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Venu V, Harjunmaa E, Dreau A, Brady S, Absher D, Kingsley DM, Jones FC. Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish. Nat Ecol Evol 2024; 8:1337-1352. [PMID: 38839849 PMCID: PMC11239493 DOI: 10.1038/s41559-024-02434-4] [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: 08/21/2023] [Accepted: 05/02/2024] [Indexed: 06/07/2024]
Abstract
Despite deep evolutionary conservation, recombination rates vary greatly across the genome and among individuals, sexes and populations. Yet the impact of this variation on adaptively diverging populations is not well understood. Here we characterized fine-scale recombination landscapes in an adaptively divergent pair of marine and freshwater populations of threespine stickleback from River Tyne, Scotland. Through whole-genome sequencing of large nuclear families, we identified the genomic locations of almost 50,000 crossovers and built recombination maps for marine, freshwater and hybrid individuals at a resolution of 3.8 kb. We used these maps to quantify the factors driving variation in recombination rates. We found strong heterochiasmy between sexes but also differences in recombination rates among ecotypes. Hybrids showed evidence of significant recombination suppression in overall map length and in individual loci. Recombination rates were lower not only within individual marine-freshwater-adaptive loci, but also between loci on the same chromosome, suggesting selection on linked gene 'cassettes'. Through temporal sampling along a natural hybrid zone, we found that recombinants showed traits associated with reduced fitness. Our results support predictions that divergence in cis-acting recombination modifiers, whose functions are disrupted in hybrids, may play an important role in maintaining differences among adaptively diverging populations.
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Affiliation(s)
- Vrinda Venu
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- Los Alamos National Laboratory, New Mexico, NM, USA.
| | - Enni Harjunmaa
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- CeGAT GmbH, Tübingen, Germany
| | - Andreea Dreau
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Evotec SE 'Campus Curie', Toulouse, France
| | - Shannon Brady
- Deptartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - David M Kingsley
- Deptartment of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands.
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2
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Vanagas L, Muñoz D, Cristaldi C, Ganuza A, Nájera R, Bonardi MC, Turowski VR, Guzman F, Deng B, Kim K, Sullivan WJ, Angel SO. Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194943. [PMID: 37217032 PMCID: PMC10524646 DOI: 10.1016/j.bbagrm.2023.194943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B.Z. The combination of PTMs and the use of histone variants are important for gene regulation in T. gondii, offering new targets for drug development. In this work, T. gondii parasites were generated in which the 5 N-terminal acetylatable lysines in H2B.Z were mutated to either alanine (c-Myc-A) or arginine (c-Myc-R). The c-Myc-A mutant displayed no phenotype over than a mild defect in its ability to kill mice. The c-Myc-R mutant presented an impaired ability to grow and an increase in differentiation to latent bradyzoites. The c-Myc-R mutant was also more sensitive to DNA damage, displayed no virulence in mice, and provided protective immunity against future infection. While nucleosome composition was unaltered, key genes were abnormally expressed during in vitro bradyzoite differentiation. Our results show that regulation of the N-terminal positive charge patch of H2B.Z is important for these processes. We also show that acetylated N-terminal H2B.Z interacts with some unique proteins compared to its unacetylated counterpart; the acetylated peptide pulled down proteins associated with chromosome maintenance/segregation and cell cycle, suggesting a link between H2B.Z acetylation status and mitosis.
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Affiliation(s)
- Laura Vanagas
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina.
| | - Daniela Muñoz
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Agustina Ganuza
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Rosario Nájera
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Mabel C Bonardi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina
| | - Valeria R Turowski
- Laboratorio de Bioquímica y Biología Celular de Parásitos, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA Chascomús, Prov. Buenos Aires, Argentina
| | - Fanny Guzman
- Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaiso, Av. Universidad 330 Curauma, Valparaiso, Chile
| | - Bin Deng
- Department of Biology and VBRN, University of Vermont, VT, USA
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - William J Sullivan
- Department of Pharmacology and Toxicology, Indiana School of Medicine, Indianapolis, IN 46202, USA
| | - Sergio O Angel
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, B7130IIWA, Chascomús, Prov. Buenos Aires, Argentina.
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3
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Vanagas L, Muñoz D, Cristaldi C, Ganuza A, Nájera R, Bonardi MC, Turowski VR, Guzman F, Deng B, Kim K, Sullivan WJ, Angel SO. Histone variant H2B.Z acetylation is necessary for maintenance of Toxoplasma gondii biological fitness. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528480. [PMID: 36824796 PMCID: PMC9949044 DOI: 10.1101/2023.02.14.528480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B.Z. The combination of PTMs and the use of histone variants is important for gene regulation in T. gondii, offering new targets for drug development. In this work, T. gondii parasites were generated in which the 5 N-terminal acetylatable lysines in H2B.Z were mutated to either alanine (c-Myc-A) or arginine (c-Myc-R). c-Myc-A mutant only displayed a mild effect in its ability to kill mice. c-Myc-R mutant presented an impaired ability to grow and an increase in differentiation to latent bradyzoites. This mutant line was also more sensitive to DNA damage, displayed no virulence in mice, and provided protective immunity against future infection. While nucleosome composition was unaltered, key genes were abnormally expressed during in vitro bradyzoite differentiation. Our results show that the N-terminal positive charge patch of H2B.Z is important for these procceses. Pull down assays with acetylated N-terminal H2B.Z peptide and unacetylated one retrieved common and differential interactors. Acetylated peptide pulled down proteins associated with chromosome maintenance/segregation and cell cycle, opening the question of a possible link between H2B.Z acetylation status and mitosis.
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Affiliation(s)
- Laura Vanagas
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Daniela Muñoz
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Constanza Cristaldi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Agustina Ganuza
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Rosario Nájera
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Mabel C. Bonardi
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Valeria R. Turowski
- Laboratorio de Bioquímica y Biología Celular de Parásitos, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
| | - Fanny Guzman
- Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaiso. Av. Universidad 330 Curauma, Valparaiso
| | - Bin Deng
- Department of Biology and VBRN, University of Vermont, Vermont, USA
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612
| | - William J. Sullivan
- Department of Pharmacology and Toxicology, Indiana School of Medicine, Indianapolis, Indiana 46202, USA
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, INTECH, CONICET-UNSAM, Av. Intendente Marino Km. 8.2, C.C 164, (B7130IIWA), Chascomús, Prov. Buenos Aires, Argentina
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Integration of Transcriptome and Epigenome to Identify and Develop Prognostic Markers for Ovarian Cancer. JOURNAL OF ONCOLOGY 2022; 2022:3744466. [PMID: 36081667 PMCID: PMC9448543 DOI: 10.1155/2022/3744466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/04/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022]
Abstract
DNA methylation is a widely researched epigenetic modification. It is associated with the occurrence and development of cancer and has helped evaluate patients' prognoses. However, most existing DNA methylation prognosis models have not simultaneously considered the changes of the downstream transcriptome. Methods. The RNA-Sequencing data and DNA methylation omics data of ovarian cancer patients were downloaded from The Cancer Genome Atlas (TCGA) database. The Consensus Cluster Plus algorithm was used to construct the methylated molecular subtypes of the ovary. Lasso regression was employed to build a multi-gene signature. An independent data set was applied to verify the prognostic value of the signature. The Gene Set Variation Analysis (GSVA) was used to carry out the enrichment analysis of the pathways linked to the gene signature. The IMvigor 210 cohort was used to explore the predictive efficacy of the gene signature for immunotherapy response. Results. We distinguished ovarian cancer samples into two subtypes with different prognosis, based on the omics data of DNA methylation. Differentially expressed genes and enrichment analysis among subtypes indicated that DNA methylation was related to fatty acid metabolism and the extracellular matrix (ECM)-receptor. Furthermore, we constructed an 8-gene signature, which proved to be efficient and stable in predicting prognostics in ovarian cancer patients with different data sets and distinctive pathological characteristics. Finally, the 8-gene signature could predict patients' responses to immunotherapy. The polymerase chain reaction experiment was further used to verify the expression of 8 genes. Conclusion. We analyzed the prognostic value of the related genes of methylation in ovarian cancer. The 8-gene signature predicted the prognosis and immunotherapy response of ovarian cancer patients well and is expected to be valuable in clinical application.
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Multi-color dSTORM microscopy in Hormad1-/- spermatocytes reveals alterations in meiotic recombination intermediates and synaptonemal complex structure. PLoS Genet 2022; 18:e1010046. [PMID: 35857787 PMCID: PMC9342782 DOI: 10.1371/journal.pgen.1010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 08/01/2022] [Accepted: 06/15/2022] [Indexed: 12/05/2022] Open
Abstract
Recombinases RAD51 and its meiosis-specific paralog DMC1 accumulate on single-stranded DNA (ssDNA) of programmed DNA double strand breaks (DSBs) in meiosis. Here we used three-color dSTORM microscopy, and a mouse model with severe defects in meiotic DSB formation and synapsis (Hormad1-/-) to obtain more insight in the recombinase accumulation patterns in relation to repair progression. First, we used the known reduction in meiotic DSB frequency in Hormad1-/- spermatocytes to be able to conclude that the RAD51/DMC1 nanofoci that preferentially localize at distances of ~300 nm form within a single DSB site, whereas a second preferred distance of ~900 nm, observed only in wild type, represents inter-DSB distance. Next, we asked whether the proposed role of HORMAD1 in repair inhibition affects the RAD51/DMC1 accumulation patterns. We observed that the two most frequent recombinase configurations (1 DMC1 and 1 RAD51 nanofocus (D1R1), and D2R1) display coupled frequency dynamics over time in wild type, but were constant in the Hormad1-/- model, indicating that the lifetime of these intermediates was altered. Recombinase nanofoci were also smaller in Hormad1-/- spermatocytes, consistent with changes in ssDNA length or protein accumulation. Furthermore, we established that upon synapsis, recombinase nanofoci localized closer to the synaptonemal complex (SYCP3), in both wild type and Hormad1-/- spermatocytes. Finally, the data also revealed a hitherto unknown function of HORMAD1 in inhibiting coil formation in the synaptonemal complex. SPO11 plays a similar but weaker role in coiling and SYCP1 had the opposite effect. Using this large super-resolution dataset, we propose models with the D1R1 configuration representing one DSB end containing recombinases, and the other end bound by other ssDNA binding proteins, or both ends loaded by the two recombinases, but in below-resolution proximity. This may then often evolve into D2R1, then D1R2, and finally back to D1R1, when DNA synthesis has commenced. In order to correctly pair homologous chromosomes in the first meiotic prophase, repair of programmed double strand breaks (DSBs) is essential. By unravelling molecular details of the protein assemblies at single DSBs, using super-resolution microscopy, we aim to understand the dynamics of repair intermediates and their functions. We investigated the localization of the two recombinases RAD51 and DMC1 in wild type and HORMAD1-deficient cells. HORMAD1 is involved in multiple aspects of homologous chromosome association: it regulates formation and repair of DSBs, and it stimulates formation of the synaptonemal complex (SC), the macromolecular protein assembly that connects paired chromosomes. RAD51 and DMC1 enable chromosome pairing by promoting the invasions of the intact chromatids by single-stranded DNA ends that result from DSBs. We found that in absence of HORMAD1, RAD51 and DMC1 showed small but significant morphological and positional changes, combined with altered kinetics of specific RAD51/DMC1 configurations. We also determined that there is a generally preferred distance of ~900 nm between meiotic DSBs along the SC. Finally, we observed changes in the structure of the SC in Hormad1-/- spermatocytes. This study contributes to a better understanding of the molecular details of meiotic homologous recombination and the role of HORMAD1 in meiotic prophase.
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Trichoderma reesei Rad51 tolerates mismatches in hybrid meiosis with diverse genome sequences. Proc Natl Acad Sci U S A 2021; 118:2007192118. [PMID: 33593897 PMCID: PMC7923544 DOI: 10.1073/pnas.2007192118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Sexual eukaryotes fall into two groups with respect to their RecA-like recombinases. The first group possesses Rad51 (ubiquitous) and Dmc1 (meiosis-specific), which cooperate to conduct interhomolog recombination in zygotes with high sequence heterogeneity. Interestingly, Dmc1 was lost from the second group of eukaryotic organisms. Here we used the industrial workhorse fungus Trichoderma reesei to address if and how Rad51-only eukaryotes carry out hybrid meiosis. We show that T. reesei Rad51 (TrRad51) is indispensable for interhomolog recombination during meiosis and that TrRad51, like Saccharomyces cerevisiae Dmc1, possesses a better mismatch tolerability than S. cerevisiae Rad51. Our results indicate that the ancestral TrRad51 evolved to acquire Dmc1-like properties by adopting multiple structural variations in the L1 and L2 DNA-binding loops. Most eukaryotes possess two RecA-like recombinases (ubiquitous Rad51 and meiosis-specific Dmc1) to promote interhomolog recombination during meiosis. However, some eukaryotes have lost Dmc1. Given that mammalian and yeast Saccharomyces cerevisiae (Sc) Dmc1 have been shown to stabilize recombination intermediates containing mismatches better than Rad51, we used the Pezizomycotina filamentous fungus Trichoderma reesei to address if and how Rad51-only eukaryotes conduct interhomolog recombination in zygotes with high sequence heterogeneity. We applied multidisciplinary approaches (next- and third-generation sequencing technology, genetics, cytology, bioinformatics, biochemistry, and single-molecule biophysics) to show that T. reesei Rad51 (TrRad51) is indispensable for interhomolog recombination during meiosis and, like ScDmc1, TrRad51 possesses better mismatch tolerance than ScRad51 during homologous recombination. Our results also indicate that the ancestral TrRad51 evolved to acquire ScDmc1-like properties by creating multiple structural variations, including via amino acid residues in the L1 and L2 DNA-binding loops.
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Luo SC, Yeh HY, Lan WH, Wu YM, Yang CH, Chang HY, Su GC, Lee CY, Wu WJ, Li HW, Ho MC, Chi P, Tsai MD. Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures. Nat Commun 2021; 12:115. [PMID: 33446654 PMCID: PMC7809202 DOI: 10.1038/s41467-020-20258-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/23/2020] [Indexed: 11/24/2022] Open
Abstract
Both high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases. RAD51 and DMC1 recombinases catalyse high-fidelity and mismatch tolerant recombination, processes that are indispensable for the maintenance of genomic integrity. Here, the authors via cryo-EM, molecular dynamics simulation and functional analysis elucidate the structural difference between RAD51 and DMC1 with regard to mismatch tolerance.
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Affiliation(s)
- Shih-Chi Luo
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wei-Hsuan Lan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yi-Min Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Guan-Chin Su
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chia-Yi Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Peter Chi
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan.
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Abstract
Accurate DNA repair and replication are critical for genomic stability and cancer prevention. RAD51 and its gene family are key regulators of DNA fidelity through diverse roles in double-strand break repair, replication stress, and meiosis. RAD51 is an ATPase that forms a nucleoprotein filament on single-stranded DNA. RAD51 has the function of finding and invading homologous DNA sequences to enable accurate and timely DNA repair. Its paralogs, which arose from ancient gene duplications of RAD51, have evolved to regulate and promote RAD51 function. Underscoring its importance, misregulation of RAD51, and its paralogs, is associated with diseases such as cancer and Fanconi anemia. In this review, we focus on the mammalian RAD51 structure and function and highlight the use of model systems to enable mechanistic understanding of RAD51 cellular roles. We also discuss how misregulation of the RAD51 gene family members contributes to disease and consider new approaches to pharmacologically inhibit RAD51.
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Affiliation(s)
- Braulio Bonilla
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - Sarah R Hengel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - McKenzie K Grundy
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA;
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Mota MBS, Carvalho MA, Monteiro ANA, Mesquita RD. DNA damage response and repair in perspective: Aedes aegypti, Drosophila melanogaster and Homo sapiens. Parasit Vectors 2019; 12:533. [PMID: 31711518 PMCID: PMC6849265 DOI: 10.1186/s13071-019-3792-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023] Open
Abstract
Background The maintenance of genomic integrity is the responsibility of a complex network, denominated the DNA damage response (DDR), which controls the lesion detection and DNA repair. The main repair pathways are base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination repair (HR) and non-homologous end joining repair (NHEJ). They correct double-strand breaks (DSB), single-strand breaks, mismatches and others, or when the damage is quite extensive and repair insufficient, apoptosis is activated. Methods In this study we used the BLAST reciprocal best-hit methodology to search for DDR orthologs proteins in Aedes aegypti. We also provided a comparison between Ae. aegypti, D. melanogaster and human DDR network. Results Our analysis revealed the presence of ATR and ATM signaling, including the H2AX ortholog, in Ae. aegypti. Key DDR proteins (orthologs to RAD51, Ku and MRN complexes, XP-components, MutS and MutL) were also identified in this insect. Other proteins were not identified in both Ae. aegypti and D. melanogaster, including BRCA1 and its partners from BRCA1-A complex, TP53BP1, PALB2, POLk, CSA, CSB and POLβ. In humans, their absence affects DSB signaling, HR and sub-pathways of NER and BER. Seven orthologs not known in D. melanogaster were found in Ae. aegypti (RNF168, RIF1, WRN, RAD54B, RMI1, DNAPKcs, ARTEMIS). Conclusions The presence of key DDR proteins in Ae. aegypti suggests that the main DDR pathways are functional in this insect, and the identification of proteins not known in D. melanogaster can help fill gaps in the DDR network. The mapping of the DDR network in Ae. aegypti can support mosquito biology studies and inform genetic manipulation approaches applied to this vector.
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Affiliation(s)
- Maria Beatriz S Mota
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcelo Alex Carvalho
- Instituto Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro, RJ, Brazil
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rafael D Mesquita
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Ma HT, Niu CM, Xia J, Shen XY, Xia MM, Hu YQ, Zheng Y. Stimulated by retinoic acid gene 8 (Stra8) plays important roles in many stages of spermatogenesis. Asian J Androl 2019; 20:479-487. [PMID: 29848833 PMCID: PMC6116687 DOI: 10.4103/aja.aja_26_18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To clarify the functions and mechanism of stimulated by retinoic acid gene 8 (Stra8) in spermatogenesis, we analyzed the testes from Stra8 knockout and wild-type mice during the first wave of spermatogenesis. Comparisons showed no significant differences in morphology and number of germ cells at 11 days postpartum, while 21 differentially expressed genes (DEGs) associated with spermatogenesis were identified. We speculate that Stra8 performs many functions in different phases of spermatogenesis, such as establishment of spermatogonial stem cells, spermatogonial proliferation and self-renewal, spermatogonial differentiation and meiosis, through direct or indirect regulation of these DEGs. We therefore established a preliminary regulatory network of Stra8 during spermatogenesis. These results will provide a theoretical basis for further research on the mechanism underlying the role of Stra8 in spermatogenesis.
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Affiliation(s)
- Hai-Tao Ma
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou 225001, China.,Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou 225001, China
| | - Chang-Min Niu
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou 225001, China.,Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou 225001, China
| | - Jing Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou 225001, China.,Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou 225001, China
| | - Xue-Yi Shen
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou 225001, China.,Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou 225001, China
| | - Meng-Meng Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou 225001, China.,Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou 225001, China
| | - Yan-Qiu Hu
- Clinicial Medical College, Yangzhou University, Yangzhou 225001, China
| | - Ying Zheng
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou 225001, China.,Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou 225001, China
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11
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Steinfeld JB, Beláň O, Kwon Y, Terakawa T, Al-Zain A, Smith MJ, Crickard JB, Qi Z, Zhao W, Rothstein R, Symington LS, Sung P, Boulton SJ, Greene EC. Defining the influence of Rad51 and Dmc1 lineage-specific amino acids on genetic recombination. Genes Dev 2019; 33:1191-1207. [PMID: 31371435 PMCID: PMC6719624 DOI: 10.1101/gad.328062.119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
The vast majority of eukaryotes possess two DNA recombinases: Rad51, which is ubiquitously expressed, and Dmc1, which is meiosis-specific. The evolutionary origins of this two-recombinase system remain poorly understood. Interestingly, Dmc1 can stabilize mismatch-containing base triplets, whereas Rad51 cannot. Here, we demonstrate that this difference can be attributed to three amino acids conserved only within the Dmc1 lineage of the Rad51/RecA family. Chimeric Rad51 mutants harboring Dmc1-specific amino acids gain the ability to stabilize heteroduplex DNA joints with mismatch-containing base triplets, whereas Dmc1 mutants with Rad51-specific amino acids lose this ability. Remarkably, RAD-51 from Caenorhabditis elegans, an organism without Dmc1, has acquired "Dmc1-like" amino acids. Chimeric C. elegans RAD-51 harboring "canonical" Rad51 amino acids gives rise to toxic recombination intermediates, which must be actively dismantled to permit normal meiotic progression. We propose that Dmc1 lineage-specific amino acids involved in the stabilization of heteroduplex DNA joints with mismatch-containing base triplets may contribute to normal meiotic recombination.
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Affiliation(s)
- Justin B Steinfeld
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Ondrej Beláň
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Tsuyoshi Terakawa
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Amr Al-Zain
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Michael J Smith
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - J Brooks Crickard
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Zhi Qi
- Center for Quantitative Biology, Peking University-Tsinghua University Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York 10032, USA
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12
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Yamada S, Kim S, Tischfield SE, Jasin M, Lange J, Keeney S. Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice. Cell Cycle 2017; 16:1870-1884. [PMID: 28820351 PMCID: PMC5638367 DOI: 10.1080/15384101.2017.1361065] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/27/2017] [Accepted: 07/25/2017] [Indexed: 11/12/2022] Open
Abstract
The SPO11-generated DNA double-strand breaks (DSBs) that initiate meiotic recombination occur non-randomly across genomes, but mechanisms shaping their distribution and repair remain incompletely understood. Here, we expand on recent studies of nucleotide-resolution DSB maps in mouse spermatocytes. We find that trimethylation of histone H3 lysine 36 around DSB hotspots is highly correlated, both spatially and quantitatively, with trimethylation of H3 lysine 4, consistent with coordinated formation and action of both PRDM9-dependent histone modifications. In contrast, the DSB-responsive kinase ATM contributes independently of PRDM9 to controlling hotspot activity, and combined action of ATM and PRDM9 can explain nearly two-thirds of the variation in DSB frequency between hotspots. DSBs were modestly underrepresented in most repetitive sequences such as segmental duplications and transposons. Nonetheless, numerous DSBs form within repetitive sequences in each meiosis and some classes of repeats are preferentially targeted. Implications of these findings are discussed for evolution of PRDM9 and its role in hybrid strain sterility in mice. Finally, we document the relationship between mouse strain-specific DNA sequence variants within PRDM9 recognition motifs and attendant differences in recombination outcomes. Our results provide further insights into the complex web of factors that influence meiotic recombination patterns.
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Affiliation(s)
- Shintaro Yamada
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seoyoung Kim
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sam E. Tischfield
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julian Lange
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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13
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Mek1 Down Regulates Rad51 Activity during Yeast Meiosis by Phosphorylation of Hed1. PLoS Genet 2016; 12:e1006226. [PMID: 27483004 PMCID: PMC4970670 DOI: 10.1371/journal.pgen.1006226] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/08/2016] [Indexed: 11/24/2022] Open
Abstract
During meiosis, programmed double strand breaks (DSBs) are repaired preferentially between homologs to generate crossovers that promote proper chromosome segregation at Meiosis I. In many organisms, there are two strand exchange proteins, Rad51 and the meiosis-specific Dmc1, required for interhomolog (IH) bias. This bias requires the presence, but not the strand exchange activity of Rad51, while Dmc1 is responsible for the bulk of meiotic recombination. How these activities are regulated is less well established. In dmc1Δ mutants, Rad51 is actively inhibited, thereby resulting in prophase arrest due to unrepaired DSBs triggering the meiotic recombination checkpoint. This inhibition is dependent upon the meiosis-specific kinase Mek1 and occurs through two different mechanisms that prevent complex formation with the Rad51 accessory factor Rad54: (i) phosphorylation of Rad54 by Mek1 and (ii) binding of Rad51 by the meiosis-specific protein Hed1. An open question has been why inhibition of Mek1 affects Hed1 repression of Rad51. This work shows that Hed1 is a direct substrate of Mek1. Phosphorylation of Hed1 at threonine 40 helps suppress Rad51 activity in dmc1Δ mutants by promoting Hed1 protein stability. Rad51-mediated recombination occurring in the absence of Hed1 phosphorylation results in a significant increase in non-exchange chromosomes despite wild-type levels of crossovers, confirming previous results indicating a defect in crossover assurance. We propose that Rad51 function in meiosis is regulated in part by the coordinated phosphorylation of Rad54 and Hed1 by Mek1. Sexual reproduction requires the formation of haploid gametes by a highly conserved, specialized cell division called meiosis. Failures in meiotic chromosome segregation lead to chromosomally imbalanced gametes that cause infertility and birth defects such as Trisomy 21 in humans. Meiotic crossovers, initiated by programmed double strand breaks (DSBs), are critical for proper chromosome segregation. Interhomolog strand invasion requires the presence of Rad51, and the strand invasion activity of the meiosis-specific recombinase Dmc1. The meiosis-specific kinase, Mek1, is a key regulator of meiotic recombination, promoting interhomolog strand invasion and recombination pathway choice. Rad51 activity during meiosis is inhibited by preventing the Rad51 protein from forming complexes with an accessory factor, Rad54, in two ways: (1) Mek1 phosphorylation of Rad54 and (2) binding of Rad51 by a meiosis-specific protein, Hed1. Why inactivation of Mek1 affects Hed1-mediated repression of Rad51 was previously unknown. This work demonstrates that Mek1 regulates the ability of Hed1 to inhibit Rad51 by direct phosphorylation of Hed1. Therefore in meiosis, Rad51 activity is regulated in part by the coordinated phosphorylation of both Rad54 and Hed1 by Mek1.
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