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Davison C, Harzman H, Nicholson J, Entriken S, Mobley K, Krull A, Singhal M, Skow C, Matthews N, Kopp L, Gillette B, Weide TJ, Hukvari JR, Stumpf SC, Feldmann OM, McGrail M, Srivastava R, Essner JJ. Tagging the tjp1a Gene in Zebrafish with Monomeric Red Fluorescent Protein Using Biotin Homology Arms. Zebrafish 2024; 21:191-197. [PMID: 38621205 PMCID: PMC11035848 DOI: 10.1089/zeb.2023.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024] Open
Abstract
Tjp1a and other tight junction and adherens proteins play important roles in cell-cell adhesion, scaffolding, and forming seals between cells in epithelial and endothelial tissues. In this study, we labeled Tjp1a of zebrafish with the monomeric red fluorescent protein (mRFP) using CRISPR/Cas9-mediated targeted integration of biotin-labeled polymerase chain reaction (PCR) generated templates. Labeling Tjp1a with RFP allowed us to follow membrane and junctional dynamics of epithelial and endothelial cells throughout zebrafish embryo development. For targeted integration, we used short 35 bp homology arms on each side of the Cas9 genomic target site at the C-terminal of the coding sequence in tjp1a. Through PCR using 5' biotinylated primers containing the homology arms, we generated a double-stranded template for homology directed repair containing a flexible linker followed by RFP. Cas9 protein was complexed with the tjp1a gRNA before mixing with the repair template and microinjected into one-cell zebrafish embryos. We confirmed and recovered a precise integration allele at the desired site at the tjp1a C-terminus. Examination of fluorescence reveals RFP cell-cell junctional labeling using confocal imaging. We are currently using this stable tjp1a-mRFPis86 line to examine the behavior and interactions between cells during vascular formation in zebrafish.
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Affiliation(s)
- Connor Davison
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Hamelynn Harzman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Jessie Nicholson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Seth Entriken
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Kierinn Mobley
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Abigail Krull
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Manik Singhal
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Caleb Skow
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Nathan Matthews
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Lindsey Kopp
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Benjamin Gillette
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Tyler J. Weide
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Jana R. Hukvari
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Sofia C.P. Stumpf
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Olivia M. Feldmann
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Renu Srivastava
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
| | - Jeffrey J. Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA
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2
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Warner JF, Besemer R, Schickle A, Borbee E, Changsut IV, Sharp K, Babonis LS. Microinjection, gene knockdown, and CRISPR-mediated gene knock-in in the hard coral, Astrangia poculata. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567385. [PMID: 38948709 PMCID: PMC11213136 DOI: 10.1101/2023.11.16.567385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including the sea anemone, Nematostella vectensis . Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata . We present methods for gene knockdown using short hairpin RNAs, gene overexpression using exogenous mRNAs, and endogenous gene tagging using CRISPR-mediated gene knock-in. Combined with our ability to control spawning in the laboratory, these tools make A. poculata a tractable experimental system for investigative studies of coral development. Further application of these tools will enable functional analyses of embryonic patterning and morphogenesis across Anthozoa and open new frontiers in coral biology research. Summary Statement This study reports the development of the first transgenic knock-in coral, providing the opportunity to track the behavior of various cell types during early coral development.
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3
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Clark B, Kuwalekar M, Fischer B, Woltering J, Biran J, Juntti S, Kratochwil CF, Santos ME, Almeida MV. Genome editing in East African cichlids and tilapias: state-of-the-art and future directions. Open Biol 2023; 13:230257. [PMID: 38018094 PMCID: PMC10685126 DOI: 10.1098/rsob.230257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
African cichlid fishes of the Cichlidae family are a group of teleosts important for aquaculture and research. A thriving research community is particularly interested in the cichlid radiations of the East African Great Lakes. One key goal is to pinpoint genetic variation underlying phenotypic diversification, but the lack of genetic tools has precluded thorough dissection of the genetic basis of relevant traits in cichlids. Genome editing technologies are well established in teleost models like zebrafish and medaka. However, this is not the case for emerging model organisms, such as East African cichlids, where these technologies remain inaccessible to most laboratories, due in part to limited exchange of knowledge and expertise. The Cichlid Science 2022 meeting (Cambridge, UK) hosted for the first time a Genome Editing Workshop, where the community discussed recent advances in genome editing, with an emphasis on CRISPR/Cas9 technologies. Based on the workshop findings and discussions, in this review we define the state-of-the-art of cichlid genome editing, share resources and protocols, and propose new possible avenues to further expand the cichlid genome editing toolkit.
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Affiliation(s)
- Bethan Clark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Muktai Kuwalekar
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Joost Woltering
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg 78457, Germany
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Scott Juntti
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Claudius F. Kratochwil
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Uusimaa 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Uusimaa 00014, Finland
| | | | - Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
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4
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Aboouf MA, Gorr TA, Hamdy NM, Gassmann M, Thiersch M. Myoglobin in Brown Adipose Tissue: A Multifaceted Player in Thermogenesis. Cells 2023; 12:2240. [PMID: 37759463 PMCID: PMC10526770 DOI: 10.3390/cells12182240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Brown adipose tissue (BAT) plays an important role in energy homeostasis by generating heat from chemical energy via uncoupled oxidative phosphorylation. Besides its high mitochondrial content and its exclusive expression of the uncoupling protein 1, another key feature of BAT is the high expression of myoglobin (MB), a heme-containing protein that typically binds oxygen, thereby facilitating the diffusion of the gas from cell membranes to mitochondria of muscle cells. In addition, MB also modulates nitric oxide (NO•) pools and can bind C16 and C18 fatty acids, which indicates a role in lipid metabolism. Recent studies in humans and mice implicated MB present in BAT in the regulation of lipid droplet morphology and fatty acid shuttling and composition, as well as mitochondrial oxidative metabolism. These functions suggest that MB plays an essential role in BAT energy metabolism and thermogenesis. In this review, we will discuss in detail the possible physiological roles played by MB in BAT thermogenesis along with the potential underlying molecular mechanisms and focus on the question of how BAT-MB expression is regulated and, in turn, how this globin regulates mitochondrial, lipid, and NO• metabolism. Finally, we present potential MB-mediated approaches to augment energy metabolism, which ultimately could help tackle different metabolic disorders.
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Affiliation(s)
- Mostafa A. Aboouf
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Thomas A. Gorr
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
| | - Nadia M. Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Max Gassmann
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
| | - Markus Thiersch
- Institute of Veterinary Physiology, University of Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
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5
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Palmiotti A, Lichak MR, Shih PY, Kwon YM, Bendesky A. Genetic manipulation of betta fish. Front Genome Ed 2023; 5:1167093. [PMID: 37545763 PMCID: PMC10401044 DOI: 10.3389/fgeed.2023.1167093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/07/2023] [Indexed: 08/08/2023] Open
Abstract
Betta splendens, also known as Siamese fighting fish or "betta," is a freshwater fish species renowned for its astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l, and mitfa, and analyzed their effects on viability and pigmentation. Furthermore, we knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.
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Affiliation(s)
- Alec Palmiotti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Madison R. Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Pei-Yin Shih
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Young Mi Kwon
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
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6
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Bedbrook CN, Nath RD, Nagvekar R, Deisseroth K, Brunet A. Rapid and precise genome engineering in a naturally short-lived vertebrate. eLife 2023; 12:80639. [PMID: 37191291 DOI: 10.7554/elife.80639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The African turquoise killifish is a powerful vertebrate system to study complex phenotypes at scale, including aging and age-related disease. Here, we develop a rapid and precise CRISPR/Cas9-mediated knock-in approach in the killifish. We show its efficient application to precisely insert fluorescent reporters of different sizes at various genomic loci in order to drive cell-type- and tissue-specific expression. This knock-in method should allow the establishment of humanized disease models and the development of cell-type-specific molecular probes for studying complex vertebrate biology.
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Affiliation(s)
- Claire N Bedbrook
- Department of Genetics, Stanford University, Stanford, United States
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, United States
| | - Rahul Nagvekar
- Department of Genetics, Stanford University, Stanford, United States
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, United States
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, United States
- Glenn Laboratories for the Biology of Aging at Stanford, Stanford, United States
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, United States
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7
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Mi J, Andersson O. Efficient knock-in method enabling lineage tracing in zebrafish. Life Sci Alliance 2023; 6:e202301944. [PMID: 36878640 PMCID: PMC9990459 DOI: 10.26508/lsa.202301944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Here, we devised a cloning-free 3' knock-in strategy for zebrafish using PCR amplified dsDNA donors that avoids disrupting the targeted genes. The dsDNA donors carry genetic cassettes coding for fluorescent proteins and Cre recombinase in frame with the endogenous gene but separated from it by self-cleavable peptides. Primers with 5' AmC6 end-protections generated PCR amplicons with increased integration efficiency that were coinjected with preassembled Cas9/gRNA ribonucleoprotein complexes for early integration. We targeted four genetic loci (krt92, nkx6.1, krt4, and id2a) and generated 10 knock-in lines, which function as reporters for the endogenous gene expression. The knocked-in iCre or CreERT2 lines were used for lineage tracing, which suggested that nkx6.1 + cells are multipotent pancreatic progenitors that gradually restrict to the bipotent duct, whereas id2a + cells are multipotent in both liver and pancreas and gradually restrict to ductal cells. In addition, the hepatic id2a + duct show progenitor properties upon extreme hepatocyte loss. Thus, we present an efficient and straightforward knock-in technique with widespread use for cellular labelling and lineage tracing.
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Affiliation(s)
- Jiarui Mi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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8
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Zhang Z, Wang J, Li J, Liu X, Liu L, Zhao C, Tao W, Wang D, Wei J. Establishment of an Integrated CRISPR/Cas9 Plasmid System for Simple and Efficient Genome Editing in Medaka In Vitro and In Vivo. BIOLOGY 2023; 12:biology12020336. [PMID: 36829610 PMCID: PMC9953409 DOI: 10.3390/biology12020336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Although CRISPR/Cas9 has been used in gene manipulation of several fish species in vivo, its application in fish cultured cells is still challenged and limited. In this study, we established an integrated CRISPR/Cas9 plasmid system and evaluated its efficiency of gene knock-out or knock-in at a specific site in medaka (Oryzias latipes) in vitro and in vivo. By using the enhanced green fluorescent protein reporter plasmid pGNtsf1, we demonstrate that pCas9-U6sgRNA driven by endogenous U6 promoter (pCas9-mU6sgRNA) mediated very high gene editing efficiency in medaka cultured cells, but not by exogenous U6 promoters. After optimizing the conditions, the gene editing efficiencies of eight sites targeting for four endogenous genes were calculated, and the highest was up to 94% with no detectable off-target. By one-cell embryo microinjection, pCas9-mU6sgRNA also mediated efficient gene knock-out in vivo. Furthermore, pCas9-mU6sgRNA efficiently mediated gene knock-in at a specific site in medaka cultured cells as well as embryos. Collectively, our study demonstrates that the genetic relationship of U6 promoter is critical to gene editing efficiency in medaka cultured cells, and a simple and efficient system for medaka genome editing in vitro and in vivo has been established. This study provides an insight into other fish genome editing and promotes gene functional analysis.
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Affiliation(s)
- Zeming Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jie Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
- Sichuan Province Yuechi Middle School, Guang’an 638300, China
| | - Jianeng Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiang Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Lei Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Changle Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
- Correspondence: (D.W.); (J.W.)
| | - Jing Wei
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
- Correspondence: (D.W.); (J.W.)
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9
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Palmiotti A, Lichak MR, Shih PY, Bendesky A. Genetic manipulation of betta fish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528733. [PMID: 36824853 PMCID: PMC9948955 DOI: 10.1101/2023.02.16.528733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Betta splendens , also known as Siamese fighting fish or 'betta', are renowned for their astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l , and mitfa , and analyzed their effects on viability and pigmentation. Furthermore, we successfully knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.
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Affiliation(s)
- Alec Palmiotti
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Madison R Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Present address: Department of Ecology and Evolutionary Biology, Princeton University, NJ, USA
| | - Pei-Yin Shih
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
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10
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Hara R, Ansai S, Kinoshita M. Genome Editing of Medaka. Methods Mol Biol 2023; 2637:325-339. [PMID: 36773158 DOI: 10.1007/978-1-0716-3016-7_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Medaka (Oryzias latipes), along with zebrafish (Danio rerio), is a useful experimental model fish. Here, we describe a simple method for generating medaka gene knockout strains using an automated microchip electrophoresis system. We also describe a method for targeted gene knockin using a plasmid carrying a sequence that does not cause off-target effects in medaka. Additionally, knockin method without plasmid cloning is described.
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Affiliation(s)
- Rie Hara
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
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11
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Oulhen N, Morita S, Warner JF, Wessel G. CRISPR/Cas9 knockin methodology for the sea urchin embryo. Mol Reprod Dev 2023; 90:69-72. [PMID: 36719060 PMCID: PMC9979971 DOI: 10.1002/mrd.23672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Affiliation(s)
- Nathalie Oulhen
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Shumpei Morita
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
- Present Address: Asamushi Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, Aomori, Aomori, 039-3501, Japan
| | - Jacob F. Warner
- Department of Biology and Marine Biology. University of North Carolina Wilmington, Wilmington, NC 28403
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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12
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Santos ME, Lopes JF, Kratochwil CF. East African cichlid fishes. EvoDevo 2023; 14:1. [PMID: 36604760 PMCID: PMC9814215 DOI: 10.1186/s13227-022-00205-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Cichlid fishes are a very diverse and species-rich family of teleost fishes that inhabit lakes and rivers of India, Africa, and South and Central America. Research has largely focused on East African cichlids of the Rift Lakes Tanganyika, Malawi, and Victoria that constitute the biodiversity hotspots of cichlid fishes. Here, we give an overview of the study system, research questions, and methodologies. Research on cichlid fishes spans many disciplines including ecology, evolution, physiology, genetics, development, and behavioral biology. In this review, we focus on a range of organismal traits, including coloration phenotypes, trophic adaptations, appendages like fins and scales, sensory systems, sex, brains, and behaviors. Moreover, we discuss studies on cichlid phylogenies, plasticity, and general evolutionary patterns, ranging from convergence to speciation rates and the proximate and ultimate mechanisms underlying these processes. From a methodological viewpoint, the last decade has brought great advances in cichlid fish research, particularly through the advent of affordable deep sequencing and advances in genetic manipulations. The ability to integrate across traits and research disciplines, ranging from developmental biology to ecology and evolution, makes cichlid fishes a fascinating research system.
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Affiliation(s)
- M. Emília Santos
- grid.5335.00000000121885934Department of Zoology, University of Cambridge, Cambridge, UK
| | - João F. Lopes
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Claudius F. Kratochwil
- grid.7737.40000 0004 0410 2071Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
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13
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Endogenous tagging of multiple cellular components in the sea anemone Nematostella vectensis. Proc Natl Acad Sci U S A 2023; 120:e2215958120. [PMID: 36574688 PMCID: PMC9910423 DOI: 10.1073/pnas.2215958120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The cnidarian Nematostella vectensis has developed into a powerful model system to study the mechanisms underlying animal development, regeneration, and evolution. However, despite the significant progress in the molecular and genetic approaches in this sea anemone, endogenous protein tagging is still challenging. Here, we report a robust method for knock in for Nematostella using CRISPR/Cas9. As an outcome, we generate endogenously tagged proteins that label core molecular components of several cellular apparatus, including the nuclear envelope, cytoskeleton, cell adhesion, endoplasmic reticulum, cell trafficking, and extracellular matrix. Using live imaging, we monitor the dynamics of vesicular trafficking and endoplasmic reticulum in embryos, as well as cell contractility during the peristaltic wave of a primary polyp. This advancement in gene editing expands the molecular tool kit of Nematostella and enables experimental avenues to interrogate the cell biology of cnidarians.
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