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Puthumana J, Chandrababu A, Sarasan M, Joseph V, Singh ISB. Genetic improvement in edible fish: status, constraints, and prospects on CRISPR-based genome engineering. 3 Biotech 2024; 14:44. [PMID: 38249355 PMCID: PMC10796887 DOI: 10.1007/s13205-023-03891-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 12/17/2023] [Indexed: 01/23/2024] Open
Abstract
Conventional selective breeding in aquaculture has been effective in genetically enhancing economic traits like growth and disease resistance. However, its advances are restricted by heritability, the extended period required to produce a strain with desirable traits, and the necessity to target multiple characteristics simultaneously in the breeding programs. Genome editing tools like zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) are promising for faster genetic improvement in fishes. CRISPR/Cas9 technology is the least expensive, most precise, and well compatible with multiplexing of all genome editing approaches, making it a productive and highly targeted approach for developing customized fish strains with specified characteristics. As a result, the use of CRISPR/Cas9 technology in aquaculture is rapidly growing, with the main traits researched being reproduction and development, growth, pigmentation, disease resistance, trans-GFP utilization, and omega-3 metabolism. However, technological obstacles, such as off-target effects, ancestral genome duplication, and mosaicism in founder population, need to be addressed to achieve sustainable fish production. Furthermore, present regulatory and risk assessment frameworks are inadequate to address the technical hurdles of CRISPR/Cas9, even though public and regulatory approval is critical to commercializing novel technology products. In this review, we examine the potential of CRISPR/Cas9 technology for the genetic improvement of edible fish, the technical, ethical, and socio-economic challenges to using it in fish species, and its future scope for sustainable fish production.
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Affiliation(s)
- Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Aswathy Chandrababu
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - Valsamma Joseph
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
| | - I. S. Bright Singh
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, 16 Kerala India
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Strømsnes TAH, Schmidke SE, Azad M, Singstad Ø, Grønsberg IM, Dalmo RA, Okoli AS. CRISPR/Cas9-Mediated Gene Editing in Salmonids Cells and Efficient Establishment of Edited Clonal Cell Lines. Int J Mol Sci 2022; 23:ijms232416218. [PMID: 36555862 PMCID: PMC9787932 DOI: 10.3390/ijms232416218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Finfish production has seen over three-fold increase in the past 30 years (1990-2020), and Atlantic salmon (A. salmon; salmo salar) accounted for approximately 32.6% of the total marine and coastal aquaculture of all finfish species in the year 2020, making it one of the most profitable farmed fish species globally. This growth in production is, however, threatened by a number of problems which can be solved using the CRISPR/Cas technology. In vitro applications of CRISPR/Cas using cell lines can complement its in vivo applications, but salmonids-derived cell lines are difficult to gene edit because they grow slowly, are difficult to transfect and isolate single clones of gene-edited cells. While clonal isolation of the gene-edited Chinook salmon cell line (CHSE-214) has successfully been performed, there is no report of successful clonal isolation of the gene-edited A. salmon ASK-1 and SHK-1cell lines. In the current study, two gene loci-cr2 and mmp9 of A. salmon-were efficiently edited using the ribonucleoprotein (RNP) and plasmid CRISPR/Cas9 strategies. Edited cells were enriched using flow cytometer-activated cell sorting (FACS), followed by clonal isolation and expansion of edited cells. The study both confirms the recent report of the highly efficient editing of these widely used model cell lines, as well as extends the frontline in the single-cell cloning of gene-edited salmonids cells. The report also highlights the pitfalls and future directions in the application of CRISPR/Cas9 in these cells.
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Affiliation(s)
- Trygve A. H. Strømsnes
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusveien 21, 9019 Tromsø, Norway
| | - Sebastian E. Schmidke
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusveien 21, 9019 Tromsø, Norway
| | - Mitra Azad
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusveien 21, 9019 Tromsø, Norway
| | - Øyvind Singstad
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusveien 21, 9019 Tromsø, Norway
| | - Idun M. Grønsberg
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusveien 21, 9019 Tromsø, Norway
| | - Roy A. Dalmo
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Muninbakken 21, 9019 Tromsø, Norway
| | - Arinze S. Okoli
- NORCE Norwegian Research Centre AS, Climate & Environment Division, Siva Innovasjonssenter, Sykehusveien 21, 9019 Tromsø, Norway
- Correspondence:
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Pulido-Quetglas C, Johnson R. Designing libraries for pooled CRISPR functional screens of long noncoding RNAs. Mamm Genome 2022; 33:312-327. [PMID: 34533605 PMCID: PMC9114037 DOI: 10.1007/s00335-021-09918-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/09/2021] [Indexed: 02/01/2023]
Abstract
Human and other genomes encode tens of thousands of long noncoding RNAs (lncRNAs), the vast majority of which remain uncharacterised. High-throughput functional screening methods, notably those based on pooled CRISPR-Cas perturbations, promise to unlock the biological significance and biomedical potential of lncRNAs. Such screens are based on libraries of single guide RNAs (sgRNAs) whose design is critical for success. Few off-the-shelf libraries are presently available, and lncRNAs tend to have cell-type-specific expression profiles, meaning that library design remains in the hands of researchers. Here we introduce the topic of pooled CRISPR screens for lncRNAs and guide readers through the three key steps of library design: accurate annotation of transcript structures, curation of optimal candidate sets, and design of sgRNAs. This review is a starting point and reference for researchers seeking to design custom CRISPR screening libraries for lncRNAs.
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Affiliation(s)
- Carlos Pulido-Quetglas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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Okoli AS, Blix T, Myhr AI, Xu W, Xu X. Sustainable use of CRISPR/Cas in fish aquaculture: the biosafety perspective. Transgenic Res 2021; 31:1-21. [PMID: 34304349 PMCID: PMC8821480 DOI: 10.1007/s11248-021-00274-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/03/2021] [Indexed: 12/18/2022]
Abstract
Aquaculture is becoming the primary source of seafood for human diets, and farmed fish aquaculture is one of its fastest growing sectors. The industry currently faces several challenges including infectious and parasitic diseases, reduced viability, fertility reduction, slow growth, escapee fish and environmental pollution. The commercialization of the growth-enhanced AquAdvantage salmon and the CRISPR/Cas9-developed tilapia (Oreochromis niloticus) proffers genetic engineering and genome editing tools, e.g. CRISPR/Cas, as potential solutions to these challenges. Future traits being developed in different fish species include disease resistance, sterility, and enhanced growth. Despite these notable advances, off-target effect and non-clarification of trait-related genes among other technical challenges hinder full realization of CRISPR/Cas potentials in fish breeding. In addition, current regulatory and risk assessment frameworks are not fit-for purpose regarding the challenges of CRISPR/Cas notwithstanding that public and regulatory acceptance are key to commercialization of products of the new technology. In this study, we discuss how CRISPR/Cas can be used to overcome some of these limitations focusing on diseases and environmental release in farmed fish aquaculture. We further present technical limitations, regulatory and risk assessment challenges of the use of CRISPR/Cas, and proffer research strategies that will provide much-needed data for regulatory decisions, risk assessments, increased public awareness and sustainable applications of CRISPR/Cas in fish aquaculture with emphasis on Atlantic salmon (Salmo salar) breeding.
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Affiliation(s)
- Arinze S Okoli
- GenØk -Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway.
| | - Torill Blix
- GenØk -Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway.,The Norwegian College of Fishery Science, The Arctic University of Norway (UiT), Tromsø, Norway
| | - Anne I Myhr
- GenØk -Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
| | - Wenteng Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaodong Xu
- Qingdao Vland Biotech Company Group, Qingdao, 266061, China
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Abstract
RNA-Seq is nowadays an indispensable approach for comparative transcriptome profiling in model and nonmodel organisms. Analyzing RNA-Seq data from nonmodel organisms poses unique challenges, due to unavailability of a high-quality genome reference and to relative sparsity of tools for downstream functional analyses. In this chapter, we provide an overview of the analysis steps in RNA-Seq projects of nonmodel organisms, while elaborating on aspects that are unique to this analysis. These will include (1) strategic decisions that have to be made in advance, regarding sequencing technology and reference to use; (2) how to search for available draft genomes, and, if necessary, how to improve their gene prediction and annotation; (3) how to clean raw reads before de novo assembly; (4) how to separate the reads in RNA-Seq projects of symbiont organisms; (5) how to design and carry out a de novo transcriptome assembly that will be comprehensive and reliable; (6) how to assess transcriptome quality; (7) when and how to reduce redundancy in the transcriptome; (8) techniques and considerations in transcriptome functional annotation; (9) quantitating transcript abundance in the face of high transcriptome redundancy; and, most importantly, (10) how to achieve functional enrichment testing using available tools which either support a large range of species or enable a universal, non-species-specific analysis.Throughout the chapter, we will refer to a variety of useful software tools. For the initial analysis steps involving high-volume data, these will include Linux-based programs. For the later steps, we will describe both Linux and R packages for advanced users, as well as many user-friendly tools for nonprogrammers. Finally, we will present a full workflow for RNA-Seq analysis of nonmodel organisms using the NeatSeq-Flow platform, which can be used locally through a user-friendly interface.
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Affiliation(s)
- Vered Chalifa-Caspi
- Bioinformatics Core Facility, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Bick JT, Zeng S, Robinson MD, Ulbrich SE, Bauersachs S. Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5539597. [PMID: 31353404 PMCID: PMC6661403 DOI: 10.1093/database/baz086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 03/08/2019] [Accepted: 06/05/2019] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing technologies and the availability of an increasing number of mammalian and other genomes allow gene expression studies, particularly RNA sequencing, in many non-model organisms. However, incomplete genome annotation and assignments of genes to functional annotation databases can lead to a substantial loss of information in downstream data analysis. To overcome this, we developed Mammalian Annotation Database tool (MAdb, https://madb.ethz.ch) to conveniently provide homologous gene information for selected mammalian species. The assignment between species is performed in three steps: (i) matching official gene symbols, (ii) using ortholog information contained in Ensembl Compara and (iii) pairwise BLAST comparisons of all transcripts. In addition, we developed a new tool (AnnOverlappeR) for the reliable assignment of the National Center for Biotechnology Information (NCBI) and Ensembl gene IDs. The gene lists translated to gene IDs of well-annotated species such as a human can be used for improved functional annotation with relevant tools based on Gene Ontology and molecular pathway information. We tested the MAdb on a published RNA-seq data set for the pig and showed clearly improved overrepresentation analysis results based on the assigned human homologous gene identifiers. Using the MAdb revealed a similar list of human homologous genes and functional annotation results regardless of whether starting with gene IDs from NCBI or Ensembl. The MAdb database is accessible via a web interface and a Galaxy application.
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Affiliation(s)
- Jochen T Bick
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Shuqin Zeng
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.,Genetics and Functional Genomics, Vetsuisse Faculty Zurich, University of Zurich, Zurich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Susanne E Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Stefan Bauersachs
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.,Genetics and Functional Genomics, Vetsuisse Faculty Zurich, University of Zurich, Zurich, Switzerland
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