opinion in Urology. Current world literature. Curr Opin Urol 2010; 20:533-8. [PMID: 20940575 DOI: 10.1097/mou.0b013e32834028bc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
36
|
|
37
|
Tamowski S, Aston KI, Carrell DT. The use of transgenic mouse models in the study of male infertility. Syst Biol Reprod Med 2010; 56:260-73. [PMID: 20536325 DOI: 10.3109/19396368.2010.485244] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Over the past few decades with the rapid advances in embryo and embryonic stem cell manipulation techniques, transgenic mouse models have emerged as a powerful tool for the study of gene function and complex diseases including male infertility. In this review we give a brief history of the development of tools for the production of transgenic mouse models. This spans the advances from early pronuclear injection to the use of targeted embryonic stem cells to produce gene targeted, conditional, and inducible knockout mouse models. Lastly we provide a few examples to illustrate the utility of mouse models in the study of male infertility.
Collapse
Affiliation(s)
- Susan Tamowski
- Transgenic and Gene Targeting Mouse Core, University of Utah School of Medicine, Salt Lake City, Utah 84108, USA
| | | | | |
Collapse
|
38
|
Extraordinary molecular evolution in the PRDM9 fertility gene. PLoS One 2009; 4:e8505. [PMID: 20041164 PMCID: PMC2794550 DOI: 10.1371/journal.pone.0008505] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 12/06/2009] [Indexed: 11/19/2022] Open
Abstract
Recent work indicates that allelic incompatibility in the mouse PRDM9 (Meisetz) gene can cause hybrid male sterility, contributing to genetic isolation and potentially speciation. The only phenotype of mouse PRDM9 knockouts is a meiosis I block that causes sterility in both sexes. The PRDM9 gene encodes a protein with histone H3(K4) trimethyltransferase activity, a KRAB domain, and a DNA-binding domain consisting of multiple tandem C2H2 zinc finger (ZF) domains. We have analyzed human coding polymorphism and interspecies evolutionary changes in the PRDM9 gene. The ZF domains of PRDM9 are evolving very rapidly, with compelling evidence of positive selection in primates. Positively selected amino acids are predominantly those known to make nucleotide specific contacts in C2H2 zinc fingers. These results suggest that PRDM9 is subject to recurrent selection to change DNA-binding specificity. The human PRDM9 protein is highly polymorphic in its ZF domains and nearly all polymorphisms affect the same nucleotide contact residues that are subject to positive selection. ZF domain nucleotide sequences are strongly homogenized within species, indicating that interfinger recombination contributes to their evolution. PRDM9 has previously been assumed to be a transcription factor required to induce meiosis specific genes, a role that is inconsistent with its molecular evolution. We suggest instead that PRDM9 is involved in some aspect of centromere segregation conflict and that rapidly evolving centromeric DNA drives changes in PRDM9 DNA-binding domains.
Collapse
|
39
|
Oliver PL, Goodstadt L, Bayes JJ, Birtle Z, Roach KC, Phadnis N, Beatson SA, Lunter G, Malik HS, Ponting CP. Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet 2009; 5:e1000753. [PMID: 19997497 PMCID: PMC2779102 DOI: 10.1371/journal.pgen.1000753] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 11/04/2009] [Indexed: 12/12/2022] Open
Abstract
The onset of prezygotic and postzygotic barriers to gene flow between populations is a hallmark of speciation. One of the earliest postzygotic isolating barriers to arise between incipient species is the sterility of the heterogametic sex in interspecies' hybrids. Four genes that underlie hybrid sterility have been identified in animals: Odysseus, JYalpha, and Overdrive in Drosophila and Prdm9 (Meisetz) in mice. Mouse Prdm9 encodes a protein with a KRAB motif, a histone methyltransferase domain and several zinc fingers. The difference of a single zinc finger distinguishes Prdm9 alleles that cause hybrid sterility from those that do not. We find that concerted evolution and positive selection have rapidly altered the number and sequence of Prdm9 zinc fingers across 13 rodent genomes. The patterns of positive selection in Prdm9 zinc fingers imply that rapid evolution has acted on the interface between the Prdm9 protein and the DNA sequences to which it binds. Similar patterns are apparent for Prdm9 zinc fingers for diverse metazoans, including primates. Indeed, allelic variation at the DNA–binding positions of human PRDM9 zinc fingers show significant association with decreased risk of infertility. Prdm9 thus plays a role in determining male sterility both between species (mouse) and within species (human). The recurrent episodes of positive selection acting on Prdm9 suggest that the DNA sequences to which it binds must also be evolving rapidly. Our findings do not identify the nature of the underlying DNA sequences, but argue against the proposed role of Prdm9 as an essential transcription factor in mouse meiosis. We propose a hypothetical model in which incompatibilities between Prdm9-binding specificity and satellite DNAs provide the molecular basis for Prdm9-mediated hybrid sterility. We suggest that Prdm9 should be investigated as a candidate gene in other instances of hybrid sterility in metazoans. Speciation, the process by which one species splits into two, involves reproductive barriers between previously interbreeding populations. The question of how speciation occurs has rightly occupied the attention of biologists since before Darwin's “On the Origin of Species.” Studies of recently diverged species have revealed the presence of hybrid sterility genes (colloquially referred to as “speciation genes”), alleles of which are associated with sterility of interspecies hybrids. Mouse Prdm9 is the only known such gene in vertebrate animals. Here we report that the Prdm9 protein has evolved extremely rapidly in its DNA-binding domain, comprising an array of “zinc fingers.” This suggests that hybrid sterility may arise from a mismatch between the DNA-binding specificity of Prdm9 and rapidly evolving DNA. We propose that Prdm9 binds to satellite-DNA repeats evolving rapidly within and between different species. Prdm9 evolution is unusual because other hybrid sterility genes appear only to evolve rapidly in isolated bursts, whereas Prdm9 has evolved rapidly over 700 million years, in many rodent species, diverse primates and other metazoans. This leads to the tantalizing possibility that Prdm9 may have served as a “speciation gene” on other occasions in metazoan evolution, a possibility that will now need to be investigated.
Collapse
Affiliation(s)
- Peter L. Oliver
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Leo Goodstadt
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Joshua J. Bayes
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Zoë Birtle
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Kevin C. Roach
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Nitin Phadnis
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Scott A. Beatson
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Gerton Lunter
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (CPP); (HSM)
| | - Chris P. Ponting
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (CPP); (HSM)
| |
Collapse
|