1
|
Phipps J, Dubrana K. DNA Repair in Space and Time: Safeguarding the Genome with the Cohesin Complex. Genes (Basel) 2022; 13:198. [PMID: 35205243 PMCID: PMC8872453 DOI: 10.3390/genes13020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
DNA double-strand breaks (DSBs) are a deleterious form of DNA damage, which must be robustly addressed to ensure genome stability. Defective repair can result in chromosome loss, point mutations, loss of heterozygosity or chromosomal rearrangements, which could lead to oncogenesis or cell death. We explore the requirements for the successful repair of DNA DSBs by non-homologous end joining and homology-directed repair (HDR) mechanisms in relation to genome folding and dynamics. On the occurrence of a DSB, local and global chromatin composition and dynamics, as well as 3D genome organization and break localization within the nuclear space, influence how repair proceeds. The cohesin complex is increasingly implicated as a key regulator of the genome, influencing chromatin composition and dynamics, and crucially genome organization through folding chromosomes by an active loop extrusion mechanism, and maintaining sister chromatid cohesion. Here, we consider how this complex is now emerging as a key player in the DNA damage response, influencing repair pathway choice and efficiency.
Collapse
Affiliation(s)
| | - Karine Dubrana
- UMR Stabilité Génétique Cellules Souches et Radiations, INSERM, iRCM/IBFJ CEA, Université de Paris and Université Paris-Saclay, F-92265 Fontenay-aux-Roses, France;
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Murakami H, Mu X, Keeney S. How do small chromosomes know they are small? Maximizing meiotic break formation on the shortest yeast chromosomes. Curr Genet 2021; 67:431-437. [PMID: 33604699 PMCID: PMC8141002 DOI: 10.1007/s00294-021-01160-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
Abstract
The programmed formation of DNA double-strand breaks (DSBs) in meiotic prophase I initiates the homologous recombination process that yields crossovers between homologous chromosomes, a prerequisite to accurately segregating chromosomes during meiosis I (MI). In the budding yeast Saccharomyces cerevisiae, proteins required for meiotic DSB formation (DSB proteins) accumulate to higher levels specifically on short chromosomes to ensure that these chromosomes make DSBs. We previously demonstrated that as-yet undefined cis-acting elements preferentially recruit DSB proteins and promote higher levels of DSBs and recombination and that these intrinsic features are subject to selection pressure to maintain the hyperrecombinogenic properties of short chromosomes. Thus, this targeted boosting of DSB protein binding may be an evolutionarily recurrent strategy to mitigate the risk of meiotic mis-segregation caused by karyotypic constraints. However, the underlining mechanisms are still elusive. Here, we discuss possible scenarios in which components of the meiotic chromosome axis (Red1 and Hop1) bind to intrinsic features independent of the meiosis-specific cohesin subunit Rec8 and DNA replication, promoting preferential binding of DSB proteins to short chromosomes. We also propose a model where chromosome position in the nucleus, influenced by centromeres, promotes the short-chromosome boost of DSB proteins.
Collapse
Affiliation(s)
- Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Xiaojing Mu
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Graduate School of Medical Sciences, Cornell University, New York, NY, 10021, USA
| | - Scott Keeney
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Weill Graduate School of Medical Sciences, Cornell University, New York, NY, 10021, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| |
Collapse
|
4
|
Brossas C, Valton AL, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau MN. Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. EMBO J 2020; 39:e99520. [PMID: 32935369 PMCID: PMC7604622 DOI: 10.15252/embj.201899520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/31/2020] [Accepted: 08/25/2020] [Indexed: 12/27/2022] Open
Abstract
Vertebrate genomes replicate according to a precise temporal program strongly correlated with their organization into A/B compartments. Until now, the molecular mechanisms underlying the establishment of early-replicating domains remain largely unknown. We defined two minimal cis-element modules containing a strong replication origin and chromatin modifier binding sites capable of shifting a targeted mid-late-replicating region for earlier replication. The two origins overlap with a constitutive or a silent tissue-specific promoter. When inserted side-by-side, these modules advance replication timing over a 250 kb region through the cooperation with one endogenous origin located 30 kb away. Moreover, when inserted at two chromosomal sites separated by 30 kb, these two modules come into close physical proximity and form an early-replicating domain establishing more contacts with active A compartments. The synergy depends on the presence of the active promoter/origin. Our results show that clustering of strong origins located at active promoters can establish early-replicating domains.
Collapse
Affiliation(s)
- Caroline Brossas
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Anne-Laure Valton
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sergey V Venev
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Antonin Counillon
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Marc Laurent
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Coralie Goncalves
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Bénédicte Duriez
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| | - Franck Picard
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marie-Noëlle Prioleau
- CNRS, Institut Jacques Monod, Equipe Labellisée Association Pour la Recherche sur le Cancer, Université de Paris, Paris, France
| |
Collapse
|
5
|
Guin K, Chen Y, Mishra R, Muzaki SRBM, Thimmappa BC, O'Brien CE, Butler G, Sanyal A, Sanyal K. Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres. eLife 2020; 9:e58556. [PMID: 32469306 PMCID: PMC7292649 DOI: 10.7554/elife.58556] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Centromeres of Candida albicans form on unique and different DNA sequences but a closely related species, Candida tropicalis, possesses homogenized inverted repeat (HIR)-associated centromeres. To investigate the mechanism of centromere type transition, we improved the fragmented genome assembly and constructed a chromosome-level genome assembly of C. tropicalis by employing PacBio sequencing, chromosome conformation capture sequencing (3C-seq), chromoblot, and genetic analysis of engineered aneuploid strains. Further, we analyzed the 3D genome organization using 3C-seq data, which revealed spatial proximity among the centromeres as well as telomeres of seven chromosomes in C. tropicalis. Intriguingly, we observed evidence of inter-centromeric translocations in the common ancestor of C. albicans and C. tropicalis. Identification of putative centromeres in closely related Candida sojae, Candida viswanathii and Candida parapsilosis indicates loss of ancestral HIR-associated centromeres and establishment of evolutionary new centromeres (ENCs) in C. albicans. We propose that spatial proximity of the homologous centromere DNA sequences facilitated karyotype rearrangements and centromere type transitions in human pathogenic yeasts of the CUG-Ser1 clade.
Collapse
Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Radha Mishra
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | | | - Bhagya C Thimmappa
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| | - Caoimhe E O'Brien
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Geraldine Butler
- School Of Biomolecular & Biomed Science, Conway Institute of Biomolecular and Biomedical Research, University College DublinDublinIreland
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological UniversitySingaporeSingapore
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific ResearchBangaloreIndia
| |
Collapse
|
6
|
The Rabl configuration limits topological entanglement of chromosomes in budding yeast. Sci Rep 2019; 9:6795. [PMID: 31043625 PMCID: PMC6494875 DOI: 10.1038/s41598-019-42967-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022] Open
Abstract
The three dimensional organization of genomes remains mostly unknown due to their high degree of condensation. Biophysical studies predict that condensation promotes the topological entanglement of chromatin fibers and the inhibition of function. How organisms balance between functionally active genomes and a high degree of condensation remains to be determined. Here we hypothesize that the Rabl configuration, characterized by the attachment of centromeres and telomeres to the nuclear envelope, helps to reduce the topological entanglement of chromosomes. To test this hypothesis we developed a novel method to quantify chromosome entanglement complexity in 3D reconstructions obtained from Chromosome Conformation Capture (CCC) data. Applying this method to published data of the yeast genome, we show that computational models implementing the attachment of telomeres or centromeres alone are not sufficient to obtain the reduced entanglement complexity observed in 3D reconstructions. It is only when the centromeres and telomeres are attached to the nuclear envelope (i.e. the Rabl configuration) that the complexity of entanglement of the genome is comparable to that of the 3D reconstructions. We therefore suggest that the Rabl configuration is an essential player in the simplification of the entanglement of chromatin fibers.
Collapse
|
7
|
Bordelet H, Dubrana K. Keep moving and stay in a good shape to find your homologous recombination partner. Curr Genet 2019; 65:29-39. [PMID: 30097675 PMCID: PMC6342867 DOI: 10.1007/s00294-018-0873-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 01/02/2023]
Abstract
Genomic DNA is constantly exposed to damage. Among the lesion in DNA, double-strand breaks (DSB), because they disrupt the two strands of the DNA double helix, are the more dangerous. DSB are repaired through two evolutionary conserved mechanisms: Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). Whereas NHEJ simply reseals the double helix with no or minimal processing, HR necessitates the formation of a 3'ssDNA through the processing of DSB ends by the resection machinery and relies on the recognition and pairing of this 3'ssDNA tails with an intact homologous sequence. Despite years of active research on HR, the manner by which the two homologous sequences find each other in the crowded nucleus, and how this modulates HR efficiency, only recently emerges. Here, we review recent advances in our understanding of the factors limiting the search of a homologous sequence during HR.
Collapse
Affiliation(s)
- Hélène Bordelet
- Laboratoire Instabilité et Organisation Nucléaire, iRCM, IBFJ, DRF, CEA. 2 INSERM, U967. 3 Université Paris Diderot et Paris Saclay, UMR967, Fontenay-aux-roses, 92265, France
| | - Karine Dubrana
- Laboratoire Instabilité et Organisation Nucléaire, iRCM, IBFJ, DRF, CEA. 2 INSERM, U967. 3 Université Paris Diderot et Paris Saclay, UMR967, Fontenay-aux-roses, 92265, France.
| |
Collapse
|
8
|
Mercy G, Mozziconacci J, Scolari VF, Yang K, Zhao G, Thierry A, Luo Y, Mitchell LA, Shen M, Shen Y, Walker R, Zhang W, Wu Y, Xie ZX, Luo Z, Cai Y, Dai J, Yang H, Yuan YJ, Boeke JD, Bader JS, Muller H, Koszul R. 3D organization of synthetic and scrambled chromosomes. Science 2017; 355:355/6329/eaaf4597. [PMID: 28280150 DOI: 10.1126/science.aaf4597] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 02/01/2017] [Indexed: 11/02/2022]
Abstract
Although the design of the synthetic yeast genome Sc2.0 is highly conservative with respect to gene content, the deletion of several classes of repeated sequences and the introduction of thousands of designer changes may affect genome organization and potentially alter cellular functions. We report here the Hi-C-determined three-dimensional (3D) conformations of Sc2.0 chromosomes. The absence of repeats leads to a smoother contact pattern and more precisely tractable chromosome conformations, and the large-scale genomic organization is globally unaffected by the presence of synthetic chromosome(s). Two exceptions are synIII, which lacks the silent mating-type cassettes, and synXII, specifically when the ribosomal DNA is moved to another chromosome. We also exploit the contact maps to detect rearrangements induced in SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) strains.
Collapse
Affiliation(s)
- Guillaume Mercy
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France.,Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 6), Paris 75005, France
| | - Julien Mozziconacci
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR7600, Université Pierre et Marie Curie (Université Paris 6), Sorbonne Universités, Paris, France
| | - Vittore F Scolari
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| | - Kun Yang
- Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Guanghou Zhao
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Agnès Thierry
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France.,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| | - Yisha Luo
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Michael Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Yue Shen
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, Qingdao 266555, China.,School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Roy Walker
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Weimin Zhang
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yi Wu
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ze-Xiong Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhouqing Luo
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Junbiao Dai
- Key Laboratory for Industrial Biocatalysis (Ministry of Education), Key Laboratory of Bioinformatics (Ministry of Education), Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanming Yang
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, Langone Medical Center, New York University, New York, NY 10016, USA
| | - Joel S Bader
- Department of Biomedical Engineering and High-Throughput Biology Center, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Héloïse Muller
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. .,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| | - Romain Koszul
- Spatial Regulation of Genomes, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France. .,UMR3525, Centre National de la Recherche Scientifique (CNRS), Paris 75015, France
| |
Collapse
|
9
|
Lazar-Stefanita L, Scolari VF, Mercy G, Muller H, Guérin TM, Thierry A, Mozziconacci J, Koszul R. Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle. EMBO J 2017; 36:2684-2697. [PMID: 28729434 PMCID: PMC5599795 DOI: 10.15252/embj.201797342] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
Duplication and segregation of chromosomes involves dynamic reorganization of their internal structure by conserved architectural proteins, including the structural maintenance of chromosomes (SMC) complexes cohesin and condensin. Despite active investigation of the roles of these factors, a genome-wide view of dynamic chromosome architecture at both small and large scale during cell division is still missing. Here, we report the first comprehensive 4D analysis of the higher-order organization of the Saccharomyces cerevisiae genome throughout the cell cycle and investigate the roles of SMC complexes in controlling structural transitions. During replication, cohesion establishment promotes numerous long-range intra-chromosomal contacts and correlates with the individualization of chromosomes, which culminates at metaphase. In anaphase, mitotic chromosomes are abruptly reorganized depending on mechanical forces exerted by the mitotic spindle. Formation of a condensin-dependent loop bridging the centromere cluster with the rDNA loci suggests that condensin-mediated forces may also directly facilitate segregation. This work therefore comprehensively recapitulates cell cycle-dependent chromosome dynamics in a unicellular eukaryote, but also unveils new features of chromosome structural reorganization during highly conserved stages of cell division.
Collapse
Affiliation(s)
- Luciana Lazar-Stefanita
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, Complexité du Vivant, Paris, France
| | - Vittore F Scolari
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Guillaume Mercy
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
- Sorbonne Universités, UPMC Université Paris 6, Complexité du Vivant, Paris, France
| | - Héloise Muller
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Thomas M Guérin
- Laboratoire Télomères et Réparation du Chromosome, CEA, INSERM, UMR 967, IRCM, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Agnès Thierry
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| | - Julien Mozziconacci
- Sorbonne Universités, Theoretical Physics for Condensed Matter Lab, UPMC Université Paris 06, Paris, France
- CNRS, UMR 7600, Paris, France
| | - Romain Koszul
- Institut Pasteur, Department Genomes and Genetics, Unité Régulation Spatiale des Génomes, Paris, France
- CNRS, UMR 3525, Paris, France
- Institut Pasteur, CNRS Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), USR 3756, Paris, France
| |
Collapse
|
10
|
Revealing Sister Chromatid Interactions with the loxP/Cre Recombination Assay. Methods Mol Biol 2017. [PMID: 28842873 DOI: 10.1007/978-1-4939-7098-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Sister chromatid cohesion is a transient state during replication in bacteria. It has been recently demonstrated that the extent of contact between cohesive sisters during the cell cycle is dependent on topoisomerase IV activity, suggesting that topological links hold sister chromatids together. In the present protocol, we describe a simple method to quantify the frequency of the contacts between two cohesive sister chromatids. This method relies on a site specific recombination assay between loxP sites upon Cre induction.
Collapse
|
11
|
Batté A, Brocas C, Bordelet H, Hocher A, Ruault M, Adjiri A, Taddei A, Dubrana K. Recombination at subtelomeres is regulated by physical distance, double-strand break resection and chromatin status. EMBO J 2017; 36:2609-2625. [PMID: 28754657 DOI: 10.15252/embj.201796631] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 11/09/2022] Open
Abstract
Homologous recombination (HR) is a conserved mechanism that repairs broken chromosomes via intact homologous sequences. How different genomic, chromatin and subnuclear contexts influence HR efficiency and outcome is poorly understood. We developed an assay to assess HR outcome by gene conversion (GC) and break-induced replication (BIR), and discovered that subtelomeric double-stranded breaks (DSBs) are preferentially repaired by BIR despite the presence of flanking homologous sequences. Overexpression of a silencing-deficient SIR3 mutant led to active grouping of telomeres and specifically increased the GC efficiency between subtelomeres. Thus, physical distance limits GC at subtelomeres. However, the repair efficiency between reciprocal intrachromosomal and subtelomeric sequences varies up to 15-fold, depending on the location of the DSB, indicating that spatial proximity is not the only limiting factor for HR EXO1 deletion limited the resection at subtelomeric DSBs and improved GC efficiency. The presence of repressive chromatin at subtelomeric DSBs also favoured recombination, by counteracting EXO1-mediated resection. Thus, repressive chromatin promotes HR at subtelomeric DSBs by limiting DSB resection and protecting against genetic information loss.
Collapse
Affiliation(s)
- Amandine Batté
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France.,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| | - Clémentine Brocas
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France.,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| | - Hélène Bordelet
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France.,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| | - Antoine Hocher
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Myriam Ruault
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Adouda Adjiri
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR3664, Paris, France
| | - Karine Dubrana
- Institute of Molecular and Cellular Radiobiology, CEA/DRF, Fontenay-aux-Roses cedex, France .,Inserm U967, Fontenay-aux-Roses cedex, France.,Université Paris-Diderot et Université Paris-Sud, UMR967, Fontenay-aux-Roses cedex, France
| |
Collapse
|
12
|
Position effects influencing intrachromosomal repair of a double-strand break in budding yeast. PLoS One 2017; 12:e0180994. [PMID: 28700723 PMCID: PMC5507452 DOI: 10.1371/journal.pone.0180994] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/23/2017] [Indexed: 12/23/2022] Open
Abstract
Repair of a double-strand break (DSB) by an ectopic homologous donor sequence is subject to the three-dimensional arrangement of chromosomes in the nucleus of haploid budding yeast. The data for interchromosomal recombination suggest that searching for homology is accomplished by a random collision process, strongly influenced by the contact probability of the donor and recipient sequences. Here we explore how recombination occurs on the same chromosome and whether there are additional constraints imposed on repair. Specifically, we examined how intrachromosomal repair is affected by the location of the donor sequence along the 813-kb chromosome 2 (Chr2), with a site-specific DSB created on the right arm (position 625 kb). Repair correlates well with contact frequencies determined by chromosome conformation capture-based studies (r = 0.85). Moreover, there is a profound constraint imposed by the anchoring of the centromere (CEN2, position 238 kb) to the spindle pole body. Sequences at the same distance on either side of CEN2 are equivalently constrained in recombining with a DSB located more distally on one arm, suggesting that sequences on the opposite arm from the DSB are not otherwise constrained in their interaction with the DSB. The centromere constraint can be partially relieved by inducing transcription through the centromere to inactivate CEN2 tethering. In diploid cells, repair of a DSB via its allelic donor is strongly influenced by the presence and the position of an ectopic intrachromosomal donor.
Collapse
|
13
|
Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ. The dynamic three-dimensional organization of the diploid yeast genome. eLife 2017; 6. [PMID: 28537556 PMCID: PMC5476426 DOI: 10.7554/elife.23623] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/22/2017] [Indexed: 12/14/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. However, even in this well-studied model, it is unclear how homolog pairing in diploids or environmental conditions influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation using a polymer model, we observe significant homolog proximity that increases in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1-TDA1 alleles specifically under galactose induction and saturated growth. This pairing is accompanied by relocalization to the nuclear periphery and requires Nup2, suggesting a role for nuclear pore complexes. Together, these results reveal that the diploid yeast genome has a dynamic and complex 3D organization. DOI:http://dx.doi.org/10.7554/eLife.23623.001 Most of the DNA in human, yeast and other eukaryotic cells is packaged into long thread-like structures called chromosomes within a compartment of the cell called the nucleus. The chromosomes are folded to fit inside the nucleus and this organization influences how the DNA is read, copied, and repaired. The folding of chromosomes must be robust in order to protect the organism’s genetic material and yet be flexible enough to allow different parts of the DNA to be accessed in response to different signals. A biochemical technique called Hi-C can be used to detect the points of contact between different regions of a chromosome and between different chromosomes, thereby providing information on how the chromosomes are folded and arranged inside the nucleus. However, most animal cells contain two copies of each chromosome, and the Hi-C method is not able to distinguish between identical copies of chromosomes. As such, it remains unclear how much the chromosomes that can form pairs actually stick together in a cell’s nucleus. Unlike humans and most organisms, two distantly related budding yeast species can mate to produce a “hybrid” in which the chromosome copies can easily be distinguished from each other. Kim et al. now use Hi-C to analyze how chromosomes are organized in hybrid budding yeast cells. The experiments reveal that the copies of a chromosome contact each other more frequently than would be expected by chance. This is especially true for certain chromosomal regions and in hybrid yeast cells that are running out of their preferred nutrient, glucose. In these cells, the regions of both copies of chromosome 13 near a gene called TDA1 are pulled to the edge of the nucleus, which helps the copies to pair up and the gene to become active. The protein encoded by TDA1 then helps turn on other genes that allow the yeast to use nutrients other than glucose. Many questions remain about how and why DNA is organized the way it is, both in yeast and in other organisms. These findings will help guide future experiments testing how the two copies of each chromosome pair, as well as what purpose, if any, this pairing might serve for the cell. A better understanding of the fundamental process of DNA organization and its implications may ultimately lead to improved treatments for genetic diseases including developmental disorders and cancers. DOI:http://dx.doi.org/10.7554/eLife.23623.002
Collapse
Affiliation(s)
- Seungsoo Kim
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Ivan Liachko
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Donna G Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kate Cook
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, United States
| |
Collapse
|
14
|
Gladyshev E, Kleckner N. Recombination-independent recognition of DNA homology for repeat-induced point mutation. Curr Genet 2016; 63:389-400. [PMID: 27628707 DOI: 10.1007/s00294-016-0649-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/04/2016] [Accepted: 09/06/2016] [Indexed: 12/31/2022]
Abstract
Numerous cytogenetic observations have shown that homologous chromosomes (or individual chromosomal loci) can engage in specific pairing interactions in the apparent absence of DNA breakage and recombination, suggesting that canonical recombination-mediated mechanisms may not be the only option for sensing DNA/DNA homology. One proposed mechanism for such recombination-independent homology recognition involves direct contacts between intact double-stranded DNA molecules. The strongest in vivo evidence for the existence of such a mechanism is provided by the phenomena of homology-directed DNA modifications in fungi, known as repeat-induced point mutation (RIP, discovered in Neurospora crassa) and methylation-induced premeiotically (MIP, discovered in Ascobolus immersus). In principle, Neurospora RIP can detect the presence of gene-sized DNA duplications irrespectively of their origin, underlying nucleotide sequence, coding capacity or relative, as well as absolute positions in the genome. Once detected, both sequence copies are altered by numerous cytosine-to-thymine (C-to-T) mutations that extend specifically over the duplicated region. We have recently shown that Neurospora RIP does not require MEI-3, the only RecA/Rad51 protein in this organism, consistent with a recombination-independent mechanism. Using an ultra-sensitive assay for RIP mutation, we have defined additional features of this process. We have shown that RIP can detect short islands of homology of only three base-pairs as long as many such islands are arrayed with a periodicity of 11 or 12 base-pairs along a pair of DNA molecules. While the presence of perfect homology is advantageous, it is not required: chromosomal segments with overall sequence identity of only 35-36 % can still be recognized by RIP. Importantly, in order for this process to work efficiently, participating DNA molecules must be able to co-align along their lengths. Based on these findings, we have proposed a model, in which sequence homology is detected by direct interactions between slightly-extended double-stranded DNAs. As a next step, it will be important to determine if the uncovered principles also apply to other processes that involve recombination-independent interactions between homologous chromosomal loci in vivo as well as to protein-free DNA/DNA interactions that were recently observed under biologically relevant conditions in vitro.
Collapse
Affiliation(s)
- Eugene Gladyshev
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Room NW140, Cambridge, MA, 02138, USA.
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Room NW140, Cambridge, MA, 02138, USA.
| |
Collapse
|
15
|
Sekan AS, Isayenkov SV, Blume YB. Development of marker-free transformants by site-specific recombinases. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715060080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
16
|
Solis-Escalante D, van den Broek M, Kuijpers NGA, Pronk JT, Boles E, Daran JM, Daran-Lapujade P. The genome sequence of the popular hexose-transport-deficient Saccharomyces cerevisiae strain EBY.VW4000 reveals LoxP/Cre-induced translocations and gene loss. FEMS Yeast Res 2015; 15:fou004. [PMID: 25673752 DOI: 10.1093/femsyr/fou004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Saccharomyces cerevisiae harbours a large group of tightly controlled hexose transporters with different characteristics. Construction and characterization of S. cerevisiae EBY.VW4000, a strain devoid of glucose import, was a milestone in hexose-transporter research. This strain has become a widely used platform for discovery and characterization of transporters from a wide range of organisms. To abolish glucose uptake, 21 genes were knocked out, involving 16 successive deletion rounds with the LoxP/Cre system. Although such intensive modifications are known to increase the risk of genome alterations, the genome of EBY.VW4000 has hitherto not been characterized. Based on a combination of whole genome sequencing, karyotyping and molecular confirmation, the present study reveals that construction of EBY.VW4000 resulted in gene losses and chromosomal rearrangements. Recombinations between the LoxP scars have led to the assembly of four neo-chromosomes, truncation of two chromosomes and loss of two subtelomeric regions. Furthermore, sporulation and spore germination are severely impaired in EBY.VW4000. Karyotyping of the EBY.VW4000 lineage retraced its current chromosomal architecture to four translocations events occurred between the 6th and the 12th rounds of deletion. The presented data facilitate further studies on EBY.VW4000 and highlight the risks of genome alterations associated with repeated use of the LoxP/Cre system.
Collapse
Affiliation(s)
- Daniel Solis-Escalante
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Niels G A Kuijpers
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands Platform Green Synthetic Biology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Eckhard Boles
- Institute for Molecular Biosciences, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands Platform Green Synthetic Biology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology Julianalaan 67, 2628 BC Delft, The Netherlands
| |
Collapse
|
17
|
Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
Collapse
|
18
|
Zickler D, Kleckner N. Recombination, Pairing, and Synapsis of Homologs during Meiosis. Cold Spring Harb Perspect Biol 2015; 7:cshperspect.a016626. [PMID: 25986558 DOI: 10.1101/cshperspect.a016626] [Citation(s) in RCA: 512] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recombination is a prominent feature of meiosis in which it plays an important role in increasing genetic diversity during inheritance. Additionally, in most organisms, recombination also plays mechanical roles in chromosomal processes, most notably to mediate pairing of homologous chromosomes during prophase and, ultimately, to ensure regular segregation of homologous chromosomes when they separate at the first meiotic division. Recombinational interactions are also subject to important spatial patterning at both early and late stages. Recombination-mediated processes occur in physical and functional linkage with meiotic axial chromosome structure, with interplay in both directions, before, during, and after formation and dissolution of the synaptonemal complex (SC), a highly conserved meiosis-specific structure that links homolog axes along their lengths. These diverse processes also are integrated with recombination-independent interactions between homologous chromosomes, nonhomology-based chromosome couplings/clusterings, and diverse types of chromosome movement. This review provides an overview of these diverse processes and their interrelationships.
Collapse
Affiliation(s)
- Denise Zickler
- Institut de Génétique et Microbiologie, UMR 8621, Université Paris-Sud, 91405 Orsay, France
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| |
Collapse
|
19
|
Renkawitz J, Lademann CA, Jentsch S. Mechanisms and principles of homology search during recombination. Nat Rev Mol Cell Biol 2014; 15:369-83. [PMID: 24824069 DOI: 10.1038/nrm3805] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination is crucial for genome stability and for genetic exchange. Although our knowledge of the principle steps in recombination and its machinery is well advanced, homology search, the critical step of exploring the genome for homologous sequences to enable recombination, has remained mostly enigmatic. However, recent methodological advances have provided considerable new insights into this fundamental step in recombination that can be integrated into a mechanistic model. These advances emphasize the importance of genomic proximity and nuclear organization for homology search and the critical role of homology search mediators in this process. They also aid our understanding of how homology search might lead to unwanted and potentially disease-promoting recombination events.
Collapse
Affiliation(s)
- Jörg Renkawitz
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2] Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria. [3]
| | - Claudio A Lademann
- 1] Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [2]
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
20
|
Mirkin EV, Chang FS, Kleckner N. Protein-mediated chromosome pairing of repetitive arrays. J Mol Biol 2013; 426:550-7. [PMID: 24211468 DOI: 10.1016/j.jmb.2013.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/28/2013] [Accepted: 11/02/2013] [Indexed: 10/26/2022]
Abstract
Chromosomally integrated arrays of lacO and tetO operator sites visualized by LacI and TetR repressor proteins fused with GFP (green fluorescent protein) (or other fluorescent proteins) are widely used to monitor the behavior of chromosomal loci in various systems. However, insertion of such arrays and expression of the corresponding proteins is known to perturb genomic architecture. In several cases, juxtaposition of such arrays located on different chromosomes has been inferred to reflect pairing of the corresponding loci. Here, we report that a version of TetR-GFP mutated to disrupt GFP dimerization (TetR-A206KGFP or "TetR-kGFP") abolishes pairing of tetO arrays in vivo and brings spatial proximity of chromosomal loci marked with those arrays back to the wild-type level. These data argue that pairing of arrays is caused by GFP dimerization and thus presents an example of protein-assisted interaction in chromosomes. Arrays marked with another protein, TetR-tdTomato, which has a propensity to form intramolecular dimers instead of intermolecular dimers, also display reduced level of pairing, supporting this idea. TetR-kGFP provides an improved system for studying chromosomal loci with a low pairing background.
Collapse
Affiliation(s)
- Ekaterina V Mirkin
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Frederick S Chang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
21
|
Mirkin EV, Chang FS, Kleckner N. Dynamic trans interactions in yeast chromosomes. PLoS One 2013; 8:e75895. [PMID: 24098740 PMCID: PMC3786970 DOI: 10.1371/journal.pone.0075895] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/21/2013] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional organization of the genome is important for regulation of gene expression and maintenance of genomic stability. It also defines, and is defined by, contacts between different chromosomal loci. Interactions between loci positioned on different chromosomes, i.e. "trans" interactions are one type of such contacts. Here, we describe a case of inducible trans interaction in chromosomes of the budding yeast S. cerevisiae. Special DNA sequences, inserted in two ectopic chromosomal loci positioned in trans, pair with one another in an inducible manner. The spatial proximity diagnostic of pairing is observable by both chromosome capture analysis (3C) and epifluorescence microscopy in whole cells. Protein synthesis de novo appears to be required for this process. The three-dimensional organization of the yeast nucleus imposes a constraint on such pairing, presumably by dictating the probability with which the two sequences collide with one another.
Collapse
Affiliation(s)
- Ekaterina V. Mirkin
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Frederick S. Chang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
22
|
Agmon N, Liefshitz B, Zimmer C, Fabre E, Kupiec M. Effect of nuclear architecture on the efficiency of double-strand break repair. Nat Cell Biol 2013; 15:694-9. [PMID: 23644470 DOI: 10.1038/ncb2745] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/02/2013] [Indexed: 12/15/2022]
Abstract
The most dangerous insults to the genome's integrity are those that break both strands of the DNA. Double-strand breaks can be repaired by homologous recombination; in this conserved mechanism, a global genomic homology search finds sequences similar to those near the break, and uses them as a template for DNA synthesis and ligation. Chromosomes occupy restricted territories within the nucleus. We show that yeast genomic regions whose nuclear territories overlap recombine more efficiently than sequences located in spatially distant territories. Tethering of telomeres and centromeres reduces the efficiency of recombination between distant genomic loci, lowering the chances of non-allelic recombination. Our results challenge present models that posit an active scanning of the whole nuclear volume by the broken chromosomal end; they demonstrate that the search for homology is a limiting step in homologous recombination, and emphasize the importance of nuclear organization in genome maintenance.
Collapse
Affiliation(s)
- Neta Agmon
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | | | | | | | | |
Collapse
|
23
|
Abstract
The nuclear envelope not only compartmentalizes the genome but is also home to the SUN-KASH domain proteins, which play essential roles both in genome organization and in linking the nucleus to the cytoskeleton. In interphase fission yeast cells, centromeres are clustered near the nuclear periphery. A recent report demonstrates that the inner nuclear membrane SUN domain protein Sad1 and a novel protein Csi1 connect centromeres to the nuclear envelope and that centromere clustering during interphase is critical for the efficient capture of kinetochores by microtubules during mitosis.
Collapse
Affiliation(s)
- Haitong Hou
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | | |
Collapse
|
24
|
Renkawitz J, Lademann CA, Kalocsay M, Jentsch S. Monitoring homology search during DNA double-strand break repair in vivo. Mol Cell 2013; 50:261-72. [PMID: 23523370 DOI: 10.1016/j.molcel.2013.02.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 10/15/2012] [Accepted: 02/15/2013] [Indexed: 01/08/2023]
Abstract
Homologous recombination (HR) is crucial for genetic exchange and accurate repair of DNA double-strand breaks and is pivotal for genome integrity. HR uses homologous sequences for repair, but how homology search, the exploration of the genome for homologous DNA sequences, is conducted in the nucleus remains poorly understood. Here, we use time-resolved chromatin immunoprecipitations of repair proteins to monitor homology search in vivo. We found that homology search proceeds by a probing mechanism, which commences around the break and samples preferentially on the broken chromosome. However, elements thought to instruct chromosome loops mediate homology search shortcuts, and centromeres, which cluster within the nucleus, may facilitate homology search on other chromosomes. Our study thus reveals crucial parameters for homology search in vivo and emphasizes the importance of linear distance, chromosome architecture, and proximity for recombination efficiency.
Collapse
Affiliation(s)
- Jörg Renkawitz
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | | | | | | |
Collapse
|
25
|
Lui DY, Cahoon CK, Burgess SM. Multiple opposing constraints govern chromosome interactions during meiosis. PLoS Genet 2013; 9:e1003197. [PMID: 23341780 PMCID: PMC3547833 DOI: 10.1371/journal.pgen.1003197] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 11/12/2012] [Indexed: 11/24/2022] Open
Abstract
Homolog pairing and crossing over during meiosis I prophase is required for accurate chromosome segregation to form euploid gametes. The repair of Spo11-induced double-strand breaks (DSB) using a homologous chromosome template is a major driver of pairing in many species, including fungi, plants, and mammals. Inappropriate pairing and crossing over at ectopic loci can lead to chromosome rearrangements and aneuploidy. How (or if) inappropriate ectopic interactions are disrupted in favor of allelic interactions is not clear. Here we used an in vivo "collision" assay in budding yeast to test the contributions of cohesion and the organization and motion of chromosomes in the nucleus on promoting or antagonizing interactions between allelic and ectopic loci at interstitial chromosome sites. We found that deletion of the cohesin subunit Rec8, but not other chromosome axis proteins (e.g. Red1, Hop1, or Mek1), caused an increase in homolog-nonspecific chromosome interaction, even in the absence of Spo11. This effect was partially suppressed by expression of the mitotic cohesin paralog Scc1/Mdc1, implicating Rec8's role in cohesion rather than axis integrity in preventing nonspecific chromosome interactions. Disruption of telomere-led motion by treating cells with the actin polymerization inhibitor Latrunculin B (Lat B) elevated nonspecific collisions in rec8Δ spo11Δ. Next, using a visual homolog-pairing assay, we found that the delay in homolog pairing in mutants defective for telomere-led chromosome motion (ndj1Δ or csm4Δ) is enhanced in Lat B-treated cells, implicating actin in more than one process promoting homolog juxtaposition. We suggest that multiple, independent contributions of actin, cohesin, and telomere function are integrated to promote stable homolog-specific interactions and to destabilize weak nonspecific interactions by modulating the elastic spring-like properties of chromosomes.
Collapse
Affiliation(s)
- Doris Y. Lui
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| | - Cori K. Cahoon
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| | - Sean M. Burgess
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, United States of America
| |
Collapse
|
26
|
Penfold CA, Brown PE, Lawrence ND, Goldman ASH. Modeling meiotic chromosomes indicates a size dependent contribution of telomere clustering and chromosome rigidity to homologue juxtaposition. PLoS Comput Biol 2012; 8:e1002496. [PMID: 22570605 PMCID: PMC3342934 DOI: 10.1371/journal.pcbi.1002496] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 03/12/2012] [Indexed: 01/17/2023] Open
Abstract
Meiosis is the cell division that halves the genetic component of diploid cells to form gametes or spores. To achieve this, meiotic cells undergo a radical spatial reorganisation of chromosomes. This reorganisation is a prerequisite for the pairing of parental homologous chromosomes and the reductional division, which halves the number of chromosomes in daughter cells. Of particular note is the change from a centromere clustered layout (Rabl configuration) to a telomere clustered conformation (bouquet stage). The contribution of the bouquet structure to homologous chromosome pairing is uncertain. We have developed a new in silico model to represent the chromosomes of Saccharomyces cerevisiae in space, based on a worm-like chain model constrained by attachment to the nuclear envelope and clustering forces. We have asked how these constraints could influence chromosome layout, with particular regard to the juxtaposition of homologous chromosomes and potential nonallelic, ectopic, interactions. The data support the view that the bouquet may be sufficient to bring short chromosomes together, but the contribution to long chromosomes is less. We also find that persistence length is critical to how much influence the bouquet structure could have, both on pairing of homologues and avoiding contacts with heterologues. This work represents an important development in computer modeling of chromosomes, and suggests new explanations for why elucidating the functional significance of the bouquet by genetics has been so difficult. Organisms store their genetic material in the form of chromosomes that must be replicated and shared out during cell division. In sexual reproduction the cell division, called meiosis, halves the number of chromosomes to form gametes. This halving requires a complex reorganisation of chromosomes. Each gamete receives one maternal or one paternal copy of every chromosome. This requires a pairing process between the maternal and paternal chromosomes of each type. Once paired the two chromosomes are organised in space to bias subsequent movement in opposite directions when the nucleus divides. How chromosomes pair is of great importance to understanding fertility, and manipulating chromosomes in crops species, for which it is desirable to breed in new genes to improve hardiness or yield. We have modelled chromosomes in 3-dimensions based on the experimental organism Saccharomyces cerevisiae. We used our model to ask if various physical features of chromosomes might influence their ability to pair. We found that binding chromosome ends to the nuclear wall and pushing those ends together helps to encourage pairing along the length of chromosomes. It has long been known this special chromosome organisation occurs in live cells, but the significance of it has been difficult to determine.
Collapse
Affiliation(s)
- Christopher A. Penfold
- Department of Molecular Biology and Biotechnology, Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
- Department of Computer Science, The University of Sheffield, Sheffield, United Kingdom
- Sheffield Institute of Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
| | - Paul E. Brown
- Systems Biology Centre, University of Warwick, Coventry, United Kingdom
| | - Neil D. Lawrence
- Department of Computer Science, The University of Sheffield, Sheffield, United Kingdom
- Sheffield Institute of Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
| | - Alastair S. H. Goldman
- Department of Molecular Biology and Biotechnology, Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| |
Collapse
|
27
|
George CM, Alani E. Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA. Crit Rev Biochem Mol Biol 2012; 47:297-313. [PMID: 22494239 PMCID: PMC3337352 DOI: 10.3109/10409238.2012.675644] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Repetitive DNA is present in the eukaryotic genome in the form of segmental duplications, tandem and interspersed repeats, and satellites. Repetitive sequences can be beneficial by serving specific cellular functions (e.g. centromeric and telomeric DNA) and by providing a rapid means for adaptive evolution. However, such elements are also substrates for deleterious chromosomal rearrangements that affect fitness and promote human disease. Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination (NAHR) have provided insights into how genome stability is maintained in eukaryotes. In this review, we outline the types of repetitive sequences seen in eukaryotic genomes and how recombination mechanisms are regulated at the DNA sequence, cell organization, chromatin structure, and cell cycle control levels to prevent chromosomal rearrangements involving these sequences.
Collapse
Affiliation(s)
- Carolyn M George
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | | |
Collapse
|
28
|
Abstract
The spatial organization of genes and chromosomes plays an important role in the regulation of several DNA processes. However, the principles and forces underlying this nonrandom organization are mostly unknown. Despite its small dimension, and thanks to new imaging and biochemical techniques, studies of the budding yeast nucleus have led to significant insights into chromosome arrangement and dynamics. The dynamic organization of the yeast genome during interphase argues for both the physical properties of the chromatin fiber and specific molecular interactions as drivers of nuclear order.
Collapse
Affiliation(s)
- Christophe Zimmer
- Groupe Imagerie et Modélisation, Département Biologie Cellulaire et Infection, Institut Pasteur, F-75015 Paris, France
| | | |
Collapse
|
29
|
Wang Y, Yau YY, Perkins-Balding D, Thomson JG. Recombinase technology: applications and possibilities. PLANT CELL REPORTS 2011; 30:267-85. [PMID: 20972794 PMCID: PMC3036822 DOI: 10.1007/s00299-010-0938-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 10/06/2010] [Accepted: 10/08/2010] [Indexed: 05/02/2023]
Abstract
The use of recombinases for genomic engineering is no longer a new technology. In fact, this technology has entered its third decade since the initial discovery that recombinases function in heterologous systems (Sauer in Mol Cell Biol 7(6):2087-2096, 1987). The random insertion of a transgene into a plant genome by traditional methods generates unpredictable expression patterns. This feature of transgenesis makes screening for functional lines with predictable expression labor intensive and time consuming. Furthermore, an antibiotic resistance gene is often left in the final product and the potential escape of such resistance markers into the environment and their potential consumption raises consumer concern. The use of site-specific recombination technology in plant genome manipulation has been demonstrated to effectively resolve complex transgene insertions to single copy, remove unwanted DNA, and precisely insert DNA into known genomic target sites. Recombinases have also been demonstrated capable of site-specific recombination within non-nuclear targets, such as the plastid genome of tobacco. Here, we review multiple uses of site-specific recombination and their application toward plant genomic engineering. We also provide alternative strategies for the combined use of multiple site-specific recombinase systems for genome engineering to precisely insert transgenes into a pre-determined locus, and removal of unwanted selectable marker genes.
Collapse
Affiliation(s)
- Yueju Wang
- Department of Natural Sciences, Northeastern State University, Broken Arrow, OK 74014 USA
| | - Yuan-Yeu Yau
- Department of Plant and Microbial Biology, Plant Gene Expression Center, USDA-ARS, University of California-Berkeley, 800 Buchanan St., Albany, CA 94710 USA
| | | | - James G. Thomson
- Crop Improvement and Utilization Unit, USDA-ARS WRRC, 800 Buchanan St., Albany, CA 94710 USA
| |
Collapse
|
30
|
Genome organization influences partner selection for chromosomal rearrangements. Trends Genet 2010; 27:63-71. [PMID: 21144612 DOI: 10.1016/j.tig.2010.11.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/02/2010] [Accepted: 11/03/2010] [Indexed: 11/22/2022]
Abstract
Chromosomal rearrangements occur as a consequence of the erroneous repair of DNA double-stranded breaks, and often underlie disease. The recurrent detection of specific tumorigenic rearrangements suggests that there is a mechanism behind chromosomal partner selection involving the shape of the genome. With the advent of novel high-throughput approaches, detailed genome integrity and folding maps are becoming available. Integrating these data with knowledge of experimentally induced DNA recombination strongly suggests that partner choice in chromosomal rearrangement primarily follows the three-dimensional conformation of the genome. Local rearrangements are favored over distal and interchromosomal rearrangements. This is seen for neutral rearrangements, but not necessarily for rearrangements that drive oncogenesis. The recurrent detection of tumorigenic rearrangements probably reflects their exceptional capacity to confer growth advantage to the rare cells that contain them. The abundant presence of neutral rearrangements suggests that somatic genome variation is also common in healthy tissue.
Collapse
|
31
|
Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, Dunham MJ, Zheng Y, Koshland D. Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination. PLoS Genet 2010; 6:e1001228. [PMID: 21151956 PMCID: PMC2996329 DOI: 10.1371/journal.pgen.1001228] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Accepted: 10/29/2010] [Indexed: 01/11/2023] Open
Abstract
Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR–dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR–dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer. The human genome is structurally dynamic, frequently undergoing loss, duplication, and rearrangement of large chromosome segments. These structural changes occur both in normal and in cancerous cells and are thought to cause both benign and deleterious changes in cell function. Many of these structural alterations are generated when two dispersed repeated DNA sequences at non-allelic sites recombine during non-allelic homologous recombination (NAHR). Here we study NAHR on a genome-wide scale using the experimentally tractable budding yeast as a eukaryotic model genome with its fully sequenced family of repeated DNA elements, the Ty retrotransposons. With our novel system, we simultaneously measure the effects of known recombination parameters on the frequency of NAHR to understand which parameters most influence the occurrence of rearrangements between repetitive sequences. These findings provide a basic framework for interpreting how structural changes observed in the human genome may have arisen.
Collapse
Affiliation(s)
- Margaret L. Hoang
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Frederick J. Tan
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
| | - David C. Lai
- Baltimore Polytechnic Institute, Ingenuity Program, Baltimore, Maryland, United States of America
| | - Sue E. Celniker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Roger A. Hoskins
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Yixian Zheng
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
| | - Douglas Koshland
- Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
32
|
Cherstvy AG. DNA-DNA sequence homology recognition: physical mechanisms and open questions. J Mol Recognit 2010; 24:283-7. [DOI: 10.1002/jmr.1050] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/07/2010] [Accepted: 04/10/2010] [Indexed: 11/11/2022]
|
33
|
Uemura M, Niwa Y, Kakazu N, Adachi N, Kinoshita K. Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors. PLoS One 2010; 5:e9846. [PMID: 20352097 PMCID: PMC2844420 DOI: 10.1371/journal.pone.0009846] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/03/2010] [Indexed: 11/24/2022] Open
Abstract
Feasibility of chromosomal manipulation in mammalian cells was first reported 15 years ago. Although this technique is useful for precise understanding of gene regulation in the chromosomal context, a limited number of laboratories have used it in actual practice because of associated technical difficulties. To overcome the practical hurdles, we developed a Cre-mediated chromosomal recombination system using fluorescent proteins and various site-specific recombinases. These techniques enabled quick construction of targeting vectors, easy identification of chromosome-rearranged cells, and rearrangement leaving minimum artificial elements at junctions. Applying this system to a human cell line, we successfully recapitulated two types of pathogenic chromosomal translocations in human diseases: MYC/IgH and BCR/ABL1. By inducing recombination between two loxP sites targeted into the same chromosome, we could mark cells harboring deletion or duplication of the inter-loxP segments with different colors of fluorescence. In addition, we demonstrated that the intrachromosomal recombination frequency is inversely proportional to the distance between two recombination sites, implicating a future application of this frequency as a proximity sensor. Our method of chromosomal manipulation can be employed for particular cell types in which gene targeting is possible (e.g. embryonic stem cells). Experimental use of this system would open up new horizons in genome biology, including the establishment of cellular and animal models of diseases caused by translocations and copy-number variations.
Collapse
Affiliation(s)
- Munehiro Uemura
- Evolutionary Medicine, Shiga Medical Center Research Institute, Moriyama, Japan
| | - Youko Niwa
- Evolutionary Medicine, Shiga Medical Center Research Institute, Moriyama, Japan
| | - Naoki Kakazu
- Department of Environmental and Preventive Medicine, Shimane University School of Medicine, Izumo, Japan
| | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
| | - Kazuo Kinoshita
- Evolutionary Medicine, Shiga Medical Center Research Institute, Moriyama, Japan
- * E-mail:
| |
Collapse
|
34
|
Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres. Proc Natl Acad Sci U S A 2010; 107:2025-30. [PMID: 20080699 DOI: 10.1073/pnas.0914187107] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Physical interactions between distinct chromosomal genomic loci are important for genomic functions including recombination and gene expression, but the mechanisms by which these interactions occur remain obscure. Using telomeric association as a model system, we analyzed here the in vivo organization of chromosome ends of haploid yeast cells during interphase. We separately labeled most of the 32 subtelomeres and analyzed their positions both in nuclear space and relative to three representative reference subtelomeres by high-throughput 3D microscopy and image processing. We show that subtelomeres are positioned nonrandomly at the nuclear periphery, depending on the genomic size of their chromosome arm, centromere attachment to the microtubule organizing center (spindle pole body, SPB), and the volume of the nucleolus. The distance of subtelomeres to the SPB increases consistently with chromosome arm length up to approximately 300 kb; for larger arms the influence of chromosome arm length is weaker, but the effect of the nucleolar volume is stronger. Distances between pairs of subtelomeres also exhibit arm-length dependence and suggest, together with dynamic tracking experiments, that potential associations between subtelomeres are unexpectedly infrequent and transient. Our results suggest that interactions between subtelomeres are nonspecific and instead governed by physical constraints, including chromosome structure, attachment to the SPB, and nuclear crowding.
Collapse
|
35
|
Weinert T, Kaochar S, Jones H, Paek A, Clark AJ. The replication fork's five degrees of freedom, their failure and genome rearrangements. Curr Opin Cell Biol 2009; 21:778-84. [PMID: 19913398 DOI: 10.1016/j.ceb.2009.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/09/2009] [Accepted: 10/10/2009] [Indexed: 12/20/2022]
Abstract
Genome rearrangements are important in pathology and evolution. The thesis of this review is that the genome is in peril when replication forks stall, and stalled forks are normally rescued by error-free mechanisms. Failure of error-free mechanisms results in large-scale chromosome changes called gross chromosomal rearrangements, GCRs, by the aficionados. In this review we discuss five error-free mechanisms a replication fork may use to overcome blockage, mechanisms that are still poorly understood. We then speculate on how genome rearrangements may occur when such mechanisms fail. Replication fork recovery failure may be an important feature of the oncogenic process. (Feedback to the authors on topics discussed herein is welcome.).
Collapse
Affiliation(s)
- T Weinert
- Department of Molecular & Cell Biology, University of Arizona, Tucson, AZ 85721, USA.
| | | | | | | | | |
Collapse
|
36
|
Measurement of spatial proximity and accessibility of chromosomal loci in Saccharomyces cerevisiae using Cre/loxP site-specific recombination. Methods Mol Biol 2009. [PMID: 19799176 DOI: 10.1007/978-1-59745-527-5_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Several methods have been developed to measure interactions between homologous chromosomes during meiosis in budding yeast. These include cytological analysis of fixed, spread nuclei using fluorescence in situ hybridization (FISH) (1, 2), visualization of GFP-labeled chromosomal loci in living cells (3), and Chromosome-Conformation Capture (3C) (4). Here we describe a quantitative genetic assay that uses exogenous site-specific recombination to monitor the level of homolog associations between two defined loci in living cells of budding yeast (5). We have used the Cre/loxP assay to genetically dissect nuclear architecture and meiotic homolog pairing in budding yeast. Data obtained from this assay report on the relative spatial proximity or accessibility of two chromosomal loci located within the same strain and can be compared to measurements from different mutated strains.
Collapse
|
37
|
Assaying chromosome pairing by FISH analysis of spread Saccharomyces cerevisiae nuclei. Methods Mol Biol 2009. [PMID: 19685317 DOI: 10.1007/978-1-60761-103-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescent in situ hybridization (FISH) provides a powerful tool to study the localization of DNA sequences in relationship to one another. FISH has the advantage over other methods, notably use of GFP-tagged repressor/operator arrays, that an almost unlimited number of probes can be utilized without having to make new strains for each new locus one wants to study. Also, the number of sites that can be visualized at the same time is limited only by the number of fluorophores that are available and can be distinguished by the available microscope. Described here is a method for FISH analysis and its application to analysis of chromosome pairing during meiosis in S. cerevisiae.
Collapse
|
38
|
Robbiani DF, Bothmer A, Callen E, Reina-San-Martin B, Dorsett Y, Difilippantonio S, Bolland DJ, Chen HT, Corcoran AE, Nussenzweig A, Nussenzweig MC. AID is required for the chromosomal breaks in c-myc that lead to c-myc/IgH translocations. Cell 2008; 135:1028-38. [PMID: 19070574 DOI: 10.1016/j.cell.2008.09.062] [Citation(s) in RCA: 339] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 08/15/2008] [Accepted: 09/16/2008] [Indexed: 01/01/2023]
Abstract
Chromosomal translocation requires formation of paired double-strand DNA breaks (DSBs) on heterologous chromosomes. One of the most well characterized oncogenic translocations juxtaposes c-myc and the immunoglobulin heavy-chain locus (IgH) and is found in Burkitt's lymphomas in humans and plasmacytomas in mice. DNA breaks in IgH leading to c-myc/IgH translocations are created by activation-induced cytidine deaminase (AID) during antibody class switch recombination or somatic hypermutation. However, the source of DNA breaks at c-myc is not known. Here, we provide evidence for the c-myc promoter region being required in targeting AID-mediated DNA damage to produce DSBs in c-myc that lead to c-myc/IgH translocations in primary B lymphocytes. Thus, in addition to producing somatic mutations and DNA breaks in antibody genes, AID is also responsible for the DNA lesions in oncogenes that are required for their translocation.
Collapse
Affiliation(s)
- Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Cooperative interactions between pairs of homologous chromatids during meiosis in Saccharomyces cerevisiae. Genetics 2008; 179:1125-7. [PMID: 18558657 DOI: 10.1534/genetics.108.088567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report a novel instance of negative interference during Saccharomyces cerevisiae meiosis, where Cre-mediated recombination between pairs of allelic loxP sites is more frequent than expected. We suggest that endogenous crossover recombination mediates cooperative pairing interactions between all four chromatids of a meiotic bivalent.
Collapse
|
40
|
Sites of recombination are local determinants of meiotic homolog pairing in Saccharomyces cerevisiae. Genetics 2008; 179:773-84. [PMID: 18505886 DOI: 10.1534/genetics.107.077727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trans-acting factors involved in the early meiotic recombination pathway play a major role in promoting homolog pairing during meiosis in many plants, fungi, and mammals. Here we address whether or not allelic sites have higher levels of interaction when in cis to meiotic recombination events in the budding yeast Saccharomyces cerevisiae. We used Cre/loxP site-specific recombination to genetically measure the magnitude of physical interaction between loxP sites located at allelic positions on homologous chromosomes during meiosis. We observed nonrandom coincidence of Cre-mediated loxP recombination events and meiotic recombination events when the two occurred at linked positions. Further experiments showed that a subset of recombination events destined to become crossover products increased the frequency of nearby Cre-mediated loxP recombination. Our results support a simple physical model of homolog pairing in budding yeast, where recombination at numerous genomic positions generally serves to loosely coalign homologous chromosomes, while crossover-bound recombination intermediates locally stabilize interactions between allelic sites.
Collapse
|
41
|
Barzel A, Kupiec M. Finding a match: how do homologous sequences get together for recombination? Nat Rev Genet 2008; 9:27-37. [PMID: 18040271 DOI: 10.1038/nrg2224] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Decades of research into homologous recombination have unravelled many of the details concerning the transfer of information between two homologous sequences. By contrast, the processes by which the interacting molecules initially colocalize are largely unknown. How can two homologous needles find each other in the genomic haystack? Is homologous pairing the result of a damage-induced homology search, or is it an enduring and general feature of the genomic architecture that facilitates homologous recombination whenever and wherever damage occurs? This Review presents the homologous-pairing enigma, delineates our current understanding of the process and offers guidelines for future research.
Collapse
Affiliation(s)
- Adi Barzel
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
| | | |
Collapse
|
42
|
Molnar M, Kleckner N. Examination of interchromosomal interactions in vegetatively growing diploid Schizosaccharomyces pombe cells by Cre/loxP site-specific recombination. Genetics 2008; 178:99-112. [PMID: 18202361 PMCID: PMC2206114 DOI: 10.1534/genetics.107.082826] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 11/12/2007] [Indexed: 11/18/2022] Open
Abstract
The probability with which different regions of a genome come in contact with one another is a question of general interest. The current study addresses this subject for vegetatively growing diploid cells of fission yeast Schizosaccharomyces pombe by application of the Cre/loxP site-specific recombination assay. High levels of allelic interactions imply a tendency for chromosomes to be colocalized along their lengths. Significant homology-dependent pairing at telomere proximal loci and robust nonspecific clustering of centromeres appear to be the primary determinants of this feature. Preference for direct homolog-directed interactions at interstitial chromosomal regions was ambiguous, perhaps as a consequence of chromosome flexibility and the constraints and dynamic nature of the nucleus. Additional features of the data provide evidence for chromosome territories and reveal an intriguing phenomenon in which interaction frequencies are favored for nonhomologous loci that are located at corresponding relative (rather than absolute) positions within their respective chromosome arms. The latter feature, and others, can be understood as manifestations of transient, variable, and/or occasional nonspecific telomeric associations. We discuss the factors whose interplay sets the probabilities of chromosomal interactions in this organism and implications of the inferred organization for ectopic recombination.
Collapse
Affiliation(s)
- Monika Molnar
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | | |
Collapse
|
43
|
Conrad MN, Lee CY, Wilkerson JL, Dresser ME. MPS3 mediates meiotic bouquet formation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2007; 104:8863-8. [PMID: 17495028 PMCID: PMC1885593 DOI: 10.1073/pnas.0606165104] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In meiotic prophase, telomeres associate with the nuclear envelope and accumulate adjacent to the centrosome/spindle pole to form the chromosome bouquet, a well conserved event that in Saccharomyces cerevisiae requires the meiotic telomere protein Ndj1p. Ndj1p interacts with Mps3p, a nuclear envelope SUN domain protein that is required for spindle pole body duplication and for sister chromatid cohesion. Removal of the Ndj1p-interaction domain from MPS3 creates an ndj1 Delta-like separation-of-function allele, and Ndj1p and Mps3p are codependent for stable association with the telomeres. SUN domain proteins are found in the nuclear envelope across phyla and are implicated in mediating interactions between the interior of the nucleus and the cytoskeleton. Our observations indicate a general mechanism for meiotic telomere movements.
Collapse
Affiliation(s)
- Michael N. Conrad
- *Program in Molecular, Cell and Developmental Biology, Oklahoma Medical Research Foundation Oklahoma City, OK 73104; and
| | - Chih-Ying Lee
- *Program in Molecular, Cell and Developmental Biology, Oklahoma Medical Research Foundation Oklahoma City, OK 73104; and
- Department of Cell Biology, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104
| | - Joseph L. Wilkerson
- *Program in Molecular, Cell and Developmental Biology, Oklahoma Medical Research Foundation Oklahoma City, OK 73104; and
| | - Michael E. Dresser
- *Program in Molecular, Cell and Developmental Biology, Oklahoma Medical Research Foundation Oklahoma City, OK 73104; and
- Department of Cell Biology, Oklahoma University Health Sciences Center, Oklahoma City, OK 73104
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
44
|
Barnes RL, McCulloch R. Trypanosoma brucei homologous recombination is dependent on substrate length and homology, though displays a differential dependence on mismatch repair as substrate length decreases. Nucleic Acids Res 2007; 35:3478-93. [PMID: 17478508 PMCID: PMC1904282 DOI: 10.1093/nar/gkm249] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Homologous recombination functions universally in the maintenance of genome stability through the repair of DNA breaks and in ensuring the completion of replication. In some organisms, homologous recombination can perform more specific functions. One example of this is in antigenic variation, a widely conserved mechanism for the evasion of host immunity. Trypanosoma brucei, the causative agent of sleeping sickness in Africa, undergoes antigenic variation by periodic changes in its variant surface glycoprotein (VSG) coat. VSG switches involve the activation of VSG genes, from an enormous silent archive, by recombination into specialized expression sites. These reactions involve homologous recombination, though they are characterized by an unusually high rate of switching and by atypical substrate requirements. Here, we have examined the substrate parameters of T. brucei homologous recombination. We show, first, that the reaction is strictly dependent on substrate length and that it is impeded by base mismatches, features shared by homologous recombination in all organisms characterized. Second, we identify a pathway of homologous recombination that acts preferentially on short substrates and is impeded to a lesser extent by base mismatches and the mismatch repair machinery. Finally, we show that mismatches during T. brucei recombination may be repaired by short-patch mismatch repair.
Collapse
Affiliation(s)
| | - Richard McCulloch
- *To whom correspondence should be addressed. Tel: 0044 141 330 5946; Fax: 0044 141 330 5422;
| |
Collapse
|
45
|
Schildkraut E, Miller CA, Nickoloff JA. Transcription of a donor enhances its use during double-strand break-induced gene conversion in human cells. Mol Cell Biol 2006; 26:3098-105. [PMID: 16581784 PMCID: PMC1446947 DOI: 10.1128/mcb.26.8.3098-3105.2006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Homologous recombination (HR) mediates accurate repair of double-strand breaks (DSBs) but carries the risk of large-scale genetic change, including loss of heterozygosity, deletions, inversions, and translocations. Nearly one-third of the human genome consists of repetitive sequences, and DSB repair by HR often requires choices among several homologous repair templates, including homologous chromosomes, sister chromatids, and linked or unlinked repeats. Donor preference during DSB-induced gene conversion was analyzed by using several HR substrates with three copies of neo targeted to a human chromosome. Repair of I-SceI nuclease-induced DSBs in one neo (the recipient) required a choice between two donor neo genes. When both donors were downstream, there was no significant bias for proximal or distal donors. When donors flanked the recipient, we observed a marked (85%) preference for the downstream donor. Reversing the HR substrate in the chromosome eliminated this preference, indicating that donor choice is influenced by factors extrinsic to the HR substrate. Prior indirect evidence suggested that transcription might increase donor use. We tested this question directly and found that increased transcription of a donor enhances its use during gene conversion. A preference for transcribed donors would minimize the use of nontranscribed (i.e., pseudogene) templates during repair and thus help maintain genome stability.
Collapse
Affiliation(s)
- Ezra Schildkraut
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA.
| | | | | |
Collapse
|
46
|
Lui DY, Peoples-Holst TL, Mell JC, Wu HY, Dean EW, Burgess SM. Analysis of close stable homolog juxtaposition during meiosis in mutants of Saccharomyces cerevisiae. Genetics 2006; 173:1207-22. [PMID: 16648640 PMCID: PMC1526657 DOI: 10.1534/genetics.105.050658] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A unique aspect of meiosis is the segregation of homologous chromosomes at the meiosis I division. The pairing of homologous chromosomes is a critical aspect of meiotic prophase I that aids proper disjunction at anaphase I. We have used a site-specific recombination assay in Saccharomyces cerevisiae to examine allelic interaction levels during meiosis in a series of mutants defective in recombination, chromatin structure, or intracellular movement. Red1, a component of the chromosome axis, and Mnd1, a chromosome-binding protein that facilitates interhomolog interaction, are critical for achieving high levels of allelic interaction. Homologous recombination factors (Sae2, Rdh54, Rad54, Rad55, Rad51, Sgs1) aid in varying degrees in promoting allelic interactions, while the Srs2 helicase appears to play no appreciable role. Ris1 (a SWI2/SNF2 related protein) and Dot1 (a histone methyltransferase) appear to play minor roles. Surprisingly, factors involved in microtubule-mediated intracellular movement (Tub3, Dhc1, and Mlp2) appear to play no appreciable role in homolog juxtaposition, unlike their counterparts in fission yeast. Taken together, these results support the notion that meiotic recombination plays a major role in the high levels of homolog interaction observed during budding yeast meiosis.
Collapse
Affiliation(s)
- Doris Y Lui
- Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA
| | | | | | | | | | | |
Collapse
|
47
|
Zickler D. From early homologue recognition to synaptonemal complex formation. Chromosoma 2006; 115:158-74. [PMID: 16570189 DOI: 10.1007/s00412-006-0048-6] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Revised: 12/20/2005] [Accepted: 12/21/2005] [Indexed: 10/24/2022]
Abstract
This review focuses on various aspects of chromosome homology searching and their relationship to meiotic and vegetative pairing and to the silencing of unpaired copies of genes. Chromosome recognition and pairing is a prominent characteristic of meiosis; however, for some organisms, this association (complete or partial) is also a normal part of nuclear organization. The multiple mechanisms suggested to contribute to homologous pairing are analyzed. Recognition of DNA/DNA homology also plays an important role in detecting DNA segments that are present in inappropriate number of copies before and during meiosis. In this context, the mechanisms of methylation induced premeiotically, repeat-induced point mutation, meiotic silencing by unpaired DNA, and meiotic sex chromosome inactivation will be discussed. Homologue juxtaposition during meiotic prophase can be divided into three mechanistically distinct steps, namely, recognition, presynaptic alignment, and synapsis by the synaptonemal complex (SC). In most organisms, these three steps are distinguished by their dependence on DNA double-strand breaks (DSBs). The coupling of SC initiation to (and downstream effects of) DSB formation and the exceptions to this dependency are discussed. Finally, this review addresses the specific factors that appear to promote chromosome movement at various stages of meiotic prophase, most particularly at the bouquet stage, and on their significance for homologue pairing and/or achieving a final pachytene configuration.
Collapse
Affiliation(s)
- Denise Zickler
- Université Paris-Sud, Institut de Génétique et Microbiologie, 91405, Orsay, France.
| |
Collapse
|
48
|
Gerton JL, Hawley RS. Homologous chromosome interactions in meiosis: diversity amidst conservation. Nat Rev Genet 2005; 6:477-87. [PMID: 15931171 DOI: 10.1038/nrg1614] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proper chromosome segregation is crucial for preventing fertility problems, birth defects and cancer. During mitotic cell divisions, sister chromatids separate from each other to opposite poles, resulting in two daughter cells that each have a complete copy of the genome. Meiosis poses a special problem in which homologous chromosomes must first pair and then separate at the first meiotic division before sister chromatids separate at the second meiotic division. So, chromosome interactions between homologues are a unique feature of meiosis and are essential for proper chromosome segregation. Pairing and locking together of homologous chromosomes involves recombination interactions in some cases, but not in others. Although all organisms must match and lock homologous chromosomes to maintain genome integrity throughout meiosis, recent results indicate that the underlying mechanisms vary in different organisms.
Collapse
Affiliation(s)
- Jennifer L Gerton
- The Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA.
| | | |
Collapse
|
49
|
Schlecht HB, Lichten M, Goldman ASH. Compartmentalization of the yeast meiotic nucleus revealed by analysis of ectopic recombination. Genetics 2005; 168:1189-203. [PMID: 15579679 PMCID: PMC1448799 DOI: 10.1534/genetics.104.029157] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
As yeast cells enter meiosis, chromosomes move from a centromere-clustered (Rabl) to a telomere-clustered (bouquet) configuration and then to states of progressive homolog pairing where telomeres are more dispersed. It is uncertain at which stage of this process sequences commit to recombine with each other. Previous analyses using recombination between dispersed homologous sequences (ectopic recombination) support the view that, on average, homologs are aligned end to end by the time of commitment to recombination. We have undertaken further analyses incorporating new inserts, chromosome rearrangements, an alternate mode of recombination initiation, and mutants that disrupt nuclear structure or telomere metabolism. Our findings support previous conclusions and reveal that distance from the nearest telomere is an important parameter influencing recombination between dispersed sequences. In general, the farther dispersed sequences are from their nearest telomere, the less likely they are to engage in ectopic recombination. Neither the mode of initiating recombination nor the formation of the bouquet appears to affect this relationship. We suggest that aspects of telomere localization and behavior influence the organization and mobility of chromosomes along their entire length, during a critical period of meiosis I prophase that encompasses the homology search.
Collapse
Affiliation(s)
- Hélène B Schlecht
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | | | | |
Collapse
|
50
|
Peoples-Holst TL, Burgess SM. Multiple branches of the meiotic recombination pathway contribute independently to homolog pairing and stable juxtaposition during meiosis in budding yeast. Genes Dev 2005; 19:863-74. [PMID: 15805472 PMCID: PMC1074323 DOI: 10.1101/gad.1293605] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A unique aspect of meiosis is the segregation of homologous chromosomes at the meiosis I division. Homologs are physically connected prior to segregation by crossing over between nonsister chromatids. Crossovers arise from the repair of induced double-strand breaks (DSBs). In many organisms, more DSBs are formed than crossovers in a given nucleus. It has been previously suggested that repair of DSBs to noncrossover recombination products aids homolog alignment. Here we explore how two modes of the meiotic recombination pathway (crossover and noncrossover) and meiotic telomere reorganization contribute to the pairing and close juxtaposition of homologous chromosomes in budding yeast. We found that intermediates in the DSB repair pathway leading to both crossover and noncrossover recombination products contribute independently to close, stable homolog juxtaposition (CSHJ), a measurable state of homolog pairing. Analysis of the ndj1delta mutant indicates that the effect of meiotic telomere reorganization on CSHJ is exerted through recombination intermediates at interstitial chromosomal loci, perhaps through the noncrossover branch of the DSB repair pathway. We suggest that transient, early DSB-initiated interactions, including those that give rise to noncrossovers, are important for homolog recognition and juxtaposition.
Collapse
Affiliation(s)
- Tamara L Peoples-Holst
- Section of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, USA
| | | |
Collapse
|