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Szurman-Zubrzycka M, Kurowska M, Till BJ, Szarejko I. Is it the end of TILLING era in plant science? FRONTIERS IN PLANT SCIENCE 2023; 14:1160695. [PMID: 37674734 PMCID: PMC10477672 DOI: 10.3389/fpls.2023.1160695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023]
Abstract
Since its introduction in 2000, the TILLING strategy has been widely used in plant research to create novel genetic diversity. TILLING is based on chemical or physical mutagenesis followed by the rapid identification of mutations within genes of interest. TILLING mutants may be used for functional analysis of genes and being nontransgenic, they may be directly used in pre-breeding programs. Nevertheless, classical mutagenesis is a random process, giving rise to mutations all over the genome. Therefore TILLING mutants carry background mutations, some of which may affect the phenotype and should be eliminated, which is often time-consuming. Recently, new strategies of targeted genome editing, including CRISPR/Cas9-based methods, have been developed and optimized for many plant species. These methods precisely target only genes of interest and produce very few off-targets. Thus, the question arises: is it the end of TILLING era in plant studies? In this review, we recap the basics of the TILLING strategy, summarize the current status of plant TILLING research and present recent TILLING achievements. Based on these reports, we conclude that TILLING still plays an important role in plant research as a valuable tool for generating genetic variation for genomics and breeding projects.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Marzena Kurowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Zhai S, Liu H, Xia X, Li H, Cao X, He Z, Ma W, Liu C, Song J, Liu A, Zhang J, Liu J. Functional analysis of polyphenol oxidase 1 gene in common wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1171839. [PMID: 37583591 PMCID: PMC10424926 DOI: 10.3389/fpls.2023.1171839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/07/2023] [Indexed: 08/17/2023]
Abstract
Polyphenol oxidase (PPO) activity is a major cause of the undesirable brown color of wheat-based products. Ppo1, a major gene for PPO activity, was cloned based on sequence homology in previous studies; however, its function and regulation mechanism remain unclear. In this study, the function and genetic regulation of Ppo1 were analyzed using RNA interference (RNAi) and Targeting Induced Local Lesions IN Genomes (TILLING) technology, and superior mutants were identified. Compared with the control, the level of Ppo1 transcript in RNAi transgenic lines was drastically decreased by 15.5%-60.9% during grain development, and PPO activity was significantly reduced by 12.9%-20.4%, confirming the role of Ppo1 in PPO activity. Thirty-two Ppo1 mutants were identified in the ethyl methanesulfonate (EMS)-mutagenized population, including eight missense mutations, 16 synonymous mutations, and eight intron mutations. The expression of Ppo1 was reduced significantly by 6.7%-37.1% and 10.1%-54.4% in mutants M092141 (G311S) and M091098 (G299R), respectively, in which PPO activity was decreased by 29.7% and 28.8%, respectively, indicating that mutation sites of two mutants have important effects on PPO1 function. Sequence and structure analysis revealed that the two sites were highly conserved among 74 plant species, where the frequency of glycine was 94.6% and 100%, respectively, and adjacent to the entrance of the hydrophobic pocket of the active site. The M092141 and M091098 mutants can be used as important germplasms to develop wheat cultivars with low grain PPO activity. This study provided important insights into the molecular mechanism of Ppo1 and the genetic improvement of wheat PPO activity.
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Affiliation(s)
- Shengnan Zhai
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hang Liu
- Australian-China Joint Centre for Wheat Improvement, Western Australian State Agriculture Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haosheng Li
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinyou Cao
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wujun Ma
- Australian-China Joint Centre for Wheat Improvement, Western Australian State Agriculture Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Cheng Liu
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianmin Song
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Aifeng Liu
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jingjuan Zhang
- Australian-China Joint Centre for Wheat Improvement, Western Australian State Agriculture Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Jianjun Liu
- National Engineering Laboratory for Wheat and Maize, Key Laboratory of Wheat Biology and Genetic Improvement in the Northern Yellow-Huai Rivers Valley of Ministry of Agriculture and Rural Affairs, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
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Wang Y, Salt DE, Koornneef M, Aarts MGM. Construction and analysis of a Noccaea caerulescens TILLING population. BMC PLANT BIOLOGY 2022; 22:360. [PMID: 35869423 PMCID: PMC9308233 DOI: 10.1186/s12870-022-03739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Metals such as Zn or Cd are toxic to plant and humans when they are exposed in high quantities through contaminated soil or food. Noccaea caerulescens, an extraordinary Zn/Cd/Ni hyperaccumulating species, is used as a model plant for metal hyperaccumulation and phytoremediation studies. Current reverse genetic techniques to generate mutants based on transgenesis is cumbersome due to the low transformation efficiency of this species. We aimed to establish a mutant library for functional genomics by a non-transgenic approach, to identify mutants with an altered mineral profiling, and to screen for mutations in bZIP19, a regulator of Zn homeostasis in N. caerulescens. RESULTS To generate the N. caerulescens mutant library, 3000 and 5000 seeds from two sister plants of a single-seed recurrent inbred descendant of the southern French accession Saint-Félix-de-Pallières (SF) were mutagenized respectively by 0.3 or 0.4% ethyl methane sulfonate (EMS). Two subpopulations of 5000 and 7000 M2 plants were obtained after 0.3 or 0.4% EMS treatment. The 0.4% EMS treatment population had a higher mutant frequency and was used for TILLING. A High Resolution Melting curve analysis (HRM) mutation screening platform was optimized and successfully applied to detect mutations for NcbZIP19, encoding a transcription factor controlling Zn homeostasis. Of four identified point mutations in NcbZIP19, two caused non-synonymous substitutions, however, these two mutations did not alter the ionome profile compared to the wild type. Forward screening of the 0.4% EMS treatment population by mineral concentration analysis (ionomics) in leaf material of each M2 plant revealed putative mutants affected in the concentration of one or more of the 20 trace elements tested. Several of the low-Zn mutants identified in the ionomic screen did not give progeny, illustrating the importance of Zn for the species. The mutant frequency of the population was evaluated based on an average of 2.3 knockout mutants per tested monogenic locus. CONCLUSIONS The 0.4% EMS treatment population is effectively mutagenized suitable for forward mutant screens and TILLING. Difficulties in seed production in low Zn mutants, obtained by both forward and reverse genetic approach, hampered further analysis of the nature of the low Zn phenotypes.
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Affiliation(s)
- Yanli Wang
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- College of Horticulture Science & Technology, Hebei Normal University of Science & Technology, No 360, West of HeBei street, Qinhuang Dao, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Abdul Hafeez
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | | | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Li Pengtao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Maozhi Ren
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Youlu Yuan
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
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Ünal İ, Emekli-Alturfan E. Fishing for Parkinson's Disease: A review of the literature. J Clin Neurosci 2019; 62:1-6. [PMID: 30660479 DOI: 10.1016/j.jocn.2019.01.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/04/2019] [Indexed: 01/08/2023]
Abstract
Parkinson's disease (PD), the second most common neurodegenerative disorder in the world, is due to the damage or death of cells that produce dopamine in the region called the substantia nigra (SN). Model organisms are important tools in PD research. Zebrafish (Danio rerio), a small tropical freshwater fish, entered the scientific world through developmental biology studies and today has become a popular model organism for human diseases. This review will provide information on the current knowledge about the use of zebrafish in PD research.
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Affiliation(s)
- İsmail Ünal
- Department of Biochemistry, Faculty of Dentistry, Marmara University, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Department of Biochemistry, Faculty of Dentistry, Marmara University, Istanbul, Turkey.
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Paone C, Diofano F, Park DD, Rottbauer W, Just S. Genetics of Cardiovascular Disease: Fishing for Causality. Front Cardiovasc Med 2018; 5:60. [PMID: 29911105 PMCID: PMC5992778 DOI: 10.3389/fcvm.2018.00060] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/15/2018] [Indexed: 01/08/2023] Open
Abstract
Cardiovascular disease (CVD) is still the leading cause of death in all western world countries and genetic predisposition in combination with traditional risk factors frequently mediates their manifestation. Genome-wide association (GWA) studies revealed numerous potentially disease modifying genetic loci often including several SNPs and associated genes. However, pure genetic association does not prove direct or indirect relevance of the modifier region on pathogenesis, nor does it define within the associated region the exact genetic driver of the disease. Therefore, the relevance of the identified genetic disease associations needs to be confirmed either in monogenic traits or in experimental in vivo model system by functional genomic studies. In this review, we focus on the use of functional genomic approaches such as gene knock-down or CRISPR/Cas9-mediated genome editing in the zebrafish model to validate disease-associated genomic loci and to identify novel cardiovascular disease genes. We summarize the benefits of the zebrafish for cardiovascular research and highlight examples demonstrating the successful combination of GWA studies and functional genomics in zebrafish to broaden our knowledge on the genetic and molecular underpinnings of cardiovascular diseases.
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Affiliation(s)
- Christoph Paone
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Federica Diofano
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | - Deung-Dae Park
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
| | | | - Steffen Just
- Molecular Cardiology, Department of Internal Medicine II, University of Ulm, Ulm, Germany
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Gut P, Reischauer S, Stainier DYR, Arnaout R. LITTLE FISH, BIG DATA: ZEBRAFISH AS A MODEL FOR CARDIOVASCULAR AND METABOLIC DISEASE. Physiol Rev 2017; 97:889-938. [PMID: 28468832 PMCID: PMC5817164 DOI: 10.1152/physrev.00038.2016] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
The burden of cardiovascular and metabolic diseases worldwide is staggering. The emergence of systems approaches in biology promises new therapies, faster and cheaper diagnostics, and personalized medicine. However, a profound understanding of pathogenic mechanisms at the cellular and molecular levels remains a fundamental requirement for discovery and therapeutics. Animal models of human disease are cornerstones of drug discovery as they allow identification of novel pharmacological targets by linking gene function with pathogenesis. The zebrafish model has been used for decades to study development and pathophysiology. More than ever, the specific strengths of the zebrafish model make it a prime partner in an age of discovery transformed by big-data approaches to genomics and disease. Zebrafish share a largely conserved physiology and anatomy with mammals. They allow a wide range of genetic manipulations, including the latest genome engineering approaches. They can be bred and studied with remarkable speed, enabling a range of large-scale phenotypic screens. Finally, zebrafish demonstrate an impressive regenerative capacity scientists hope to unlock in humans. Here, we provide a comprehensive guide on applications of zebrafish to investigate cardiovascular and metabolic diseases. We delineate advantages and limitations of zebrafish models of human disease and summarize their most significant contributions to understanding disease progression to date.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sven Reischauer
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Didier Y R Stainier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rima Arnaout
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
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Zhai S, Li G, Sun Y, Song J, Li J, Song G, Li Y, Ling H, He Z, Xia X. Genetic analysis of phytoene synthase 1 (Psy1) gene function and regulation in common wheat. BMC PLANT BIOLOGY 2016; 16:228. [PMID: 27769185 PMCID: PMC5073469 DOI: 10.1186/s12870-016-0916-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/06/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Phytoene synthase 1 (PSY1) is the most important regulatory enzyme in carotenoid biosynthesis, whereas its function is hardly known in common wheat. The aims of the present study were to investigate Psy1 function and genetic regulation using reverse genetics approaches. RESULTS Transcript levels of Psy1 in RNAi transgenic lines were decreased by 54-76 % and yellow pigment content (YPC) was reduced by 26-35 % compared with controls, confirming the impact of Psy1 on carotenoid accumulation. A series of candidate genes involved in secondary metabolic pathways and core metabolic processes responded to Psy1 down-regulation. The aspartate rich domain (DXXXD) was important for PSY1 function, and conserved nucleotides adjacent to the domain influenced YPC by regulating gene expression, enzyme activity or alternative splicing. Compensatory responses analysis indicated that three Psy1 homoeologs may be coordinately regulated under normal conditions, but separately regulated under stress. The period 14 days post anthesis (DPA) was found to be a key regulation node during grain development. CONCLUSION The findings define key aspects of flour color regulation in wheat and facilitate the genetic improvement of wheat quality targeting color/nutritional specifications required for specific end products.
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Affiliation(s)
- Shengnan Zhai
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Genying Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Youwei Sun
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jianmin Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Jihu Li
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Guoqi Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Yulian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye Bei Road, Jinan, Shandong 250100 China
| | - Hongqing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
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Ogino K, Hirata H. Defects of the Glycinergic Synapse in Zebrafish. Front Mol Neurosci 2016; 9:50. [PMID: 27445686 PMCID: PMC4925712 DOI: 10.3389/fnmol.2016.00050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/13/2016] [Indexed: 12/26/2022] Open
Abstract
Glycine mediates fast inhibitory synaptic transmission. Physiological importance of the glycinergic synapse is well established in the brainstem and the spinal cord. In humans, the loss of glycinergic function in the spinal cord and brainstem leads to hyperekplexia, which is characterized by an excess startle reflex to sudden acoustic or tactile stimulation. In addition, glycinergic synapses in this region are also involved in the regulation of respiration and locomotion, and in the nociceptive processing. The importance of the glycinergic synapse is conserved across vertebrate species. A teleost fish, the zebrafish, offers several advantages as a vertebrate model for research of glycinergic synapse. Mutagenesis screens in zebrafish have isolated two motor defective mutants that have pathogenic mutations in glycinergic synaptic transmission: bandoneon (beo) and shocked (sho). Beo mutants have a loss-of-function mutation of glycine receptor (GlyR) β-subunit b, alternatively, sho mutant is a glycinergic transporter 1 (GlyT1) defective mutant. These mutants are useful animal models for understanding of glycinergic synaptic transmission and for identification of novel therapeutic agents for human diseases arising from defect in glycinergic transmission, such as hyperekplexia or glycine encephalopathy. Recent advances in techniques for genome editing and for imaging and manipulating of a molecule or a physiological process make zebrafish more attractive model. In this review, we describe the glycinergic defective zebrafish mutants and the technical advances in both forward and reverse genetic approaches as well as in vivo visualization and manipulation approaches for the study of the glycinergic synapse in zebrafish.
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Affiliation(s)
- Kazutoyo Ogino
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University Sagamihara, Japan
| | - Hiromi Hirata
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University Sagamihara, Japan
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Shen Y, Pan G, Lübberstedt T. Haploid Strategies for Functional Validation of Plant Genes. Trends Biotechnol 2016; 33:611-620. [PMID: 26409779 DOI: 10.1016/j.tibtech.2015.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 01/11/2023]
Abstract
Increasing knowledge of plant genome sequences requires the development of more reliable and efficient genetic approaches for genotype-phenotype validation. Functional identification of plant genes is generally achieved by a combination of creating genetic modifications and observing the according phenotype, which begins with forward-genetic methods represented by random physical and chemical mutagenesis and move towards reverse-genetic tools as targeted genome editing. A major bottleneck is time need to produce modified homozygous genotypes that can actually be used for phenotypic validation. Herein, we comprehensively address and compare available experimental approaches for functional validation of plant genes, and propose haploid strategies to reduce the time needed and cost consumed for establishing gene function.
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Affiliation(s)
- Yaou Shen
- Maize Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China; Department of Agronomy, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA.
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, 211 Huimin Road, Wenjiang District, Chengdu, 611130, China
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University, 100 Osborn Drive, Ames, IA 50011, USA.
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Zhao S, Huang J, Ye J. A fresh look at zebrafish from the perspective of cancer research. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:80. [PMID: 26260237 PMCID: PMC4531851 DOI: 10.1186/s13046-015-0196-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 07/28/2015] [Indexed: 12/31/2022]
Abstract
Zebrafish represent a vertebrate model organism that has been widely, and increasingly, employed over the last decade in the study of developmental processes, wound healing, microbe-host interactions, and drug screening. With the increase in the laboratory use of zebrafish, several advantages, such as a high genetic homology to humans and transparent embryos, which allow clear disease evaluation, have greatly widened its use as a model for studying tumor development in vivo. The use of zebrafish has been applied in several areas of cancer research, mainly in the following domains: (1) establishing cancer models by carcinogenic chemical, genetic technology, and xenotransplantation; (2) evaluating tumor angiogenesis; (3) studying tumor metastasis; and (4) anti-tumor drug screening and drug toxicity evaluation. In this study, we provide a comprehensive overview of the role of zebrafish in order to underline the advantages of using them as a model organism in cancer research. Several related successful events are also reviewed.
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Affiliation(s)
- Shuai Zhao
- Department of Surgical oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jian Huang
- Department of Surgical oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
| | - Jun Ye
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China.
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Cheng J, Salentijn EMJ, Huang B, Denneboom C, Qi W, Dechesne AC, Krens FA, Visser RGF, van Loo EN. Detection of induced mutations in CaFAD2 genes by next-generation sequencing leading to the production of improved oil composition in Crambe abyssinica. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:471-81. [PMID: 25393152 DOI: 10.1111/pbi.12269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 08/10/2014] [Accepted: 08/20/2014] [Indexed: 05/09/2023]
Abstract
Crambe abyssinica is a hexaploid oil crop for industrial applications. An increase of erucic acid (C22:1) and reduction of polyunsaturated fatty acid (PUFA) contents in crambe oil is a valuable improvement. An increase in oleic acid (C18:1), a reduction in PUFA and possibly an increase in C22:1 can be obtained by down-regulating the expression of fatty acid desaturase2 genes (CaFAD2), which code for the enzyme that converts C18:1 into C18:2. We conducted EMS-mutagenesis in crambe, followed by Illumina sequencing, to screen mutations in three expressed CaFAD2 genes. Two novel analysis strategies were used to detect mutation sites. In the first strategy, mutation detection targeted specific sequence motifs. In the second strategy, every nucleotide position in a CaFAD2 fragment was tested for the presence of mutations. Seventeen novel mutations were detected in 1100 one-dimensional pools (11 000 individuals) in three expressed CaFAD2 genes, including non-sense mutations and mis-sense mutations in CaFAD2-C1, -C2 and -C3. The homozygous non-sense mutants for CaFAD2-C3 resulted in a 25% higher content of C18:1 and 25% lower content of PUFA compared to the wild type. The mis-sense mutations only led to small changes in oil composition. Concluding, targeted mutation detection using NGS in a polyploid was successfully applied and it was found that a non-sense mutation in even a single CaFAD2 gene can lead to changes in crambe oil composition. Stacking the mutations in different CaFAD2 may gain additional changes in C18:1 and PUFA contents.
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Affiliation(s)
- Jihua Cheng
- Wageningen UR Plant Breeding, Wageningen, The Netherlands; College of Life Science, Hubei University, Hubei, China
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15
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Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB. Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis. BMC Genomics 2015; 16:83. [PMID: 25886285 PMCID: PMC4457992 DOI: 10.1186/s12864-015-1263-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive. RESULTS Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified. CONCLUSIONS Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.
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Affiliation(s)
- Luyuan Pan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA. .,Current Address: China Zebrafish Resource Center, Institute of Hydrobiology CAS, 430072, Wuhan, China.
| | - Arish N Shah
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA.
| | - Ian G Phelps
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA. .,Biology Department, University of Washington, Seattle, WA, USA.
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17
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18
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Wager K, Mahmood F, Russell C. Modelling inborn errors of metabolism in zebrafish. J Inherit Metab Dis 2014; 37:483-95. [PMID: 24797558 DOI: 10.1007/s10545-014-9696-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/13/2014] [Accepted: 02/17/2014] [Indexed: 12/22/2022]
Abstract
The majority of human inborn errors of metabolism are fatal multisystem disorders that lack proper treatment and have a poorly understood mechanistic basis. Novel technologies are required to address this issue, and the use of zebrafish to model these diseases is an emerging field. Here we present the published zebrafish models of inborn metabolic diseases, discuss their validity, and review the novel mechanistic insights that they have provided. We also review the available methods for creating and studying zebrafish disease models, advantages and disadvantages of using this model organism, and successful examples of the use of zebrafish for drug discovery and development. Using a zebrafish to model inborn errors of metabolism in vivo, although still in its infancy, shows promise for a deeper understanding of disease pathomechanisms, onset, and progression, and also for the development of specific therapies.
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Affiliation(s)
- Kim Wager
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
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19
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Poloni A, Schirawski J. Red card for pathogens: phytoalexins in sorghum and maize. Molecules 2014; 19:9114-33. [PMID: 24983861 PMCID: PMC6271655 DOI: 10.3390/molecules19079114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/26/2014] [Accepted: 06/26/2014] [Indexed: 12/11/2022] Open
Abstract
Cereal crop plants such as maize and sorghum are constantly being attacked by a great variety of pathogens that cause large economic losses. Plants protect themselves against pathogens by synthesizing antimicrobial compounds, which include phytoalexins. In this review we summarize the current knowledge on phytoalexins produced by sorghum (luteolinidin, apigeninidin) and maize (zealexin, kauralexin, DIMBOA and HDMBOA). For these molecules, we highlight biosynthetic pathways, known intermediates, proposed enzymes, and mechanisms of elicitation. Finally, we discuss the involvement of phytoalexins in plant resistance and their possible application in technology, medicine and agriculture. For those whose world is round we tried to set the scene in the context of a hypothetical football game in which pathogens fight with phytoalexins on the different playing fields provided by maize and sorghum.
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Affiliation(s)
- Alana Poloni
- Department of Microbial Genetics, Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany.
| | - Jan Schirawski
- Department of Microbial Genetics, Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany.
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Chen L, Hao L, Parry MAJ, Phillips AL, Hu YG. Progress in TILLING as a tool for functional genomics and improvement of crops. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:425-43. [PMID: 24618006 DOI: 10.1111/jipb.12192] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/11/2014] [Indexed: 05/18/2023]
Abstract
Food security is a global concern and substantial yield increases in crops are required to feed the growing world population. Mutagenesis is an important tool in crop improvement and is free of the regulatory restrictions imposed on genetically modified organisms. Targeting Induced Local Lesions in Genomes (TILLING), which combines traditional chemical mutagenesis with high-throughput genome-wide screening for point mutations in desired genes, offers a powerful way to create novel mutant alleles for both functional genomics and improvement of crops. TILLING is generally applicable to genomes whether small or large, diploid or even allohexaploid, and shows great potential to address the major challenge of linking sequence information to the function of genes and to modulate key traits for plant breeding. TILLING has been successfully applied in many crop species and recent progress in TILLING is summarized below, especially on the developments in mutation detection technology, application of TILLING in gene functional studies and crop breeding. The potential of TILLING/EcoTILLING for functional genetics and crop improvement is also discussed. Furthermore, a small-scale forward strategy including backcross and selfing was conducted to release the potential mutant phenotypes masked in M2 (or M3) plants.
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Affiliation(s)
- Liang Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
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21
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Love DR, Lan CC, Dodd A, Shelling AN, McNabb WC, Ferguson LR. Modeling inflammatory bowel disease: the zebrafish as a way forward. Expert Rev Mol Diagn 2014; 7:177-93. [PMID: 17331065 DOI: 10.1586/14737159.7.2.177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The zebrafish has proved to be an informative model of vertebrate development and, more recently, an emerging model of human disease. The realization of the full potential of the zebrafish as a disease model lies in two interdependent areas. The first is an appreciation that the often overlooked strength of this species lies in allowing the design of experiments that address the interplay of genetics and the environment in a manipulable manner. The second is in the application and further development of gene targeting approaches. These twin features will be addressed in this review in the context of modeling inflammatory bowel disease.
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Affiliation(s)
- Donald R Love
- University of Auckland, School of Biological Sciences, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand.
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Wells R, Trick M, Soumpourou E, Clissold L, Morgan C, Werner P, Gibbard C, Clarke M, Jennaway R, Bancroft I. The control of seed oil polyunsaturate content in the polyploid crop species Brassica napus. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:349-362. [PMID: 24489479 PMCID: PMC3901927 DOI: 10.1007/s11032-013-9954-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/05/2013] [Indexed: 05/18/2023]
Abstract
Many important plant species have polyploidy in their recent ancestry, complicating inferences about the genetic basis of trait variation. Although the principal locus controlling the proportion of polyunsaturated fatty acids (PUFAs) in seeds of Arabidopsis thaliana is known (fatty acid desaturase 2; FAD2), commercial cultivars of a related crop, oilseed rape (Brassica napus), with very low PUFA content have yet to be developed. We showed that a cultivar of oilseed rape with lower than usual PUFA content has non-functional alleles at three of the four orthologous FAD2 loci. To explore the genetic basis further, we developed an ethyl methanesulphonate mutagenised population, JBnaCAB_E, and used it to identify lines that also carried mutations in the remaining functional copy. This confirmed the hypothesised basis of variation, resulting in an allelic series of mutant lines showing a spectrum of PUFA contents of seed oil. Several lines had PUFA content of ~6 % and oleic acid content of ~84 %, achieving a long-standing industry objective: very high oleic, very low PUFA rapeseed without the use of genetic modification technology. The population contains a high rate of mutations and represents an important resource for research in B. napus.
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Affiliation(s)
- Rachel Wells
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Leah Clissold
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Colin Morgan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Peter Werner
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | - Carl Gibbard
- KWS UK Ltd., 56 Church Street, Thriplow, Hertfordshire, SG8 7RE UK
| | | | - Richard Jennaway
- Saaten-Union UK Ltd., Rosalie Field Station, Bradley Road, Cowlinge, Newmarket, Suffolk, CB8 9HU UK
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Department of Biology, University of York, Heslington, York, YO41 5DD UK
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Wells R, Trick M, Fraser F, Soumpourou E, Clissold L, Morgan C, Pauquet J, Bancroft I. Sequencing-based variant detection in the polyploid crop oilseed rape. BMC PLANT BIOLOGY 2013; 13:111. [PMID: 23915099 PMCID: PMC3750413 DOI: 10.1186/1471-2229-13-111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 07/23/2013] [Indexed: 05/24/2023]
Abstract
BACKGROUND The detection and exploitation of genetic variation underpins crop improvement. However, the polyploid nature of the genomes of many of our most important crops represents a barrier, particularly for the analysis of variation within genes. To overcome this, we aimed to develop methodologies based on amplicon sequencing that involve the incorporation of barcoded amplification tags (BATs) into PCR products. RESULTS A protocol was developed to tag PCR products with 5' 6-base oligonucleotide barcode extensions before pooling for sequencing library production using standard Illumina adapters. A computational method was developed for the de-convolution of products and the robust detection and scoring of sequence variants. Using this methodology, amplicons targeted to gene sequences were screened across a B. napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome. Furthermore, using one-dimensional 8-fold pooling, 4608 lines of a B. napus mutation population were screened for induced mutations in a locus-specific amplicon (an orthologue of GL2.b) and mixed product of three co-amplified loci (orthologues of FAD2), identifying 10 and 41 mutants respectively. CONCLUSIONS The utilisation of barcode tags to de-convolute pooled PCR products in multiplexed, variation screening via Illumina sequencing provides a cost effective method for SNP genotyping and mutation detection and, potentially, markers for causative changes, even in polyploid species. Combining this approach with existing Illumina multiplexing workflows allows the analysis of thousands of lines cheaply and efficiently in a single sequencing run with minimal library production costs.
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Affiliation(s)
- Rachel Wells
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Trick
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Fiona Fraser
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Leah Clissold
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Colin Morgan
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jérôme Pauquet
- BIOGEMMA S.A.S., Chemin de Panedautes, Domaine de Sandreau, 31700, Mondonville, France
| | - Ian Bancroft
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Present address: Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
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Bastidas RJ, Elwell CA, Engel JN, Valdivia RH. Chlamydial intracellular survival strategies. Cold Spring Harb Perspect Med 2013; 3:a010256. [PMID: 23637308 DOI: 10.1101/cshperspect.a010256] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen and the causative agent of blinding trachoma. Although Chlamydia is protected from humoral immune responses by residing within remodeled intracellular vacuoles, it still must contend with multilayered intracellular innate immune defenses deployed by its host while scavenging for nutrients. Here we provide an overview of Chlamydia biology and highlight recent findings detailing how this vacuole-bound pathogen manipulates host-cellular functions to invade host cells and maintain a replicative niche.
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Affiliation(s)
- Robert J Bastidas
- Department of Molecular Genetics and Microbiology, Center for Microbial Pathogenesis, Duke University Medical Center, Durham, NC 27710, USA
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25
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Kettleborough RNW, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E, Stemple DL. A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature 2013; 496:494-7. [PMID: 23594742 PMCID: PMC3743023 DOI: 10.1038/nature11992] [Citation(s) in RCA: 447] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 02/07/2013] [Indexed: 01/11/2023]
Abstract
Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in model vertebrate organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes, this number falls considerably short of the more than 22,000 mouse protein-coding genes. Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning, insertional mutagenesis, antisense morpholino oligonucleotides, targeted re-sequencing, and zinc finger and TAL endonucleases have made substantial contributions to our understanding of the biological activity of vertebrate genes, but again the number of genes studied falls well short of the more than 26,000 zebrafish protein-coding genes. Importantly, for both mice and zebrafish, none of these strategies are particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Here we describe an active project that aims to identify and phenotype the disruptive mutations in every zebrafish protein-coding gene, using a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis. So far we have identified potentially disruptive mutations in more than 38% of all known zebrafish protein-coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1,000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.
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Affiliation(s)
- Ross N W Kettleborough
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING. PLoS One 2012. [PMID: 23185237 PMCID: PMC3504036 DOI: 10.1371/journal.pone.0047284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Information on polymorphic DNA in organelle genomes is essential for evolutionary and ecological studies. However, it is challenging to perform high-throughput investigations of chloroplast and mitochondrial DNA polymorphisms. In recent years, EcoTILLING stands out as one of the most universal, low-cost, and high-throughput reverse genetic methods, and the identification of natural genetic variants can provide much information about gene function, association mapping and linkage disequilibrium analysis and species evolution. Until now, no report exists on whether this method is applicable to organelle genomes and to what extent it can be used. Methodology/Principal Findings To address this problem, we adapted the CEL I-based heteroduplex cleavage strategy used in Targeting Induced Local Lesions in Genomes (TILLING) for the discovery of nucleotide polymorphisms in organelle genomes. To assess the applicability and accuracy of this technology, designated ORG-EcoTILLING, at different taxonomic levels, we sampled two sets of taxa representing accessions from the Brassicaceae with three chloroplast genes (accD, matK and rbcL) and one mitochondrial gene (atp6). The method successfully detected nine, six and one mutation sites in the accD, matK and rbcL genes, respectively, in 96 Brassica accessions. These mutations were confirmed by DNA sequencing, with 100% accuracy at both inter- and intraspecific levels. We also detected 44 putative mutations in accD in 91 accessions from 45 species and 29 genera of seven tribes. Compared with DNA sequencing results, the false negative rate was 36%. However, 17 SNPs detected in atp6 were completely identical to the sequencing results. Conclusions/Significance These results suggest that ORG-EcoTILLING is a powerful and cost-effective alternative method for high-throughput genome-wide assessment of inter- and intraspecific chloroplast and mitochondrial DNA polymorphisms. It will play an important role in evolutionary and ecological biology studies, in identification of related genes associated with agronomic importance such as high yield and improved cytoplasmic quality, and for identifying mitochondrial point mutations responsible for diseases in humans and other animals.
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Abstract
Zebrafish have been widely used as a model system for studying developmental processes, but in the last decade, they have also emerged as a valuable system for modeling human disease. The development and function of zebrafish organs are strikingly similar to those of humans, and the ease of creating mutant or transgenic fish has facilitated the generation of disease models. Here, we highlight the use of zebrafish for defining disease pathways and for discovering new therapies.
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Affiliation(s)
- Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
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28
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Gruszka D, Marzec M, Szarejko I. The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair. BMC PLANT BIOLOGY 2012; 12:88. [PMID: 22697361 PMCID: PMC3410793 DOI: 10.1186/1471-2229-12-88] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/14/2012] [Indexed: 05/29/2023]
Abstract
BACKGROUND The high level of conservation of genes that regulate DNA replication and repair indicates that they may serve as a source of information on the origin and evolution of the species and makes them a reliable system for the identification of cross-species homologs. Studies that had been conducted to date shed light on the processes of DNA replication and repair in bacteria, yeast and mammals. However, there is still much to be learned about the process of DNA damage repair in plants. DESCRIPTION These studies, which were conducted mainly using bioinformatics tools, enabled the list of genes that participate in various pathways of DNA repair in Arabidopsis thaliana (L.) Heynh to be outlined; however, information regarding these mechanisms in crop plants is still very limited. A similar, functional approach is particularly difficult for a species whose complete genomic sequences are still unavailable. One of the solutions is to apply ESTs (Expressed Sequence Tags) as the basis for gene identification. For the construction of the barley EST DNA Replication and Repair Database (bEST-DRRD), presented here, the Arabidopsis nucleotide and protein sequences involved in DNA replication and repair were used to browse for and retrieve the deposited sequences, derived from four barley (Hordeum vulgare L.) sequence databases, including the "Barley Genome version 0.05" database (encompassing ca. 90% of barley coding sequences) and from two databases covering the complete genomes of two monocot models: Oryza sativa L. and Brachypodium distachyon L. in order to identify homologous genes. Sequences of the categorised Arabidopsis queries are used for browsing the repositories, which are located on the ViroBLAST platform. The bEST-DRRD is currently used in our project during the identification and validation of the barley genes involved in DNA repair. CONCLUSIONS The presented database provides information about the Arabidopsis genes involved in DNA replication and repair, their expression patterns and models of protein interactions. It was designed and established to provide an open-access tool for the identification of monocot homologs of known Arabidopsis genes that are responsible for DNA-related processes. The barley genes identified in the project are currently being analysed to validate their function.
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Affiliation(s)
- Damian Gruszka
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, Jagiellonska 28, 40-032, Katowice, Poland
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29
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Lin YY. Muscle diseases in the zebrafish. Neuromuscul Disord 2012; 22:673-84. [PMID: 22647769 DOI: 10.1016/j.nmd.2012.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 04/09/2012] [Accepted: 04/23/2012] [Indexed: 10/28/2022]
Abstract
Animal models in biomedical research are important for understanding the pathological mechanisms of human diseases at a molecular and cellular level. Several aspects of mammalian animals, however, may limit their use in modelling neuromuscular disorders. Many attributes of zebrafish (Danio rerio) are complementary to mammalian experimental systems, establishing the zebrafish as a powerful model organism in disease biology. This review focuses on a number of key studies using the zebrafish to model hereditary muscle diseases with additional emphasis on recent advances in zebrafish functional genomics and drug discovery. Increasing research in zebrafish disease models, combined with knowledge from mammalian models, will bring novel insights into the disease pathogenesis of neuromuscular disorders, as well as facilitate the development of effective therapeutic strategies.
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Affiliation(s)
- Yung-Yao Lin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom.
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30
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Harrison RJ. Understanding genetic variation and function- the applications of next generation sequencing. Semin Cell Dev Biol 2012; 23:230-6. [DOI: 10.1016/j.semcdb.2012.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/31/2022]
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Pearl EJ, Grainger RM, Guille M, Horb ME. Development of Xenopus resource centers: the National Xenopus Resource and the European Xenopus Resource Center. Genesis 2012; 50:155-63. [PMID: 22253050 PMCID: PMC3778656 DOI: 10.1002/dvg.22013] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/09/2012] [Indexed: 12/25/2022]
Abstract
Xenopus is an essential vertebrate model system for biomedical research that has contributed to important discoveries in many disciplines, including cell biology, molecular biology, physiology, developmental biology, and neurobiology. However, unlike other model systems no central repository/stock center for Xenopus had been established until recently. Similar to mouse, zebrafish, and fly communities, which have established stock centers, Xenopus researchers need to maintain and distribute rapidly growing numbers of inbred, mutant, and transgenic frog strains, along with DNA and protein resources, and individual laboratories struggle to accomplish this efficiently. In the last 5 years, two resource centers were founded to address this need: the European Xenopus Resource Center (EXRC) at the University of Portsmouth in England, and the National Xenopus Resource (NXR) at the Marine Biological Laboratory in Woods Hole, MA. These two centers work together to provide resources and support to the Xenopus research community. The EXRC and NXR serve as stock centers and acquire, produce, maintain and distribute mutant, inbred and transgenic Xenopus laevis and Xenopus tropicalis lines. Independently, the EXRC is a repository for Xenopus cDNAs, fosmids, and antibodies; it also provides oocytes and wild-type frogs within the United Kingdom. The NXR will complement these services by providing research training and promoting intellectual interchange through hosting mini-courses and workshops and offering space for researchers to perform short-term projects at the Marine Biological Laboratory. Together the EXRC and NXR will enable researchers to improve productivity by providing resources and expertise to all levels, from graduate students to experienced PIs. These two centers will also enable investigators that use other animal systems to take advantage of Xenopus' unique experimental features to complement their studies.
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Affiliation(s)
- Esther J. Pearl
- National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
| | - Robert M. Grainger
- University of Virginia Department of Biology, Gilmer Hall, University of Virginia, Charlottesville, VA 22904, USA
| | - Matthew Guille
- European Xenopus Resource Center, St Michael’s Building, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Marko E. Horb
- National Xenopus Resource, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA 02543, USA
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI USA
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA USA
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Abstract
Xenopus tropicalis was introduced as a model system for genetic, and then genomic research, in the early 1990s, complementing work on the widely used model organism Xenopus laevis. Its shorter generation time and diploid genome has facilitated a number of experimental approaches. It has permitted multigenerational experiments (e.g., preparation of transgenic lines and generation of mutant lines) that have added powerful approaches for research by the Xenopus community. As a diploid animal, its simpler genome was sequenced before X. laevis, and has provided a highly valuable resource indispensable for all Xenopus researchers. As more sophisticated transgenic technologies for manipulating gene expression are developed, and mutations, particularly null mutations, are identified in widely studied genes involved in critical cellular and developmental processes, researchers will increasingly turn to X. tropicalis for definitive analysis of complex genetic pathways. This chapter describes the historical and conceptual development of X. tropicalis as a genetic and genomic model system for higher vertebrate development.
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Affiliation(s)
- Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
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Harland RM, Grainger RM. Xenopus research: metamorphosed by genetics and genomics. Trends Genet 2011; 27:507-15. [PMID: 21963197 PMCID: PMC3601910 DOI: 10.1016/j.tig.2011.08.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/25/2011] [Accepted: 08/25/2011] [Indexed: 01/18/2023]
Abstract
Research using Xenopus takes advantage of large, abundant eggs and readily manipulated embryos in addition to conserved cellular, developmental and genomic organization with mammals. Research on Xenopus has defined key principles of gene regulation and signal transduction, embryonic induction, morphogenesis and patterning as well as cell cycle regulation. Genomic and genetic advances in this system, including the development of Xenopus tropicalis as a genetically tractable complement to the widely used Xenopus laevis, capitalize on the classical strengths and wealth of achievements. These attributes provide the tools to tackle the complex biological problems of the new century, including cellular reprogramming, organogenesis, regeneration, gene regulatory networks and protein interactions controlling growth and development, all of which provide insights into a multitude of human diseases and their potential treatments.
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Affiliation(s)
- Richard M Harland
- Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California Berkeley, CA 94720, USA
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Abstract
Zebrafish studies in the past two decades have made major contributions to our understanding of hematopoiesis and its associated disorders. The zebrafish has proven to be a powerful organism for studies in this area owing to its amenability to large-scale genetic and chemical screening. In addition, the externally fertilized and transparent embryos allow convenient genetic manipulation and in vivo imaging of normal and aberrant hematopoiesis. This review discusses available methods for studying hematopoiesis in zebrafish, summarizes key recent advances in this area, and highlights the current and potential contributions of zebrafish to the discovery and development of drugs to treat human blood disorders.
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Affiliation(s)
- Lili Jing
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
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Abstract
A central goal of modern neuroscience is to obtain a mechanistic understanding of higher brain functions under healthy and diseased conditions. Addressing this challenge requires rigorous experimental and theoretical analysis of neuronal circuits. Recent advances in optogenetics, high-resolution in vivo imaging, and reconstructions of synaptic wiring diagrams have created new opportunities to achieve this goal. To fully harness these methods, model organisms should allow for a combination of genetic and neurophysiological approaches in vivo. Moreover, the brain should be small in terms of neuron numbers and physical size. A promising vertebrate organism is the zebrafish because it is small, it is transparent at larval stages and it offers a wide range of genetic tools and advantages for neurophysiological approaches. Recent studies have highlighted the potential of zebrafish for exhaustive measurements of neuronal activity patterns, for manipulations of defined cell types in vivo and for studies of causal relationships between circuit function and behavior. In this article, we summarize background information on the zebrafish as a model in modern systems neuroscience and discuss recent results.
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Affiliation(s)
- Rainer W Friedrich
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstr. 66, CH-4058 Basel, Switzerland.
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Agrawal GK, Bourguignon J, Rolland N, Ephritikhine G, Ferro M, Jaquinod M, Alexiou KG, Chardot T, Chakraborty N, Jolivet P, Doonan JH, Rakwal R. Plant organelle proteomics: collaborating for optimal cell function. MASS SPECTROMETRY REVIEWS 2011; 30:772-853. [PMID: 21038434 DOI: 10.1002/mas.20301] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/10/2023]
Abstract
Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), P.O. Box 13265, Sanepa, Kathmandu, Nepal.
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Barkley NA, Wang ML. Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals. Curr Genomics 2011; 9:212-26. [PMID: 19452039 PMCID: PMC2682938 DOI: 10.2174/138920208784533656] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 04/24/2008] [Accepted: 04/28/2008] [Indexed: 11/22/2022] Open
Abstract
With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed.
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Affiliation(s)
- N A Barkley
- USDA-ARS, Plant Genetic Resources Conservation Unit (PGRCU), 1109 Experiment Street, Griffin, GA 30223, USA
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Brownfield L, Köhler C. Unreduced gamete formation in plants: mechanisms and prospects. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1659-68. [PMID: 21109579 DOI: 10.1093/jxb/erq371] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyploids, organisms with more than two sets of chromosomes, are widespread in flowering plants, including many important crop species. Increases in ploidy level are believed to arise commonly through the production of gametes that have not had their ploidy level reduced during meiosis. Although there have been cytological descriptions of unreduced gamete formation in a number of plants, until recently none of the underlying genes or molecular mechanisms involved in unreduced gamete production have been described. The recent discovery of several genes in which mutations give rise to a high frequency of unreduced gametes in the model plant Arabidopsis thaliana opens the door to the elucidation of this important event and its manipulation in crop species. Here this recent progress is reviewed and the identified genes and the mechanism by which the loss of protein function leads to the formation of unreduced gametes are discussed. The potential to use the knowledge gained from Arabidopsis mutants to design tools and develop techniques to engineer unreduced gamete production in important crop species for use in plant breeding is also discussed.
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Affiliation(s)
- Lynette Brownfield
- Department of Biology and Zurich-Basel Plant Science Center, Swiss Federal Institute of Technology, ETH Centre, Zurich, Switzerland
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Lin YY, White RJ, Torelli S, Cirak S, Muntoni F, Stemple DL. Zebrafish Fukutin family proteins link the unfolded protein response with dystroglycanopathies. Hum Mol Genet 2011; 20:1763-75. [PMID: 21317159 PMCID: PMC3071672 DOI: 10.1093/hmg/ddr059] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Allelic mutations in putative glycosyltransferase genes, fukutin and fukutin-related protein (fkrp), lead to a wide range of muscular dystrophies associated with hypoglycosylation of α-dystroglycan, commonly referred to as dystroglycanopathies. Defective glycosylation affecting dystroglycan–ligand interactions is considered to underlie the disease pathogenesis. We have modelled dystroglycanopathies in zebrafish using a novel loss-of-function dystroglycan allele and by inhibition of Fukutin family protein activities. We show that muscle pathology in embryos lacking Fukutin or FKRP is different from loss of dystroglycan. In addition to hypoglycosylated α-dystroglycan, knockdown of Fukutin or FKRP leads to a notochord defect and a perturbation of laminin expression before muscle degeneration. These are a consequence of endoplasmic reticulum stress and activation of the unfolded protein response (UPR), preceding loss of dystroglycan–ligand interactions. Together, our results suggest that Fukutin family proteins may play important roles in protein secretion and that the UPR may contribute to the phenotypic spectrum of some dystroglycanopathies in humans.
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Affiliation(s)
- Yung-Yao Lin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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41
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Abstract
Myelin is a vertebrate adaptation that allows for the rapid propagation of action potentials along axons. Specialized glial cells-oligodendrocytes in the central nervous system (CNS) and Schwann cells in the peripheral nervous system (PNS)-form myelin by repeatedly wrapping axon segments. Debilitating diseases result from the disruption of myelin, including multiple sclerosis and Charcot-Marie-Tooth peripheral neuropathies. The process of myelination involves extensive communication between glial cells and the associated neurons. The past few years have seen important progress in understanding the molecular basis of the signals that coordinate the development of these fascinating cells. This review highlights recent advances in myelination deriving from studies in the zebrafish model system, with a primary focus on the PNS. While Neuregulin1-ErbB signaling has long been known to play important roles in peripheral myelin development, work in zebrafish has elucidated its roles in Schwann cell migration and radial sorting of axons in vivo. Forward genetic screens in zebrafish have also uncovered new genes required for development of myelinated axons, including gpr126, which encodes a G-protein coupled receptor required for Schwann cells to progress beyond the promyelinating stage. In addition, work in zebrafish uncovered new roles for Schwann cells themselves, including in regulating the boundary between the PNS and CNS and positioning a nerve after its initial outgrowth.
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42
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Winkler S, Gscheidel N, Brand M. Mutant generation in vertebrate model organisms by TILLING. Methods Mol Biol 2011; 770:475-504. [PMID: 21805277 DOI: 10.1007/978-1-61779-210-6_19] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
TILLING (Targeting Induced Local Lesions IN Genomes) is a popular reverse genetic approach that has been successfully applied in several genetic model organisms such as zebrafish, rat, Drosophila, Arabidopsis, or medaka. In contrast to classical targeted knockout technologies that work in mice by directly targeting a gene of interest, TILLING follows an indirect strategy. The first step of the TILLING pipeline is the generation of a TILLING library that consists of large numbers of mutagenized individuals. In a second step, these individuals are screened for mutations in any gene of interest. Screening is performed by PCR amplification of specific exons from each individual of a library followed by mutation detection. This could be done, for example, by direct re-sequencing of PCR fragments or alternatively, by CEL1 endonuclease-mediated mutation discovery. Individuals carrying potentially deleterious point mutations are isolated from the library and mutant lines are established. TILLING allows the identification of a whole range of point mutations, covering nonsense, splice site, and missense mutations in only one screening round, because the generation of mutations by mutagenesis as well as the screening tools is not biased. Potential knockout mutations are initially the mutations of choice, but TILLING screens can also be used to isolate allelic series of point mutations ranging from complete null phenotypes to hypomorphic or even dominant-negative or conditional alleles. These allelic series can be helpful for a comprehensive functional analysis of a gene of interest. TILLING is applicable to any kind of genetically tractable model organism, as long as this model organism is amenable to chemical mutagenesis, and genomic sequence information for a gene of interest is available. This chapter describes the design and pipeline of a TILLING facility as we are currently operating it for zebrafish in Dresden. Protocols for mutation detection by direct re-sequencing are described in detail. However, alternatives to this pipeline do exist and will be mentioned briefly.
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Affiliation(s)
- Sylke Winkler
- Dresden TILLING Project, c/o MPI CBG, Dresden, Germany.
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43
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Abstract
Since the initial publication of this chapter in 2004, additional methodologies have been developed which could improve and/or complement the original retroviral-mediated insertional mutagenesis. Retroviral vectors have also been shown to be useful for goals other than mutagenesis. In addition, retroviral-mediated insertional mutagenesis has been applied to zebrafish for use in reverse genetics as well as forward screening. Finally, the insertional mutant collection described herein has been screened by a number of labs to find a host of mutants (with genes already identified) with developmental and/or growth defects affecting the eye, liver, skin, craniofacial skeleton, kidney, myeloid cells, hematopoietic stem cells, and axon pathfinding, as well as mutants with defects in the cell cycle or DNA damage response, altered aging properties, and modulated cardiac repolarization. The major complementary approaches and new uses of this technique include:
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Affiliation(s)
- Adam Amsterdam
- Koch Institute for Integrative Cancer Research, Massachusetts Institute for Technology, Cambridge, Massachusetts, USA
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Abstract
Lens regeneration among vertebrates is basically restricted to some amphibians. The most notable cases are the ones that occur in premetamorphic frogs and in adult newts. Frogs and newts regenerate their lens in very different ways. In frogs the lens is regenerated by transdifferentiation of the cornea and is limited only to a time before metamorphosis. On the other hand, regeneration in newts is mediated by transdifferentiation of the pigment epithelial cells of the dorsal iris and is possible in adult animals as well. Thus, the study of both systems could provide important information about the process. Molecular tools have been developed in frogs and recently also in newts. Thus, the process has been studied at the molecular and cellular levels. A synthesis describing both systems was long due. In this review we describe the process in both Xenopus and the newt. The known molecular mechanisms are described and compared.
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Affiliation(s)
- Jonathan J Henry
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA.
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Nijman IJ, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E. Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nat Methods 2010; 7:913-5. [PMID: 20953175 DOI: 10.1038/nmeth.1516] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 09/06/2010] [Indexed: 11/09/2022]
Abstract
Targeted genomic enrichment followed by next-generation DNA sequencing has dramatically increased efficiency of mutation-discovery efforts. We describe a protocol for genomic enrichment of pooled barcoded samples in a single assay that increases experimental flexibility and efficiency. We screened 770 genes (1.4 megabases) in thirty N-ethyl-N-nitrosourea (ENU)-mutagenized rats and identified known variants at >96% sensitivity as well as new mutations at a false positive rate < 1 in 8 megabases.
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Affiliation(s)
- Isaäc J Nijman
- Hubrecht Institute, Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences and the University Medical Center Utrecht, Utrecht, The Netherlands
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Fett ME, Pilsl A, Paquet D, van Bebber F, Haass C, Tatzelt J, Schmid B, Winklhofer KF. Parkin is protective against proteotoxic stress in a transgenic zebrafish model. PLoS One 2010; 5:e11783. [PMID: 20689587 PMCID: PMC2912770 DOI: 10.1371/journal.pone.0011783] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 07/01/2010] [Indexed: 02/05/2023] Open
Abstract
Background Mutations in the gene encoding the E3 ubiquitin ligase parkin (PARK2) are responsible for the majority of autosomal recessive parkinsonism. Similarly to other knockout mouse models of PD-associated genes, parkin knockout mice do not show a substantial neuropathological or behavioral phenotype, while loss of parkin in Drosophila melanogaster leads to a severe phenotype, including reduced lifespan, apoptotic flight muscle degeneration and male sterility. In order to study the function of parkin in more detail and to address possible differences in its role in different species, we chose Danio rerio as a different vertebrate model system. Methodology/Principal Findings We first cloned zebrafish parkin to compare its biochemical and functional aspects with that of human parkin. By using an antisense knockdown strategy we generated a zebrafish model of parkin deficiency (knockdown efficiency between 50% and 60%) and found that the transient knockdown of parkin does not cause morphological or behavioral alterations. Specifically, we did not observe a loss of dopaminergic neurons in parkin-deficient zebrafish. In addition, we established transgenic zebrafish lines stably expressing parkin by using a Gal4/UAS-based bidirectional expression system. While parkin-deficient zebrafish are more vulnerable to proteotoxicity, increased parkin expression protected transgenic zebrafish from cell death induced by proteotoxic stress. Conclusions/Significance Similarly to human parkin, zebrafish parkin is a stress-responsive protein which protects cells from stress-induced cell death. Our transgenic zebrafish model is a novel tool to characterize the protective capacity of parkin in vivo.
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Affiliation(s)
- Mareike E. Fett
- Neurobiochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Anna Pilsl
- Neurobiochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Dominik Paquet
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Frauke van Bebber
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Jörg Tatzelt
- Neurobiochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Bettina Schmid
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
| | - Konstanze F. Winklhofer
- Neurobiochemistry, Adolf-Butenandt-Institute, Ludwig Maximilians University, Munich, Germany
- * E-mail:
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47
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Leebens-Mack J, Soltis DE, Soltis PS. Plant reproductive genomics at the Plant and Animal Genome Conference. Comp Funct Genomics 2010; 6:159-69. [PMID: 18629227 PMCID: PMC2447523 DOI: 10.1002/cfg.469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 02/08/2005] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jim Leebens-Mack
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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48
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Genetic zebrafish models of neurodegenerative diseases. Neurobiol Dis 2010; 40:58-65. [PMID: 20493258 DOI: 10.1016/j.nbd.2010.05.017] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 05/05/2010] [Accepted: 05/11/2010] [Indexed: 11/23/2022] Open
Abstract
As a consequence of the widespread use of zebrafish in developmental biology studies, an extensive array of experimental tools and techniques has been assembled; it has recently become apparent that these might be exploited in the analysis of human neurodegenerative diseases. A surprising degree of functional conservation has been demonstrated between human genes implicated in neurodegenerative diseases and their zebrafish orthologues. In zebrafish models of recessive parkinsonism, Parkin or Pink1 knockdown gave rise to specific loss of dopamine neurons; in a zebrafish model of recessive spinal muscular atrophy, loss of Smn1 function caused specific motor axonal defects. In addition, pathological features of several dominant diseases were replicated by transgenic over-expression of mutant human proteins, including Tau, Huntingtin, and SOD1. In some cases, conservation of relevant cellular pathways was sufficient that disease-specific posttranslational changes to the respective proteins were found in the zebrafish models. These data collectively suggest that the zebrafish can be an appropriate setting in which to model the molecular events underlying human neuropsychiatric disease. Consequently, novel findings yielded by studies in zebrafish models may be applicable to human diseases; this is an exciting prospect, in view of the many potential uses of zebrafish models, for example, screening for lead therapeutic compounds, rapid functional assessments of putative modifier genes, and live observation of pathogenic mechanisms in vivo.
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McCammon JM, Amacher SL. Using zinc finger nucleases for efficient and heritable gene disruption in zebrafish. Methods Mol Biol 2010; 649:281-298. [PMID: 20680842 DOI: 10.1007/978-1-60761-753-2_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
While the experimental tools developed for zebrafish have continued to advance the organism as a laboratory model, techniques for reverse genetics remain somewhat limited in scope. Zinc finger nucleases (ZFNs), chimeric fusions between DNA-binding zinc finger proteins and the non-specific cleavage domain of the FokI endonuclease, hold great promise for targeted mutagenesis in zebrafish, as demonstrated by two recent publications (Doyon et al., 2008, Nat Biotechnol. 26, 702-708; Meng et al., 2008, Nat Biotechnol. 26, 695-701). Because ZFNs can be designed to recognize a unique sequence in the genome, they can specifically bind and cleave a target locus, creating a double-strand break (DSB) that is repaired by one of two major DNA repair pathways. Repair by one of these pathways, non-homologous end joining, is often mutagenic, allowing one to screen for induced mutations in the target locus. By injecting into zebrafish embryos RNA encoding ZFNs that target three different loci, two groups have shown that ZFNs work efficiently to induce somatic and germline mutations (reviewed in (3)). We review here protocols for injection of ZFN-encoding mRNA into zebrafish embryos, screening of injected fish for induced mutations, and subsequent recovery of the induced mutations.
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Affiliation(s)
- Jasmine M McCammon
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
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50
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Wheeler GN, Brändli AW. Simple vertebrate models for chemical genetics and drug discovery screens: Lessons from zebrafish andXenopus. Dev Dyn 2009; 238:1287-308. [DOI: 10.1002/dvdy.21967] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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