201
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Shen S, Loh TJ, Shen H, Zheng X, Shen H. CRISPR as a strong gene editing tool. BMB Rep 2017; 50:20-24. [PMID: 27616359 PMCID: PMC5319660 DOI: 10.5483/bmbrep.2017.50.1.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/16/2016] [Accepted: 09/07/2016] [Indexed: 11/20/2022] Open
Abstract
Clustered regularly-interspaced short palindromic repeats (CRISPR) is a new and effective genetic editing tool. CRISPR was initially found in bacteria to protect it from virus invasions. In the first step, specific DNA strands of virus are identified by guide RNA that is composed of crRNA and tracrRNA. Then RNAse III is required for producing crRNA from pre-crRNA. In The second step, a crRNA:tracrRNA:Cas9 complex guides RNase III to cleave target DNA. After cleavage of DNA by CRISPR-Cas9, DNA can be fixed by Non- Homologous End Joining (NHEJ) and Homology Directed Repair (HDR). Whereas NHEJ is simple and random, HDR is much more complex and accurate. Gene editing by CRISPR is able to be applied to various biological field such as agriculture and treating genetic diseases in human. [BMB Reports 2017; 50(1): 20-24].
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Affiliation(s)
- Shengfu Shen
- Willston Northampton School, Easthampton, MA 01027,
USA
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Hongling Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
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202
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Vriend LEM, Krawczyk PM. Nick-initiated homologous recombination: Protecting the genome, one strand at a time. DNA Repair (Amst) 2016; 50:1-13. [PMID: 28087249 DOI: 10.1016/j.dnarep.2016.12.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 12/17/2016] [Indexed: 01/13/2023]
Abstract
Homologous recombination (HR) is an essential, widely conserved mechanism that utilizes a template for accurate repair of DNA breaks. Some early HR models, developed over five decades ago, anticipated single-strand breaks (nicks) as initiating lesions. Subsequent studies favored a more double-strand break (DSB)-centered view of HR initiation and at present this pathway is primarily considered to be associated with DSB repair. However, mounting evidence suggests that nicks can indeed initiate HR directly, without first being converted to DSBs. Moreover, recent studies reported on novel branches of nick-initiated HR (nickHR) that rely on single-, rather than double-stranded repair templates and that are characterized by mechanistically and genetically unique properties. The physiological significance of nickHR is not well documented, but its high-fidelity nature and low mutagenic potential are relevant in recently developed, precise gene editing approaches. Here, we review the evidence for stimulation of HR by nicks, as well as the data on the interactions of nickHR with other DNA repair pathways and on its mechanistic properties. We conclude that nickHR is a bona-fide pathway for nick repair, sharing the molecular machinery with the canonical HR but nevertheless characterized by unique properties that secure its inclusion in DNA repair models and warrant future investigations.
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Affiliation(s)
- Lianne E M Vriend
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Przemek M Krawczyk
- Department of Cell Biology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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203
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Lv YH, Li XQ, Yue CW, Wang M. Application of genome editing technologies in gastrointestinal cancers. Shijie Huaren Xiaohua Zazhi 2016; 24:4772-4780. [DOI: 10.11569/wcjd.v24.i36.4772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome editing is a site-directed modification technology for gene targeting and a powerful tool to edit the target DNA by site-specific DNA knockout or knockin. Genome editing has achieved a considerable success from lower microbes to human in the past years and may play a very important role in tumor staging, precision medicine as well as prognosis evaluation in gastrointestinal cancers. This review discusses the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including transcription activator-like effector nucleases, zinc finger nucleases and the CRISPR/Cas9 system. We also summarize the progress made in applying genome editing to the research of gastrointestinal cancers.
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204
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Abstract
The recent development of CRISPR-Cas systems as easily accessible and programmable tools for genome editing and regulation is spurring a revolution in biology. Paired with the rapid expansion of reference and personalized genomic sequence information, technologies based on CRISPR-Cas are enabling nearly unlimited genetic manipulation, even in previously difficult contexts, including human cells. Although much attention has focused on the potential of CRISPR-Cas to cure Mendelian diseases, the technology also holds promise to transform the development of therapies to treat complex heritable and somatic disorders. In this Review, we discuss how CRISPR-Cas can affect the next generation of drugs by accelerating the identification and validation of high-value targets, uncovering high-confidence biomarkers and developing differentiated breakthrough therapies. We focus on the promises, pitfalls and hurdles of this revolutionary gene-editing technology, discuss key aspects of different CRISPR-Cas screening platforms and offer our perspectives on the best practices in genome engineering.
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205
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Bhattacharjee S, Nandi S. Choices have consequences: the nexus between DNA repair pathways and genomic instability in cancer. Clin Transl Med 2016; 5:45. [PMID: 27921283 PMCID: PMC5136664 DOI: 10.1186/s40169-016-0128-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background The genome is under constant assault from a multitude of sources that can lead to the formation of DNA double-stand breaks (DSBs). DSBs are cytotoxic lesions, which if left unrepaired could lead to genomic instability, cancer and even cell death. However, erroneous repair of DSBs can lead to chromosomal rearrangements and loss of heterozygosity, which in turn can also cause cancer and cell death. Hence, although the repair of DSBs is crucial for the maintenance of genome integrity the process of repair need to be well regulated and closely monitored. Main body The two most commonly used pathways to repair DSBs in higher eukaryotes include non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is considered to be error-prone, intrinsically mutagenic quick fix remedy to seal together the broken DNA ends and restart replication. In contrast, HR is a high-fidelity process that has been very well conserved from phage to humans. Here we review HR and its sub-pathways. We discuss what factors determine the sub pathway choice including etiology of the DSB, chromatin structure at the break site, processing of the DSBs and the mechanisms regulating the sub-pathway choice. We also elaborate on the potential of targeting HR genes for cancer therapy and anticancer strategies. Conclusion The DNA repair field is a vibrant one, and the stage is ripe for scrutinizing the potential treatment efficacy and future clinical applications of the pharmacological inhibitors of HR enzymes as mono- or combinatorial therapy regimes. Electronic supplementary material The online version of this article (doi:10.1186/s40169-016-0128-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Saikat Nandi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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206
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Abstract
Meiosis, the mechanism of creating haploid gametes, is a complex cellular process observed across sexually reproducing organisms. Fundamental to meiosis is the process of homologous recombination, whereby DNA double-strand breaks are introduced into the genome and are subsequently repaired to generate either noncrossovers or crossovers. Although homologous recombination is essential for chromosome pairing during prophase I, the resulting crossovers are critical for maintaining homolog interactions and enabling accurate segregation at the first meiotic division. Thus, the placement, timing, and frequency of crossover formation must be exquisitely controlled. In this review, we discuss the proteins involved in crossover formation, the process of their formation and designation, and the rules governing crossovers, all within the context of the important landmarks of prophase I. We draw together crossover designation data across organisms, analyze their evolutionary divergence, and propose a universal model for crossover regulation.
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Affiliation(s)
- Stephen Gray
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, New York 14853; ,
| | - Paula E Cohen
- Department of Biomedical Sciences and Center for Reproductive Genomics, Cornell University, Ithaca, New York 14853; ,
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207
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Calos MP. Genome Editing Techniques and Their Therapeutic Applications. Clin Pharmacol Ther 2016; 101:42-51. [PMID: 27783398 DOI: 10.1002/cpt.542] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022]
Abstract
Fueled by advances in the field of genetics, the methods available to edit DNA sequences in living cells have continued to develop steadily. These technologies directly impact the fields of gene and cell therapy, where changes in the DNA sequence of target cells offer a route to correct genetic diseases and manipulate disorders like cancer. We review here the expanding menu of genome editing techniques and how they are being applied to therapeutic targets. The methods encompass a myriad of approaches to modify the covalent structure of DNA, including the targeted creation of double-strand breaks that can catalyze genomic changes, as well as the use of retroviruses and transposons to mediate gene addition, recombinases for sequence-specific gene addition and deletion, and base repair for direct sequence changes. The continued growth of the exciting field of genome editing is opening new possibilities for therapeutic intervention.
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Affiliation(s)
- M P Calos
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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208
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Hohmann S. Nobel Yeast Research. FEMS Yeast Res 2016; 16:fow094. [PMID: 27770011 DOI: 10.1093/femsyr/fow094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/17/2016] [Accepted: 10/19/2016] [Indexed: 01/06/2023] Open
Affiliation(s)
- Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Göteborg, Sweden
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209
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Abstract
Double-strand breaks (DSBs) pose a severe challenge to genome integrity; consequently, cells have developed efficient mechanisms to repair DSBs through several pathways of homologous recombination and other nonhomologous end-joining processes. Much of our understanding of these pathways has come from the analysis of site-specific DSBs created by the HO endonuclease in the budding yeast Saccharomyces cerevisiae. I was fortunate to get in on the ground floor of analyzing the fate of synchronously induced DSBs through the study of what I coined "in vivo biochemistry." I have had the remarkable good fortune to profit from the development of new techniques that have permitted an ever more detailed dissection of these repair mechanisms, which are described here.
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Affiliation(s)
- James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02453;
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210
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Jia L, Li L, Gui T, Liu S, Li H, Han J, Guo W, Liu Y, Li J. Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination. Virol J 2016; 13:156. [PMID: 27655081 PMCID: PMC5031261 DOI: 10.1186/s12985-016-0616-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/15/2016] [Indexed: 01/27/2023] Open
Abstract
Background With increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms. Methods Near full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated. Results Pearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination. Conclusions These results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our findings will be relevant in furthering the understanding of HIV-1 recombination mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0616-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Jia
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Lin Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Tao Gui
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Siyang Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Hanping Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jingwan Han
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Wei Guo
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yongjian Liu
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Jingyun Li
- Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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211
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de Freitas MCR, Resende JA, Ferreira-Machado AB, Saji GDRQ, de Vasconcelos ATR, da Silva VL, Nicolás MF, Diniz CG. Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole. Front Microbiol 2016; 7:1465. [PMID: 27703449 PMCID: PMC5028390 DOI: 10.3389/fmicb.2016.01465] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/01/2016] [Indexed: 12/29/2022] Open
Abstract
Bacteroides fragilis, member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug. From a wild type B. fragilis ATCC 43859 four derivative strains were selected: first and fourth subcultures under metronidazole exposure and first and fourth subcultures after drug removal. According to global gene expression analysis, 2,146 protein coding genes were identified, of which a total of 1,618 (77%) were assigned to a Gene Ontology term (GO), indicating that most known cellular functions were taken. Among these 2,146 protein coding genes, 377 were shared among all strains, suggesting that they are critical for B. fragilis survival. In order to identify distinct expression patterns, we also performed a K-means clustering analysis set to 15 groups. This analysis allowed us to detect the major activated or repressed genes encoding for enzymes which act in several metabolic pathways involved in metronidazole response such as drug activation, defense mechanisms against superoxide ions, high expression level of multidrug efflux pumps, and DNA repair. The strains collected after metronidazole removal were functionally more similar to those cultured under drug pressure, reinforcing that drug-exposure lead to drastic persistent changes in the B. fragilis gene expression patterns. These results may help to elucidate B. fragilis response during metronidazole exposure, mainly at SIC, contributing with information about bacterial survival strategies under stress conditions in their environment.
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Affiliation(s)
- Michele C R de Freitas
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Juliana A Resende
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Alessandra B Ferreira-Machado
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Guadalupe D R Q Saji
- Laboratório de Bioinformática and Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Ana T R de Vasconcelos
- Laboratório de Bioinformática and Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Vânia L da Silva
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Marisa F Nicolás
- Laboratório de Bioinformática and Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Cláudio G Diniz
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
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212
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The rate of meiotic gene conversion varies by sex and age. Nat Genet 2016; 48:1377-1384. [PMID: 27643539 PMCID: PMC5083143 DOI: 10.1038/ng.3669] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 08/16/2016] [Indexed: 12/14/2022]
Abstract
Meiotic recombination involves a combination of gene conversion and crossover events that, along with mutations, produce germline genetic diversity. Here we report the discovery of 3,176 SNP and 61 indel gene conversions. Our estimate of the non-crossover (NCO) gene conversion rate (G) is 7.0 for SNPs and 5.8 for indels per megabase per generation, and the GC bias is 67.6%. For indels, we demonstrate a 65.6% preference for the shorter allele. NCO gene conversions from mothers are longer than those from fathers, and G is 2.17 times greater in mothers. Notably, G increases with the age of mothers, but not the age of fathers. A disproportionate number of NCO gene conversions in older mothers occur outside double-strand break (DSB) regions and in regions with relatively low GC content. This points to age-related changes in the mechanisms of meiotic gene conversion in oocytes.
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213
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CRISPR-Cas9 enables conditional mutagenesis of challenging loci. Sci Rep 2016; 6:32326. [PMID: 27580957 PMCID: PMC5007477 DOI: 10.1038/srep32326] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 08/05/2016] [Indexed: 11/08/2022] Open
Abstract
The International Knockout Mouse Consortium (IKMC) has produced a genome-wide collection of 15,000 isogenic targeting vectors for conditional mutagenesis in C57BL/6N mice. Although most of the vectors have been used successfully in murine embryonic stem (ES) cells, there remain a set of nearly two thousand genes that have failed to target even after several attempts. Recent attention has turned to the use of new genome editing technology for the generation of mutant alleles in mice. Here, we demonstrate how Cas9-assisted targeting can be combined with the IKMC targeting vector resource to generate conditional alleles in genes that have previously eluded targeting using conventional methods.
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214
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Talhaoui I, Bernal M, Mazón G. The nucleolytic resolution of recombination intermediates in yeast mitotic cells. FEMS Yeast Res 2016; 16:fow065. [PMID: 27509904 DOI: 10.1093/femsyr/fow065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2016] [Indexed: 12/20/2022] Open
Abstract
In mitotic cells, the repair of double-strand breaks by homologous recombination (HR) is important for genome integrity. HR requires the orchestration of a subset of pathways for timely removal of joint-molecule intermediates that would otherwise prevent segregation of chromosomes in mitosis. The use of nucleases to resolve recombination intermediates is important for chromosome segregation, but is hazardous because crossovers can result in loss of heterozygosity or chromosome rearrangements. Unregulated use of the nucleases involved in the resolution of recombination intermediates could also be a risk during replication. The yeast models (Saccharomyces cerevisae and Schizosaccharomyces pombe) have proven effective in determining the major nucleases involved in the processing of such intermediates: Mus81-Mms4 and Yen1. Mus81-Mms4 and Yen1 are regulated by the cell cycle in a gradual activation during G2/M to keep the crossing-over risk low while ensuring proper removal of HJ intermediates.
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Affiliation(s)
- Ibtissam Talhaoui
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS) UMR 8200 Genetic Stability and Oncogenesis, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Manuel Bernal
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS) UMR 8200 Genetic Stability and Oncogenesis, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Gerard Mazón
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS) UMR 8200 Genetic Stability and Oncogenesis, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
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215
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Huang J, Copenhaver GP, Ma H, Wang Y. New insights into the role of DNA synthesis in meiotic recombination. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1126-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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216
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Lin CC, Potter CJ. Editing Transgenic DNA Components by Inducible Gene Replacement in Drosophila melanogaster. Genetics 2016; 203:1613-28. [PMID: 27334272 PMCID: PMC4981265 DOI: 10.1534/genetics.116.191783] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022] Open
Abstract
Gene conversions occur when genomic double-strand DNA breaks (DSBs) trigger unidirectional transfer of genetic material from a homologous template sequence. Exogenous or mutated sequence can be introduced through this homology-directed repair (HDR). We leveraged gene conversion to develop a method for genomic editing of existing transgenic insertions in Drosophila melanogaster The clustered regularly-interspaced palindromic repeats (CRISPR)/Cas9 system is used in the H: omology A: ssisted C: RISPR K: nock-in (HACK) method to induce DSBs in a GAL4 transgene, which is repaired by a single-genomic transgenic construct containing GAL4 homologous sequences flanking a T2A-QF2 cassette. With two crosses, this technique converts existing GAL4 lines, including enhancer traps, into functional QF2 expressing lines. We used HACK to convert the most commonly-used GAL4 lines (labeling tissues such as neurons, fat, glia, muscle, and hemocytes) to QF2 lines. We also identified regions of the genome that exhibited differential efficiencies of HDR. The HACK technique is robust and readily adaptable for targeting and replacement of other genomic sequences, and could be a useful approach to repurpose existing transgenes as new genetic reagents become available.
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Affiliation(s)
- Chun-Chieh Lin
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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217
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Chugunova AA, Dontsova OA, Sergiev PV. Methods of genome engineering: a new era of molecular biology. BIOCHEMISTRY (MOSCOW) 2016; 81:662-77. [DOI: 10.1134/s0006297916070038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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218
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Selvarajah G, Selvarajah S. Model building to facilitate understanding of holliday junction and heteroduplex formation, and holliday junction resolution. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:381-390. [PMID: 26899144 DOI: 10.1002/bmb.20964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 12/30/2015] [Accepted: 01/26/2016] [Indexed: 06/05/2023]
Abstract
Students frequently expressed difficulty in understanding the molecular mechanisms involved in chromosomal recombination. Therefore, we explored alternative methods for presenting the two concepts of the double-strand break model: Holliday junction and heteroduplex formation, and Holliday junction resolution. In addition to a lecture and computer-animated video, we included a model building activity using pipe cleaners. Biotechnology undergraduates (n = 108) used the model to simulate Holliday junction and heteroduplex formation, and Holliday junction resolution. Based on student perception, an average of 12.85 and 78.35% students claimed that they completely and partially understood the two concepts, respectively. A test conducted to ascertain their understanding about the two concepts showed that 66.1% of the students provided the correct response to the three multiple choice questions. A majority of the 108 students attributed the inclusion of model building to their better understanding of Holliday junction and heteroduplex formation, and Holliday junction resolution. This underlines the importance of incorporating model building, particularly in concepts that require spatial visualization. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(4):381-390, 2016.
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219
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Extended Abstracts. Toxicol Pathol 2016. [DOI: 10.1177/019262339702500633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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220
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Choi K, Reinhard C, Serra H, Ziolkowski PA, Underwood CJ, Zhao X, Hardcastle TJ, Yelina NE, Griffin C, Jackson M, Mézard C, McVean G, Copenhaver GP, Henderson IR. Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes. PLoS Genet 2016; 12:e1006179. [PMID: 27415776 PMCID: PMC4945094 DOI: 10.1371/journal.pgen.1006179] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/15/2016] [Indexed: 12/31/2022] Open
Abstract
Meiotic crossover frequency varies extensively along chromosomes and is typically concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to occur at immunity genes, where variation may be beneficial. A major component of plant immunity is recognition of pathogen Avirulence (Avr) effectors by resistance (R) genes that encode NBS-LRR domain proteins. Therefore, we sought to test whether NBS-LRR genes would overlap with meiotic crossover hotspots using experimental genetics in Arabidopsis thaliana. NBS-LRR genes tend to physically cluster in plant genomes; for example, in Arabidopsis most are located in large clusters on the south arms of chromosomes 1 and 5. We experimentally mapped 1,439 crossovers within these clusters and observed NBS-LRR gene associated hotspots, which were also detected as historical hotspots via analysis of linkage disequilibrium. However, we also observed NBS-LRR gene coldspots, which in some cases correlate with structural heterozygosity. To study recombination at the fine-scale we used high-throughput sequencing to analyze ~1,000 crossovers within the RESISTANCE TO ALBUGO CANDIDA1 (RAC1) R gene hotspot. This revealed elevated intragenic crossovers, overlapping nucleosome-occupied exons that encode the TIR, NBS and LRR domains. The highest RAC1 recombination frequency was promoter-proximal and overlapped CTT-repeat DNA sequence motifs, which have previously been associated with plant crossover hotspots. Additionally, we show a significant influence of natural genetic variation on NBS-LRR cluster recombination rates, using crosses between Arabidopsis ecotypes. In conclusion, we show that a subset of NBS-LRR genes are strong hotspots, whereas others are coldspots. This reveals a complex recombination landscape in Arabidopsis NBS-LRR genes, which we propose results from varying coevolutionary pressures exerted by host-pathogen relationships, and is influenced by structural heterozygosity.
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Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Carsten Reinhard
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Heïdi Serra
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Piotr A. Ziolkowski
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Department of Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Charles J. Underwood
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Xiaohui Zhao
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Thomas J. Hardcastle
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Nataliya E. Yelina
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Catherine Griffin
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Jackson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, Versailles, France
| | - Gil McVean
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Ian R. Henderson
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge, United Kingdom
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221
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Apparent Epigenetic Meiotic Double-Strand-Break Disparity in Saccharomyces cerevisiae: A Meta-Analysis. Genetics 2016; 204:129-37. [PMID: 27356614 PMCID: PMC5012380 DOI: 10.1534/genetics.116.191635] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 06/23/2016] [Indexed: 11/25/2022] Open
Abstract
Previously published, and some unpublished, tetrad data from budding yeast (Saccharomyces cerevisiae) are analyzed for disparity in gene conversion, in which one allele is more often favored than the other (conversion disparity). One such disparity, characteristic of a bias in the frequencies of meiotic double-strand DNA breaks at the hotspot near the His4 locus, is found in diploids that undergo meiosis soon after their formation, but not in diploids that have been cloned and frozen. Altered meiotic DNA breakability associated with altered metabolism-related chromatin states has been previously reported. However, the above observations imply that such differing parental chromatin states can persist through at least one chromosome replication, and probably more, in a common environment. This conclusion may have implications for interpreting changes in allele frequencies in populations.
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222
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Steinert J, Schiml S, Puchta H. Homology-based double-strand break-induced genome engineering in plants. PLANT CELL REPORTS 2016; 35:1429-38. [PMID: 27084537 DOI: 10.1007/s00299-016-1981-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/31/2016] [Indexed: 05/19/2023]
Abstract
This review summarises the recent progress in DSB-induced gene targeting by homologous recombination in plants. We are getting closer to efficiently inserting genes or precisely exchanging single amino acids. Although the basic features of double-strand break (DSB)-induced genome engineering were established more than 20 years ago, only in recent years has the technique come into the focus of plant biologists. Today, most scientists apply the recently discovered CRISPR/Cas system for inducing site-specific DSBs in genes of interest to obtain mutations by non-homologous end joining (NHEJ), which is the prevailing and often imprecise mechanism of DSB repair in somatic plant cells. However, predefined changes like the site-specific insertion of foreign genes or an exchange of single amino acids can be achieved by DSB-induced homologous recombination (HR). Although DSB induction drastically enhances the efficiency of HR, the efficiency is still about two orders of magnitude lower than that of NHEJ. Therefore, significant effort have been put forth to improve DSB-induced HR based technologies. This review summarises the previous studies as well as discusses the most recent developments in using the CRISPR/Cas system to improve these processes for plants.
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Affiliation(s)
- Jeannette Steinert
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Simon Schiml
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany.
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223
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Robert T, Vrielynck N, Mézard C, de Massy B, Grelon M. A new light on the meiotic DSB catalytic complex. Semin Cell Dev Biol 2016; 54:165-76. [DOI: 10.1016/j.semcdb.2016.02.025] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/22/2016] [Indexed: 11/30/2022]
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224
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Udayakumar D, Pandita RK, Horikoshi N, Liu Y, Liu Q, Wong KK, Hunt CR, Gray NS, Minna JD, Pandita TK, Westover KD. Torin2 Suppresses Ionizing Radiation-Induced DNA Damage Repair. Radiat Res 2016; 185:527-38. [PMID: 27135971 DOI: 10.1667/rr14373.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Several classes of inhibitors of the mammalian target of rapamycin (mTOR) have been developed based on its central role in sensing growth factor and nutrient levels to regulate cellular metabolism. However, its ATP-binding site closely resembles other phosphatidylinositol 3-kinase-related kinase (PIKK) family members, resulting in reactivity with these targets that may also be therapeutically useful. The ATP-competitive mTOR inhibitor, Torin2, shows biochemical activity against the DNA repair-associated proteins ATM, ATR and DNA-PK, which raises the possibility that Torin2 and related compounds might radiosensitize cancerous tumors. In this study Torin2 was also found to enhance ionizing radiation-induced cell killing in conditions where ATM was dispensable, confirming the requirement for multiple PIKK targets. Moreover, Torin2 did not influence the initial appearance of γ-H2AX foci after irradiation but significantly delayed the disappearance of radiation-induced γ-H2AX foci, indicating a DNA repair defect. Torin2 increased the number of radiation-induced S-phase specific chromosome aberrations and reduced the frequency of radiation-induced CtIP and Rad51 foci formation, suggesting that Torin2 works by blocking homologous recombination (HR)-mediated DNA repair resulting in an S-phase specific DNA repair defect. Accordingly, Torin2 reduced HR-mediated repair of I-Sce1-induced DNA damage and contributed to replication fork stalling. We conclude that radiosensitization of tumor cells by Torin2 is associated with disrupting ATR- and ATM-dependent DNA damage responses. Our findings support the concept of developing combination cancer therapies that incorporate ionizing radiation therapy and Torin2 or compounds with similar properties.
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Affiliation(s)
- Durga Udayakumar
- a Department of Radiation Oncology and.,c Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030; and
| | - Raj K Pandita
- a Department of Radiation Oncology and.,c Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030; and
| | - Nobuo Horikoshi
- a Department of Radiation Oncology and.,c Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030; and
| | - Yan Liu
- d Center for Thoracic Oncology, Dana Farber Cancer Institute and
| | - Qingsong Liu
- e Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Kwok-Kin Wong
- d Center for Thoracic Oncology, Dana Farber Cancer Institute and
| | - Clayton R Hunt
- a Department of Radiation Oncology and.,c Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030; and
| | - Nathanael S Gray
- e Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - John D Minna
- b Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, Texas 75390
| | - Tej K Pandita
- a Department of Radiation Oncology and.,c Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030; and
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225
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Gourbal B, Théron A, Grunau C, Duval D, Mitta G. Polymorphic Mucin-Like Proteins in Schistosoma mansoni, a Variable Antigen and a Key Component of the Compatibility Between the Schistosome and Its Snail Host. Results Probl Cell Differ 2016; 57:91-108. [PMID: 26537378 DOI: 10.1007/978-3-319-20819-0_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The arms race between vertebrate hosts and parasites has led to diversification systems able to generate huge repertoires of immune recognition receptors and antigenic variants. Until recently, the invertebrate immunity was considered to be poorly specific, and consequently, antigenic variability was not expected to be high for their respective parasites. In the present chapter, we show how the study of the interaction between the snail Biomphalaria glabrata and its parasite Schistosome mansoni has shaken this paradigm. We show that the fate of the interaction between the snail and its parasite is at least partly the result of the concordance of highly variable repertoires of immune recognition receptors in the snail and corresponding antigenic variants in the parasite. We call these antigenic variants of the schistosome Schistosoma mansoni polymorphic mucins (SmPoMucs). We show that their high level of diversification is the result of a complex cascade of mechanisms, thus presenting evidence for antigenic variation in a parasite infecting an invertebrate species.
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Affiliation(s)
- Benjamin Gourbal
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - André Théron
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - Christoph Grunau
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - David Duval
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - Guillaume Mitta
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
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226
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Xu Q, Wang R, Ghanam AR, Yan G, Miao W, Song X. The key role of CYC2 during meiosis in Tetrahymena thermophila. Protein Cell 2016; 7:236-249. [PMID: 27008457 PMCID: PMC4818844 DOI: 10.1007/s13238-016-0254-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/12/2016] [Indexed: 01/30/2023] Open
Abstract
Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5-3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. To investigate the underlying mechanism of this phenomenon, a complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR.
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Affiliation(s)
- Qianlan Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai, 200031, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230071, China
| | - Ruoyu Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230071, China
| | - A R Ghanam
- School of Life Sciences, University of Science and Technology of China, Hefei, 230071, China
- Anatomy and Embryology Department, Suez Canal University, Ismailia, 41522, Egypt
| | - Guanxiong Yan
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaoyuan Song
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China.
- CAS Center for Excellence in Molecular Cell Science, Shanghai, 200031, China.
- School of Life Sciences, University of Science and Technology of China, Hefei, 230071, China.
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227
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Jagut M, Hamminger P, Woglar A, Millonigg S, Paulin L, Mikl M, Dello Stritto MR, Tang L, Habacher C, Tam A, Gallach M, von Haeseler A, Villeneuve AM, Jantsch V. Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance. PLoS Biol 2016; 14:e1002412. [PMID: 27011106 PMCID: PMC4807110 DOI: 10.1371/journal.pbio.1002412] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/19/2016] [Indexed: 11/30/2022] Open
Abstract
During the first meiotic division, crossovers (COs) between homologous chromosomes ensure their correct segregation. COs are produced by homologous recombination (HR)-mediated repair of programmed DNA double strand breaks (DSBs). As more DSBs are induced than COs, mechanisms are required to establish a regulated number of COs and to repair remaining intermediates as non-crossovers (NCOs). We show that the Caenorhabditis elegans RMI1 homolog-1 (RMH-1) functions during meiosis to promote both CO and NCO HR at appropriate chromosomal sites. RMH-1 accumulates at CO sites, dependent on known pro-CO factors, and acts to promote CO designation and enforce the CO outcome of HR-intermediate resolution. RMH-1 also localizes at NCO sites and functions in parallel with SMC-5 to antagonize excess HR-based connections between chromosomes. Moreover, RMH-1 also has a major role in channeling DSBs into an NCO HR outcome near the centers of chromosomes, thereby ensuring that COs form predominantly at off-center positions. A nematode homolog of the conserved DNA repair factor RMI1 plays multiple genetically separable roles that together ensure the faithful inheritance of intact genomes during sexual reproduction. During meiosis, faithful separation of chromosomes into gametes is essential for fertility and healthy progeny. During the first meiotic division, crossovers (CO) between parental homologs ensure their correct segregation. Programmed DNA double strand breaks (DSBs) and resection steps generate single-stranded overhangs that invade a sister chromatid of the homolog to initiate homologous recombination. This culminates in the generation of a DNA double Holliday junction (dHJ). This can be acted upon by resolvases to produce CO and non-crossover (NCO) products, depending on where the resolvases cut the DNA. Alternatively, NCOs can also be produced by decatenation via the RecQ helicase–topoisomeraseIII–Rmi1 (RTR) complex. The mammalian RTR contains a topoisomerase, Bloom’s helicase, and RMI1/2 scaffolding components. It disassembles dHJs in vitro and contributes the major NCO activity in mitosis. Here, we provide evidence that the Caenorhabditis elegans RMH-1 functions in distinct complexes during meiosis to produce both COs and NCOs in an in vivo animal model system. Strikingly, RMH-1 spatially regulates the distribution of COs on chromosomes, demonstrating that the RTR complex can act locally within specific chromosome domains.
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Affiliation(s)
- Marlène Jagut
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Patricia Hamminger
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Alexander Woglar
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sophia Millonigg
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Luis Paulin
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Martin Mikl
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Maria Rosaria Dello Stritto
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Lois Tang
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Cornelia Habacher
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
| | - Angela Tam
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Miguel Gallach
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna and Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Austria
| | - Anne M. Villeneuve
- Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Verena Jantsch
- Department of Chromosome Biology, Max F. Perutz Laboratories, Vienna Bio Center, University of Vienna, Vienna, Austria
- * E-mail:
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228
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MTE1 Functions with MPH1 in Double-Strand Break Repair. Genetics 2016; 203:147-57. [PMID: 26920759 DOI: 10.1534/genetics.115.185454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/22/2016] [Indexed: 11/18/2022] Open
Abstract
Double-strand DNA breaks occur upon exposure of cells to ionizing radiation and certain chemical agents or indirectly through replication fork collapse at DNA damage sites. If left unrepaired, double-strand breaks can cause genome instability and cell death, and their repair can result in loss of heterozygosity. In response to DNA damage, proteins involved in double-strand break repair by homologous recombination relocalize into discrete nuclear foci. We identified 29 proteins that colocalize with recombination repair protein Rad52 in response to DNA damage. Of particular interest, Ygr042w/Mte1, a protein of unknown function, showed robust colocalization with Rad52. Mte1 foci fail to form when the DNA helicase gene MPH1 is absent. Mte1 and Mph1 form a complex and are recruited to double-strand breaks in vivo in a mutually dependent manner. MTE1 is important for resolution of Rad52 foci during double-strand break repair and for suppressing break-induced replication. Together our data indicate that Mte1 functions with Mph1 in double-strand break repair.
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229
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Kolodner RD. A personal historical view of DNA mismatch repair with an emphasis on eukaryotic DNA mismatch repair. DNA Repair (Amst) 2016; 38:3-13. [PMID: 26698650 PMCID: PMC4740188 DOI: 10.1016/j.dnarep.2015.11.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 10/30/2015] [Accepted: 11/30/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Richard D Kolodner
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, Moores-UCSD Cancer Center and Institute for Molecular Medicine, University of CA, San Diego School of Medicine, La Jolla, CA 92093-0669, United States.
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230
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Manhart CM, Alani E. Roles for mismatch repair family proteins in promoting meiotic crossing over. DNA Repair (Amst) 2016; 38:84-93. [PMID: 26686657 PMCID: PMC4740264 DOI: 10.1016/j.dnarep.2015.11.024] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/14/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
The mismatch repair (MMR) family complexes Msh4-Msh5 and Mlh1-Mlh3 act with Exo1 and Sgs1-Top3-Rmi1 in a meiotic double strand break repair pathway that results in the asymmetric cleavage of double Holliday junctions (dHJ) to form crossovers. This review discusses how meiotic roles for Msh4-Msh5 and Mlh1-Mlh3 do not fit paradigms established for post-replicative MMR. We also outline models used to explain how these factors promote the formation of meiotic crossovers required for the accurate segregation of chromosome homologs during the Meiosis I division.
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Affiliation(s)
- Carol M Manhart
- Department of Molecular Biology and Genetics, Cornell University, 457 Biotechnology Building, Ithaca, NY 14853-2703, USA
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, 457 Biotechnology Building, Ithaca, NY 14853-2703, USA.
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231
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Yelina NE, Lambing C, Hardcastle TJ, Zhao X, Santos B, Henderson IR. DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis. Genes Dev 2016; 29:2183-202. [PMID: 26494791 PMCID: PMC4617981 DOI: 10.1101/gad.270876.115] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Yelina et al. show that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. This work demonstrates that DNA methylation plays a key role in establishing domains of meiotic recombination along chromosomes. During meiosis, homologous chromosomes undergo crossover recombination, which is typically concentrated in narrow hot spots that are controlled by genetic and epigenetic information. Arabidopsis chromosomes are highly DNA methylated in the repetitive centromeres, which are also crossover-suppressed. Here we demonstrate that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. However, loss of CG DNA methylation maintenance in met1 triggers epigenetic crossover remodeling at the chromosome scale, with pericentromeric decreases and euchromatic increases in recombination. We used recombination mutants that alter interfering and noninterfering crossover repair pathways (fancm and zip4) to demonstrate that remodeling primarily involves redistribution of interfering crossovers. Using whole-genome bisulfite sequencing, we show that crossover remodeling is driven by loss of CG methylation within the centromeric regions. Using cytogenetics, we profiled meiotic DNA double-strand break (DSB) foci in met1 and found them unchanged relative to wild type. We propose that met1 chromosome structure is altered, causing centromere-proximal DSBs to be inhibited from maturation into interfering crossovers. These data demonstrate that DNA methylation is sufficient to silence crossover hot spots and plays a key role in establishing domains of meiotic recombination along chromosomes.
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Affiliation(s)
- Nataliya E Yelina
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Christophe Lambing
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Xiaohui Zhao
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Bruno Santos
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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232
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Yeadon PJ, Bowring FJ, Catcheside DEA. Meiotic Recombination in Neurospora crassa Proceeds by Two Pathways with Extensive Holliday Junction Migration. PLoS One 2016; 11:e0147815. [PMID: 26812651 PMCID: PMC4727923 DOI: 10.1371/journal.pone.0147815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022] Open
Abstract
Analysis of thousands of Δmsh-2 octads using our fluorescent recombination system indicates that, as in other filamentous fungi, symmetric heteroduplex is common in the his-3 region of Neurospora crassa. Symmetric heteroduplex arises from Holliday junction migration, and we suggest this mechanism explains the high frequency of His+ spores in heteroallelic crosses in which recombination is initiated cis to the his-3 allele further from the initiator, cog+. In contrast, when recombination is initiated cis to the his-3 allele closer to cog+, His+ spores are mainly a result of synthesis-dependent strand annealing, yielding asymmetric heteroduplex. Loss of Msh-2 function increases measures of allelic recombination in both his-3 and the fluorescent marker gene, indicating that mismatches in asymmetric heteroduplex, as in Saccharomyces cerevisiae, tend to be repaired in the direction of restoration. Furthermore, the presence of substantial numbers of conversion octads in crosses lacking Msh-2 function suggests that the disjunction pathway described in S. cerevisiae is also active in Neurospora, adding to evidence for a universal model for meiotic recombination.
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Affiliation(s)
- Patricia Jane Yeadon
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
- * E-mail:
| | | | - David E. A. Catcheside
- School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
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233
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Salient Features of Endonuclease Platforms for Therapeutic Genome Editing. Mol Ther 2016; 24:422-9. [PMID: 26796671 DOI: 10.1038/mt.2016.21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Emerging gene-editing technologies are nearing a revolutionary phase in genetic medicine: precisely modifying or repairing causal genetic defects. This may include any number of DNA sequence manipulations, such as knocking out a deleterious gene, introducing a particular mutation, or directly repairing a defective sequence by site-specific recombination. All of these edits can currently be achieved via programmable rare-cutting endonucleases to create targeted DNA breaks that can engage and exploit endogenous DNA repair pathways to impart site-specific genetic changes. Over the past decade, several distinct technologies for introducing site-specific DNA breaks have been developed, yet the different biological origins of these gene-editing technologies bring along inherent differences in parameters that impact clinical implementation. This review aims to provide an accessible overview of the various endonuclease-based gene-editing platforms, highlighting the strengths and weakness of each with respect to therapeutic applications.
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234
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Maeder ML, Gersbach CA. Genome-editing Technologies for Gene and Cell Therapy. Mol Ther 2016; 24:430-46. [PMID: 26755333 PMCID: PMC4786923 DOI: 10.1038/mt.2016.10] [Citation(s) in RCA: 410] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Gene therapy has historically been defined as the addition of new genes to human cells. However, the recent advent of genome-editing technologies has enabled a new paradigm in which the sequence of the human genome can be precisely manipulated to achieve a therapeutic effect. This includes the correction of mutations that cause disease, the addition of therapeutic genes to specific sites in the genome, and the removal of deleterious genes or genome sequences. This review presents the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including zinc finger nucleases, transcription activator-like effector nucleases (TALENs), meganucleases, and the CRISPR/Cas9 system. We then summarize the progress made in applying genome editing to various areas of gene and cell therapy, including antiviral strategies, immunotherapies, and the treatment of monogenic hereditary disorders. The current challenges and future prospects for genome editing as a transformative technology for gene and cell therapy are also discussed.
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Affiliation(s)
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA
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235
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236
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Catching a (Double-Strand) Break: The Rad51 and Dmc1 Strand Exchange Proteins Can Co-occupy Both Ends of a Meiotic DNA Double-Strand Break. PLoS Genet 2016; 11:e1005741. [PMID: 26720282 PMCID: PMC4699915 DOI: 10.1371/journal.pgen.1005741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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237
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Quétier F. The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:65-76. [PMID: 26566825 DOI: 10.1016/j.plantsci.2015.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 05/23/2023]
Abstract
The first period of plant genome editing was based on Agrobacterium; chemical mutagenesis by EMS (ethyl methanesulfonate) and ionizing radiations; each of these technologies led to randomly distributed genome modifications. The second period is associated with the discoveries of homing and meganuclease enzymes during the 80s and 90s, which were then engineered to provide efficient tools for targeted editing. From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology. The latest revolution surfaced in 2013 with the CRISPR-Cas9 system, whose high efficiency and technical ease of use is really impressive; scientists can use in-house kits or commercially available kits; the only two requirements are to carefully choose the location of the DNA double strand breaks to be induced and then to order an oligonucleotide. While this close-to- ultimate toolkit for targeted editing of genomes represents dramatic scientific progress which allows the development of more complex useful agronomic traits through synthetic biology, the social acceptance of genome editing remains regularly questioned by anti-GMO citizens and organizations.
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Affiliation(s)
- Francis Quétier
- University of Evry Val d'Essonne, Evry 91025, France; Genopole, Evry 91025, France.
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238
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Lee SH, Princz LN, Klügel MF, Habermann B, Pfander B, Biertümpfel C. Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage. eLife 2015; 4:e12256. [PMID: 26682650 PMCID: PMC5039027 DOI: 10.7554/elife.12256] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/17/2015] [Indexed: 12/22/2022] Open
Abstract
Holliday junctions (HJs) are key DNA intermediates in homologous recombination. They link homologous DNA strands and have to be faithfully removed for proper DNA segregation and genome integrity. Here, we present the crystal structure of human HJ resolvase GEN1 complexed with DNA at 3.0 Å resolution. The GEN1 core is similar to other Rad2/XPG nucleases. However, unlike other members of the superfamily, GEN1 contains a chromodomain as an additional DNA interaction site. Chromodomains are known for their chromatin-targeting function in chromatin remodelers and histone(de)acetylases but they have not previously been found in nucleases. The GEN1 chromodomain directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. Structure-guided mutations in vitro and in vivo in yeast validated our mechanistic findings. Our study provides the missing structure in the Rad2/XPG family and insights how a well-conserved nuclease core acquires versatility in recognizing diverse substrates for DNA repair and maintenance.
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Affiliation(s)
- Shun-Hsiao Lee
- Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lissa Nicola Princz
- Department of Molecular Cell Biology, DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maren Felizitas Klügel
- Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Bianca Habermann
- Computational Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Department of Molecular Cell Biology, DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Biertümpfel
- Department of Structural Cell Biology, Molecular Mechanisms of DNA Repair, Max Planck Institute of Biochemistry, Martinsried, Germany
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239
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Biased Gene Conversion in Rhizobium etli Is Caused by Preferential Double-Strand Breaks on One of the Recombining Homologs. J Bacteriol 2015; 198:591-9. [PMID: 26598365 DOI: 10.1128/jb.00768-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/16/2015] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED Gene conversion, the nonreciprocal transfer of information during homologous recombination, is the main process that maintains identity between members of multigene families. Gene conversion in the nitrogenase (nifH) multigene family of Rhizobium etli was analyzed by using a two-plasmid system, where each plasmid carried a copy of nifH. One of the nifH copies was modified, creating restriction fragment length polymorphisms (RFLPs) spaced along the gene. Once the modified plasmid was introduced into R. etli, selection was done for cointegration with a resident plasmid lacking the RFLPs. Most of the cointegrate molecules harbor gene conversion events, biased toward a gain of RFLPs. This bias may be explained under the double-strand break repair model by proposing that the nifH gene lacking the RFLPs suffers a DNA double-strand break, so the incoming plasmid functions as a template for repairing the homolog on the resident plasmid. To support this proposal, we cloned an SceI site into the nifH homolog that had the RFLPs used for scoring gene conversion. In vivo expression of the meganuclease I-SceI allowed the generation of a double-strand break on this homolog. Upon introduction of this modified plasmid into an R. etli strain lacking I-SceI, biased gene conversion still favored the retention of markers on the incoming plasmid. In contrast, when the recipient strain ectopically expressed I-SceI, a dramatic reversal in gene conversion bias was seen, favoring the preservation of resident sequences. These results show that biased gene conversion is caused by preferential double-strand breaks on one of the recombining homologs. IMPORTANCE In this work, we analyzed gene conversion by using a system that entails horizontal gene transfer followed by homologous recombination in the recipient cell. Most gene conversion events are biased toward the acquisition of the incoming sequences, ranging in size from 120 bp to 800 bp. This bias is due to preferential cutting of resident DNA and can be reversed upon introduction of a double-strand break on the incoming sequence. Since conditions used in this work are similar to those in horizontal gene transfer, it provides evidence that, upon transfer, the resident DNA preferentially acquires gene variants.
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240
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Jakočiu̅nas T, Rajkumar AS, Zhang J, Arsovska D, Rodriguez A, Jendresen CB, Skjødt ML, Nielsen AT, Borodina I, Jensen MK, Keasling JD. CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae. ACS Synth Biol 2015; 4:1226-34. [PMID: 25781611 DOI: 10.1021/acssynbio.5b00007] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Homologous recombination (HR) in Saccharomyces cerevisiae has been harnessed for both plasmid construction and chromosomal integration of foreign DNA. Still, native HR machinery is not efficient enough for complex and marker-free genome engineering required for modern metabolic engineering. Here, we present a method for marker-free multiloci integration of in vivo assembled DNA parts. By the use of CRISPR/Cas9-mediated one-step double-strand breaks at single, double and triple integration sites we report the successful in vivo assembly and chromosomal integration of DNA parts. We call our method CasEMBLR and validate its applicability for genome engineering and cell factory development in two ways: (i) introduction of the carotenoid pathway from 15 DNA parts into three targeted loci, and (ii) creation of a tyrosine production strain using ten parts into two loci, simultaneously knocking out two genes. This method complements and improves the current set of tools available for genome engineering in S. cerevisiae.
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Affiliation(s)
- Tadas Jakočiu̅nas
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Arun S. Rajkumar
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jie Zhang
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Dushica Arsovska
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Angelica Rodriguez
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Christian Bille Jendresen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Mette L. Skjødt
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Alex T. Nielsen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Irina Borodina
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Michael K. Jensen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jay D. Keasling
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Physical
Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, California 94720, United States
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241
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Abstract
The ability to manipulate the genome with precise spatial and nucleotide resolution (genome editing) has been a powerful research tool. In the past decade, the tools and expertise for using genome editing in human somatic cells and pluripotent cells have increased to such an extent that the approach is now being developed widely as a strategy to treat human disease. The fundamental process depends on creating a site-specific DNA double-strand break (DSB) in the genome and then allowing the cell's endogenous DSB repair machinery to fix the break such that precise nucleotide changes are made to the DNA sequence. With the development and discovery of several different nuclease platforms and increasing knowledge of the parameters affecting different genome editing outcomes, genome editing frequencies now reach therapeutic relevance for a wide variety of diseases. Moreover, there is a series of complementary approaches to assessing the safety and toxicity of any genome editing process, irrespective of the underlying nuclease used. Finally, the development of genome editing has raised the issue of whether it should be used to engineer the human germline. Although such an approach could clearly prevent the birth of people with devastating and destructive genetic diseases, questions remain about whether human society is morally responsible enough to use this tool.
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Affiliation(s)
- Matthew Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, California 94305;
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242
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Abstract
The study of homologous recombination has its historical roots in meiosis. In this context, recombination occurs as a programmed event that culminates in the formation of crossovers, which are essential for accurate chromosome segregation and create new combinations of parental alleles. Thus, meiotic recombination underlies both the independent assortment of parental chromosomes and genetic linkage. This review highlights the features of meiotic recombination that distinguish it from recombinational repair in somatic cells, and how the molecular processes of meiotic recombination are embedded and interdependent with the chromosome structures that characterize meiotic prophase. A more in-depth review presents our understanding of how crossover and noncrossover pathways of meiotic recombination are differentiated and regulated. The final section of this review summarizes the studies that have defined defective recombination as a leading cause of pregnancy loss and congenital disease in humans.
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Affiliation(s)
- Neil Hunter
- Howard Hughes Medical Institute, Department of Microbiology & Molecular Genetics, Department of Molecular & Cellular Biology, Department of Cell Biology & Human Anatomy, University of California Davis, Davis, California 95616
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243
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Westmoreland JW, Resnick MA. Recombinational repair of radiation-induced double-strand breaks occurs in the absence of extensive resection. Nucleic Acids Res 2015; 44:695-704. [PMID: 26503252 PMCID: PMC4737140 DOI: 10.1093/nar/gkv1109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
Recombinational repair provides accurate chromosomal restitution after double-strand break (DSB) induction. While all DSB recombination repair models include 5′-3′ resection, there are no studies that directly assess the resection needed for repair between sister chromatids in G-2 arrested cells of random, radiation-induced ‘dirty’ DSBs. Using our Pulse Field Gel Electrophoresis-shift approach, we determined resection at IR-DSBs in WT and mutants lacking exonuclease1 or Sgs1 helicase. Lack of either reduced resection length by half, without decreased DSB repair or survival. In the exo1Δ sgs1Δ double mutant, resection was barely detectable, yet it only took an additional hour to achieve a level of repair comparable to WT and there was only a 2-fold dose-modifying effect on survival. Results with a Dnl4 deletion strain showed that remaining repair was not due to endjoining. Thus, similar to what has been shown for a single, clean HO-induced DSB, a severe reduction in resection tract length has only a modest effect on repair of multiple, dirty DSBs in G2-arrested cells. Significantly, this study provides the first opportunity to directly relate resection length at DSBs to the capability for global recombination repair between sister chromatids.
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Affiliation(s)
- James W Westmoreland
- Chromosome Stability Section, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Michael A Resnick
- Chromosome Stability Section, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
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244
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Stahl FFW. Serendipity and the times. BACTERIOPHAGE 2015; 5:e1059003. [PMID: 26442193 DOI: 10.1080/21597081.2015.1059003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/02/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Franklin Frank W Stahl
- Distinguished Professor Emeritus of Biology; American Cancer Society Research Professor; University of Oregon ; Eugene, OR USA
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245
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Formation of interference-sensitive meiotic cross-overs requires sufficient DNA leading-strand elongation. Proc Natl Acad Sci U S A 2015; 112:12534-9. [PMID: 26392549 DOI: 10.1073/pnas.1507165112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Meiosis halves diploid genomes to haploid and is essential for sexual reproduction in eukaryotes. Meiotic recombination ensures physical association of homologs and their subsequent accurate segregation and results in the redistribution of genetic variations among progeny. Most organisms have two classes of cross-overs (COs): interference-sensitive (type I) and -insensitive (type II) COs. DNA synthesis is essential for meiotic recombination, but whether DNA synthesis has a role in differentiating meiotic CO pathways is unknown. Here, we show that Arabidopsis POL2A, the homolog of the yeast DNA polymerase-ε (a leading-strand DNA polymerase), is required for plant fertility and meiosis. Mutations in POL2A cause reduced fertility and meiotic defects, including abnormal chromosome association, improper chromosome segregation, and fragmentation. Observation of prophase I cell distribution suggests that pol2a mutants likely delay progression of meiotic recombination. In addition, the residual COs in pol2a have reduced CO interference, and the double mutant of pol2a with mus81, which affects type II COs, displayed more severe defects than either single mutant, indicating that POL2A functions in the type I pathway. We hypothesize that sufficient leading-strand DNA elongation promotes formation of some type I COs. Given that meiotic recombination and DNA synthesis are conserved in divergent eukaryotes, this study and our previous study suggest a novel role for DNA synthesis in the differentiation of meiotic recombination pathways.
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246
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Kostylev M, Otwell AE, Richardson RE, Suzuki Y. Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies. PLoS One 2015; 10:e0137466. [PMID: 26348330 PMCID: PMC4562628 DOI: 10.1371/journal.pone.0137466] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/17/2015] [Indexed: 11/18/2022] Open
Abstract
Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six double-stranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processes associated with most common applications of DNA assembly. We demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work.
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Affiliation(s)
- Maxim Kostylev
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (YS), (MK)
| | - Anne E. Otwell
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Ruth E. Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Yo Suzuki
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (YS), (MK)
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247
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Ouedraogo JP, Arentshorst M, Nikolaev I, Barends S, Ram AFJ. I-SceI-mediated double-strand DNA breaks stimulate efficient gene targeting in the industrial fungus Trichoderma reesei. Appl Microbiol Biotechnol 2015; 99:10083-95. [PMID: 26272087 PMCID: PMC4643118 DOI: 10.1007/s00253-015-6829-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 01/24/2023]
Abstract
Targeted integration of expression cassettes for enzyme production in industrial microorganisms is desirable especially when enzyme variants are screened for improved enzymatic properties. However, currently used methods for targeted integration are inefficient and result in low transformation frequencies. In this study, we expressed the Saccharomyces cerevisiae I-SceI meganuclease to generate double-strand breaks at a defined locus in the Trichoderma reesei genome. We showed that the double-strand DNA breaks mediated by I-SceI can be efficiently repaired when an exogenous DNA cassette flanked by regions homologous to the I-SceI landing locus was added during transformation. Transformation efficiencies increased approximately sixfold compared to control transformation. Analysis of the transformants obtained via I-SceI-mediated gene targeting showed that about two thirds of the transformants resulted from a homologous recombination event at the predetermined locus. Counter selection of the transformants for the loss of the pyrG marker upon integration of the DNA cassette showed that almost all of the clones contained the cassette at the predetermined locus. Analysis of independently obtained transformants using targeted integration of a glucoamylase expression cassette demonstrated that glucoamylase production among the transformants was high and showing limited variation. In conclusion, the gene targeting system developed in this study significantly increases transformation efficiency as well as homologous recombination efficiency and omits the use of Δku70 strains. It is also suitable for high-throughput screening of enzyme variants or gene libraries in T. reesei.
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Affiliation(s)
- Jean Paul Ouedraogo
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Kluyver Centre for Genomics of Industrial Fermentation, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Kluyver Centre for Genomics of Industrial Fermentation, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Igor Nikolaev
- Dupont Industrial Biosciences, Archimedesweg 30, 2333 CN, Leiden, The Netherlands
| | - Sharief Barends
- Dupont Industrial Biosciences, Archimedesweg 30, 2333 CN, Leiden, The Netherlands
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Kluyver Centre for Genomics of Industrial Fermentation, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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248
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Keeney S, Lange J, Mohibullah N. Self-organization of meiotic recombination initiation: general principles and molecular pathways. Annu Rev Genet 2015; 48:187-214. [PMID: 25421598 DOI: 10.1146/annurev-genet-120213-092304] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recombination in meiosis is a fascinating case study for the coordination of chromosomal duplication, repair, and segregation with each other and with progression through a cell-division cycle. Meiotic recombination initiates with formation of developmentally programmed DNA double-strand breaks (DSBs) at many places across the genome. DSBs are important for successful meiosis but are also dangerous lesions that can mutate or kill, so cells ensure that DSBs are made only at the right times, places, and amounts. This review examines the complex web of pathways that accomplish this control. We explore how chromosome breakage is integrated with meiotic progression and how feedback mechanisms spatially pattern DSB formation and make it homeostatic, robust, and error correcting. Common regulatory themes recur in different organisms or in different contexts in the same organism. We review this evolutionary and mechanistic conservation but also highlight where control modules have diverged. The framework that emerges helps explain how meiotic chromosomes behave as a self-organizing system.
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Affiliation(s)
- Scott Keeney
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
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249
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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.
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250
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Finnigan GC, Thorner J. Complex in vivo Ligation Using Homologous Recombination and High-efficiency Plasmid Rescue from Saccharomyces cerevisiae. Bio Protoc 2015; 5:e1521. [PMID: 26523287 DOI: 10.21769/bioprotoc.1521] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The protocols presented here allow for the facile generation of a wide variety of complex multipart DNA constructs (tagged gene products, gene fusions, chimeric proteins, and other variants) using homologous recombination and in vivo ligation in budding yeast (Saccharomyces cerevisiae). This method is straightforward, efficient and cost-effective, and can be used both for vector creation and for subsequent one-step, high frequency integration into a chromosomal locus in yeast. The procedure utilizes PCR with extended oligonucleotide "tails" of homology between multiple fragments to allow for reassembly in yeast in a single transformation followed by a method for highly efficient plasmid extraction from yeast (for transformation into bacteria). The latter is an improvement on existing methods of yeast plasmid extraction, which, historically, has been a limiting step in recovery of desired constructs. We describe the utility and convenience of our techniques, and provide several examples.
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Affiliation(s)
- Gregory C Finnigan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, USA
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