1
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Errbii M, Gadau J, Becker K, Schrader L, Oettler J. Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior. Genome Res 2024; 34:863-876. [PMID: 38839375 PMCID: PMC11293551 DOI: 10.1101/gr.278392.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions that are enriched with TEs, that have strong haplotype divergence, or that show signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.
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Affiliation(s)
- Mohammed Errbii
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Kerstin Becker
- Cologne Center for Genomics (CCG), Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Jan Oettler
- Lehrstuhl für Zoologie/Evolutionsbiologie, University Regensburg, 93053 Regensburg, Germany
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2
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Carreira R, Lama-Diaz T, Crugeiras M, Aguado F, Sebesta M, Krejci L, Blanco M. Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors. Nucleic Acids Res 2024; 52:7012-7030. [PMID: 38832625 PMCID: PMC11229367 DOI: 10.1093/nar/gkae453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination involves the formation of branched DNA molecules that may interfere with chromosome segregation. To resolve these persistent joint molecules, cells rely on the activation of structure-selective endonucleases (SSEs) during the late stages of the cell cycle. However, the premature activation of SSEs compromises genome integrity, due to untimely processing of replication and/or recombination intermediates. Here, we used a biochemical approach to show that the budding yeast SSEs Mus81 and Yen1 possess the ability to cleave the central recombination intermediate known as the displacement loop or D-loop. Moreover, we demonstrate that, consistently with previous genetic data, the simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursor in vitro. Our results provide not only mechanistic explanation for the formation of a half-crossover, but also highlight the critical importance for precise regulation of these SSEs to prevent chromosomal rearrangements.
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Affiliation(s)
- Raquel Carreira
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Tomas Lama-Diaz
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Maria Crugeiras
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - F Javier Aguado
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
| | - Marek Sebesta
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic
| | - Miguel G Blanco
- Department of Biochemistry and Molecular Biology, CIMUS, Universidade de Santiago de Compostela-Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, A Coruña 15782, Spain
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3
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Li Y, Zhu R, Jin J, Guo H, Zhang J, He Z, Liang T, Guo L. Exploring the Role of Clustered Mutations in Carcinogenesis and Their Potential Clinical Implications in Cancer. Int J Mol Sci 2024; 25:6744. [PMID: 38928450 PMCID: PMC11203652 DOI: 10.3390/ijms25126744] [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: 04/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Abnormal cell proliferation and growth leading to cancer primarily result from cumulative genome mutations. Single gene mutations alone do not fully explain cancer onset and progression; instead, clustered mutations-simultaneous occurrences of multiple mutations-are considered to be pivotal in cancer development and advancement. These mutations can affect different genes and pathways, resulting in cells undergoing malignant transformation with multiple functional abnormalities. Clustered mutations influence cancer growth rates, metastatic potential, and drug treatment sensitivity. This summary highlights the various types and characteristics of clustered mutations to understand their associations with carcinogenesis and discusses their potential clinical significance in cancer. As a unique mutation type, clustered mutations may involve genomic instability, DNA repair mechanism defects, and environmental exposures, potentially correlating with responsiveness to immunotherapy. Understanding the characteristics and underlying processes of clustered mutations enhances our comprehension of carcinogenesis and cancer progression, providing new diagnostic and therapeutic approaches for cancer.
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Affiliation(s)
- Yi Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Rui Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaming Jin
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Haochuan Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Jiaxi Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Zhiheng He
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, School of Life Science, Nanjing Normal University, Nanjing 210023, China; (Y.L.); (R.Z.); (H.G.); (J.Z.)
| | - Li Guo
- State Key Laboratory of Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (J.J.); (Z.H.)
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4
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Ferguson S, Jones A, Murray K, Andrew RL, Schwessinger B, Bothwell H, Borevitz J. Exploring the role of polymorphic interspecies structural variants in reproductive isolation and adaptive divergence in Eucalyptus. Gigascience 2024; 13:giae029. [PMID: 38869149 PMCID: PMC11170218 DOI: 10.1093/gigascience/giae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 03/11/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024] Open
Abstract
Structural variations (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related Eucalyptus species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of Eucalyptus melliodora and Eucalyptus sideroxylon, along with recent high-quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads in E. melliodora and E. sideroxylon, respectively. Focusing on inversions and translocations, symmetric SVs that are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076 Germany
| | - Rose L Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
| | - Helen Bothwell
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens 30602 GA, United States
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2600 Australia
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5
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Hou Z, Xu Z, Wu M, Ma L, Sui L, Bian P, Wang T. Enhancement of Repeat-Mediated Deletion Rearrangement Induced by Particle Irradiation in a RecA-Dependent Manner in Escherichia coli. BIOLOGY 2023; 12:1406. [PMID: 37998005 PMCID: PMC10669199 DOI: 10.3390/biology12111406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Repeat-mediated deletion (RMD) rearrangement is a major source of genome instability and can be deleterious to the organism, whereby the intervening sequence between two repeats is deleted along with one of the repeats. RMD rearrangement is likely induced by DNA double-strand breaks (DSBs); however, it is unclear how the complexity of DSBs influences RMD rearrangement. Here, a transgenic Escherichia coli strain K12 MG1655 with a lacI repeat-controlled amp activation was used while taking advantage of particle irradiation, such as proton and carbon irradiation, to generate different complexities of DSBs. Our research confirmed the enhancement of RMD under proton and carbon irradiation and revealed a positive correlation between RMD enhancement and LET. In addition, RMD enhancement could be suppressed by an intermolecular homologous sequence, which was regulated by its composition and length. Meanwhile, RMD enhancement was significantly stimulated by exogenous λ-Red recombinase. Further results investigating its mechanisms showed that the enhancement of RMD, induced by particle irradiation, occurred in a RecA-dependent manner. Our finding has a significant impact on the understanding of RMD rearrangement and provides some clues for elucidating the repair process and possible outcomes of complex DNA damage.
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Affiliation(s)
- Zhiyang Hou
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.H.); (Z.X.); (M.W.); (P.B.)
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Science Island Branch, Graduate School of USTC, Hefei 230026, China
| | - Zelin Xu
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.H.); (Z.X.); (M.W.); (P.B.)
| | - Mengying Wu
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.H.); (Z.X.); (M.W.); (P.B.)
| | - Liqiu Ma
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413, China;
- National Innovation Center of Radiation Application, Beijing 102413, China
| | - Li Sui
- Department of Nuclear Physics, China Institute of Atomic Energy, Beijing 102413, China;
- National Innovation Center of Radiation Application, Beijing 102413, China
| | - Po Bian
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.H.); (Z.X.); (M.W.); (P.B.)
| | - Ting Wang
- Teaching and Research Section of Nuclear Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China; (Z.H.); (Z.X.); (M.W.); (P.B.)
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6
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. Genes Dev 2023; 37:621-639. [PMID: 37541760 PMCID: PMC10499017 DOI: 10.1101/gad.350618.123] [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: 03/10/2023] [Accepted: 07/14/2023] [Indexed: 08/06/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR subpathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology and results in sequence insertion without additional breaks or SVs. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Yasmina Djeghmoum
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Ruth A Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, USA;
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA
| | - Aurèle Piazza
- Laboratory of Biology and Modelling of the Cell (UMR5239), Ecole Normale Supérieure de Lyon, 69007 Lyon, France;
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7
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Reitz D, Djeghmoum Y, Watson RA, Rajput P, Argueso JL, Heyer WD, Piazza A. Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532751. [PMID: 36993162 PMCID: PMC10055120 DOI: 10.1101/2023.03.15.532751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Punctuated bursts of structural genomic variations (SVs) have been described in various organisms, but their etiology remains incompletely understood. Homologous recombination (HR) is a template-guided mechanism of repair of DNA double-strand breaks and stalled or collapsed replication forks. We recently identified a DNA break amplification and genome rearrangement pathway originating from the endonucleolytic processing of a multi-invasion (MI) DNA joint molecule formed during HR. Genome-wide sequencing approaches confirmed that multi-invasion-induced rearrangement (MIR) frequently leads to several repeat-mediated SVs and aneuploidies. Using molecular and genetic analysis, and a novel, highly sensitive proximity ligation-based assay for chromosomal rearrangement quantification, we further delineate two MIR sub-pathways. MIR1 is a universal pathway occurring in any sequence context, which generates secondary breaks and frequently leads to additional SVs. MIR2 occurs only if recombining donors exhibit substantial homology, and results in sequence insertion without additional break or SV. The most detrimental MIR1 pathway occurs late on a subset of persisting DNA joint molecules in a PCNA/Polδ-independent manner, unlike recombinational DNA synthesis. This work provides a refined mechanistic understanding of these HR-based SV formation pathways and shows that complex repeat-mediated SVs can occur without displacement DNA synthesis. Sequence signatures for inferring MIR1 from long-read data are proposed.
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Affiliation(s)
- Diedre Reitz
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Yasmina Djeghmoum
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
| | - Ruth A. Watson
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Pallavi Rajput
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, One Shields Ave, University of California, Davis, CA 95616, USA
- Department of Molecular and Cellular Biology, One Shields Ave, University of California, Davis, CA 95616, USA
| | - Aurèle Piazza
- Univ Lyon, ENS, UCBL, CNRS, INSERM, Laboratory of Biology and Modelling of the Cell, UMR5239, U 1210, F-69364, Lyon, France
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8
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Ferguson S, Jones A, Murray K, Schwessinger B, Borevitz JO. Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus. Mol Ecol 2023; 32:1271-1287. [PMID: 35810343 DOI: 10.1111/mec.16608] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/27/2022]
Abstract
Synteny, the ordering of sequences within homologous chromosomes, must be maintained within the genomes of sexually reproducing species for the sharing of alleles and production of viable, reproducing offspring. However, when the genomes of closely related species are compared, a loss of synteny is often observed. Unequal homologous recombination is the primary mechanism behind synteny loss, occurring more often in transposon rich regions, and resulting in the formation of chromosomal rearrangements. To examine patterns of synteny among three closely related, interbreeding, and wild Eucalyptus species, we assembled their genomes using long-read DNA sequencing and de novo assembly. We identify syntenic and rearranged regions between these genomes and estimate that ~48% of our genomes remain syntenic while ~36% is rearranged. We observed that rearrangements highly fragment microsynteny. Our results suggest that synteny between these species is primarily lost through small-scale rearrangements, not through sequence loss, gain, or sequence divergence. Further examination of identified rearrangements suggests that rearrangements may be altering the phenotypes of Eucalyptus species. Our study also underscores that the use of single reference genomes in genomic variation studies could lead to reference bias, especially given the scale at which we show potentially adaptive loci have highly diverged, deleted, duplicated and/or rearranged. This study provides an unbiased framework to look at potential speciation and adaptive loci among a rapidly radiating foundation species of woodland trees that are free from selective breeding seen in most crop species.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.,Weigel Department, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Justin O Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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9
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Recillas-Targa F. Cancer Epigenetics: An Overview. Arch Med Res 2022; 53:732-740. [PMID: 36411173 DOI: 10.1016/j.arcmed.2022.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/18/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022]
Abstract
Cancer is a complex disease caused by genetic and epigenetic alterations in the control of cell division. Findings from the field of cancer genomics and epigenomics have increased our understanding of the origin and evolution of tumorigenic processes, greatly advancing our knowledge of the molecular etiology of cancer. Consequently, any contemporary view of cancer research must consider tumorigenesis as a cellular phenomenon that is a result of the interplay between genetic and epigenetic mutations and their interaction with environmental factors, including our microbiome, that influences cellular metabolism and proliferation rates. The integration and better knowledge of these processes will help us to improve diagnosis, prognosis, and future genetic and epigenetic therapies. Here, I present an overview of the epigenetic processes that are affected in cancer and how they contribute to the onset and progression of the disease. Finally, I discuss how the development of sophisticated experimental approaches and computational tools, including novel ways to exploit large data sets, could contribute to the better understanding and treatment of cancer.
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Affiliation(s)
- Félix Recillas-Targa
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México.
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10
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Pascarella G, Hon CC, Hashimoto K, Busch A, Luginbühl J, Parr C, Hin Yip W, Abe K, Kratz A, Bonetti A, Agostini F, Severin J, Murayama S, Suzuki Y, Gustincich S, Frith M, Carninci P. Recombination of repeat elements generates somatic complexity in human genomes. Cell 2022; 185:3025-3040.e6. [DOI: 10.1016/j.cell.2022.06.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/30/2022] [Accepted: 06/16/2022] [Indexed: 12/14/2022]
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11
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Piazza A, Bordelet H, Dumont A, Thierry A, Savocco J, Girard F, Koszul R. Cohesin regulates homology search during recombinational DNA repair. Nat Cell Biol 2021; 23:1176-1186. [PMID: 34750581 DOI: 10.1038/s41556-021-00783-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023]
Abstract
Homologous recombination repairs DNA double-strand breaks (DSB) using an intact dsDNA molecule as a template. It entails a homology search step, carried out along a conserved RecA/Rad51-ssDNA filament assembled on each DSB end. Whether, how and to what extent a DSB impacts chromatin folding, and how this (re)organization in turns influences the homology search process, remain ill-defined. Here we characterize two layers of spatial chromatin reorganization following DSB formation in Saccharomyces cerevisiae. Although cohesin folds chromosomes into cohesive arrays of ~20-kb-long chromatin loops as cells arrest in G2/M, the DSB-flanking regions interact locally in a resection- and 9-1-1 clamp-dependent manner, independently of cohesin, Mec1ATR, Rad52 and Rad51. This local structure blocks cohesin progression, constraining the DSB region at the base of a loop. Functionally, cohesin promotes DSB-dsDNA interactions and donor identification in cis, while inhibiting them in trans. This study identifies multiple direct and indirect ways by which cohesin regulates homology search during recombinational DNA repair.
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Affiliation(s)
- Aurèle Piazza
- Institut Pasteur, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015, Paris, France.
- Université de Lyon, ENS de Lyon, Université Claude Bernard, Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, INSERM U1210, 46 allée d'Italie, 69007, Lyon, France.
| | - Hélène Bordelet
- Institut Pasteur, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015, Paris, France
- Université de Lyon, ENS de Lyon, Université Claude Bernard, Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, INSERM U1210, 46 allée d'Italie, 69007, Lyon, France
| | - Agnès Dumont
- Université de Lyon, ENS de Lyon, Université Claude Bernard, Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, INSERM U1210, 46 allée d'Italie, 69007, Lyon, France
| | - Agnès Thierry
- Institut Pasteur, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015, Paris, France
| | - Jérôme Savocco
- Université de Lyon, ENS de Lyon, Université Claude Bernard, Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, INSERM U1210, 46 allée d'Italie, 69007, Lyon, France
| | - Fabien Girard
- Institut Pasteur, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015, Paris, France
| | - Romain Koszul
- Institut Pasteur, CNRS UMR3525, Unité Régulation Spatiale des Génomes, F-75015, Paris, France.
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