1
|
Chu WK, Huang SC, Chang CF, Wu JL, Gong HY. Infertility control of transgenic fluorescent zebrafish with targeted mutagenesis of the dnd1 gene by CRISPR/Cas9 genome editing. Front Genet 2023; 14:1029200. [PMID: 36713075 PMCID: PMC9881232 DOI: 10.3389/fgene.2023.1029200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Transgenic technology and selective breeding have great potential for the genetic breeding in both edible fish and ornamental fish. The development of infertility control technologies in transgenic fish and farmed fish is the critical issue to prevent the gene flow with wild relatives. In this study, we report the genome editing of the dead end (dnd1) gene in the zebrafish model, using the CRISPR/Cas9 technology to achieve a loss-of-function mutation in both wild-type zebrafish and transgenic fluorescent zebrafish to develop complete infertility control technology of farmed fish and transgenic fish. We effectively performed targeted mutagenesis in the dnd1 gene of zebrafish with a single gRNA, which resulted in a small deletion (-7 bp) or insertion (+41 bp) in exon 2, leading to a null mutation. Heterozygotes and homozygotes of dnd1-knockout zebrafish were both selected by genotyping in the F 1 and F 2 generations. Based on a comparison of histological sections of the gonads between wild-type, heterozygous, and homozygous dnd1 zebrafish mutants, the dnd1 homozygous mutation (aa) resulted in the loss of germ cells. Still, there was no difference between the wild-type (AA) and dnd1 heterozygous (Aa) zebrafish. The homozygous dnd1 mutants of adult zebrafish and transgenic fluorescent zebrafish became all male, which had normal courtship behavior to induce wild-type female zebrafish spawning. However, they both had no sperm to fertilize the spawned eggs from wild-type females. Thus, all the unfertilized eggs died within 10 h. The targeted mutagenesis of the dnd1 gene using the CRISPR/Cas9 technology is stably heritable by crossing of fertile heterozygous mutants to obtain sterile homozygous mutants. It can be applied in the infertility control of transgenic fluorescent fish and genetically improved farmed fish by selective breeding to promote ecologically responsible aquaculture.
Collapse
Affiliation(s)
- Wai-Kwan Chu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Shih-Chin Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Ching-Fong Chang
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
| | - Jen-Leih Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan,College of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan,*Correspondence: Hong-Yi Gong,
| |
Collapse
|
2
|
Knowlton MN, Smith CL. Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. Mamm Genome 2017; 28:367-376. [PMID: 28589392 PMCID: PMC5569137 DOI: 10.1007/s00335-017-9698-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/27/2017] [Indexed: 12/29/2022]
Abstract
The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.
Collapse
Affiliation(s)
| | - Cynthia L Smith
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, 04609, USA
| |
Collapse
|
3
|
Yuan Y, Wang Y, Liu Q, Zhu F, Hong Y. Singapore grouper iridovirus protein VP088 is essential for viral infectivity. Sci Rep 2016; 6:31170. [PMID: 27498856 PMCID: PMC4976331 DOI: 10.1038/srep31170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 07/13/2016] [Indexed: 12/14/2022] Open
Abstract
Viral infection is a great challenge in healthcare and agriculture. The Singapore grouper iridovirus (SGIV) is highly infectious to numerous marine fishes and increasingly threatens mariculture and wildlife conservation. SGIV intervention is not available because little is known about key players and their precise roles in SGVI infection. Here we report the precise role of VP088 as a key player in SGIV infection. VP088 was verified as an envelope protein encoded by late gene orf088. We show that SGIV could be neutralized with an antibody against VP088. Depletion or deletion of VP088 significantly suppresses SGIV infection without altering viral gene expression and host responses. By precisely quantifying the genome copy numbers of host cells and virions, we reveal that VP088 deletion dramatically reduces SGIV infectivity through inhibiting virus entry without altering viral pathogenicity, genome stability and replication and progeny virus release. These results pinpoint that VP088 is a key player in SGIV entry and represents an ideal target for SGIV intervention.
Collapse
Affiliation(s)
- Yongming Yuan
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543, Singapore
| | - Yunzhi Wang
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543, Singapore
| | - Qizhi Liu
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543, Singapore
| | - Feng Zhu
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543, Singapore
| | - Yunhan Hong
- Department of Biological Sciences, National University of Singapore, Science Drive 4, Singapore 117543, Singapore
| |
Collapse
|
4
|
Reautschnig P, Vogel P, Stafforst T. The notorious R.N.A. in the spotlight - drug or target for the treatment of disease. RNA Biol 2016; 14:651-668. [PMID: 27415589 PMCID: PMC5449091 DOI: 10.1080/15476286.2016.1208323] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
mRNA is an attractive drug target for therapeutic interventions. In this review we highlight the current state, clinical trials, and developments in antisense therapy, including the classical approaches like RNaseH-dependent oligomers, splice-switching oligomers, aptamers, and therapeutic RNA interference. Furthermore, we provide an overview on emerging concepts for using RNA in therapeutic settings including protein replacement by in-vitro-transcribed mRNAs, mRNA as vaccines and anti-allergic drugs. Finally, we give a brief outlook on early-stage RNA repair approaches that apply endogenous or engineered proteins in combination with short RNAs or chemically stabilized oligomers for the re-programming of point mutations, RNA modifications, and frame shift mutations directly on the endogenous mRNA.
Collapse
Affiliation(s)
- Philipp Reautschnig
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| | - Paul Vogel
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| | - Thorsten Stafforst
- a Interfaculty Institute of Biochemistry, University of Tübingen Auf der Morgenstelle , Tübingen , Germany
| |
Collapse
|
5
|
Hong N, Li M, Yuan Y, Wang T, Yi M, Xu H, Zeng H, Song J, Hong Y. Dnd Is a Critical Specifier of Primordial Germ Cells in the Medaka Fish. Stem Cell Reports 2016; 6:411-21. [PMID: 26852942 PMCID: PMC4788760 DOI: 10.1016/j.stemcr.2016.01.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 11/28/2022] Open
Abstract
Primordial germ cell (PGC) specification occurs early in development. PGC specifiers have been identified in Drosophila, mouse, and human but remained elusive in most animals. Here we identify the RNA-binding protein Dnd as a critical PGC specifier in the medaka fish (Oryzias latipes). Dnd depletion specifically abolished PGCs, and its overexpression boosted PGCs. We established a single-cell culture procedure enabling lineage tracing in vitro. We show that individual blastomeres from cleavage embryos at the 32- and 64-cell stages are capable of PGC production in culture. Importantly, Dnd overexpression increases PGCs via increasing PGC precursors. Strikingly, dnd RNA forms prominent particles that segregate asymmetrically. Dnd concentrates in germ plasm and stabilizes germ plasm RNA. Therefore, Dnd is a critical specifier of fish PGCs and utilizes particle partition as a previously unidentified mechanism for asymmetric segregation. These findings offer insights into PGC specification and manipulation in medaka as a lower vertebrate model. The medaka RNA-binding protein Dnd specifies primordial germ cells Cells from medaka cleavage embryos can be singly cultured for lineage tracing The dnd RNA forms particles as a new mechanism for asymmetric segregation These findings offer new insights into PGC specification and manipulation
Collapse
Affiliation(s)
- Ni Hong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; Institute of Bioengineering and Nanotechnology, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis Way, Singapore 138669, Singapore
| | - Mingyou Li
- Ministry of Education Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai 201306, China
| | - Yongming Yuan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Tiansu Wang
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Meisheng Yi
- Laboratory of Molecular Reproductive Biology, School of Marine Sciences, Sun Yat-sen University, 135 Xingang West Road, Guangzhou 510275, China
| | - Hongyan Xu
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Huaqiang Zeng
- Institute of Bioengineering and Nanotechnology, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis Way, Singapore 138669, Singapore
| | - Jianxing Song
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| | - Yunhan Hong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
| |
Collapse
|
6
|
|
7
|
Liu Q, Wang Y, Lin F, Zhang L, Li Y, Ge R, Hong Y. Gene transfer and genome-wide insertional mutagenesis by retroviral transduction in fish stem cells. PLoS One 2015; 10:e0127961. [PMID: 26029933 PMCID: PMC4451014 DOI: 10.1371/journal.pone.0127961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/22/2015] [Indexed: 12/15/2022] Open
Abstract
Retrovirus (RV) is efficient for gene transfer and integration in dividing cells of diverse organisms. RV provides a powerful tool for insertional mutagenesis (IM) to identify and functionally analyze genes essential for normal and pathological processes. Here we report RV-mediated gene transfer and genome-wide IM in fish stem cells from medaka and zebrafish. Three RVs were produced for fish cell transduction: rvLegfp and rvLcherry produce green fluorescent protein (GFP) and mCherry fluorescent protein respectively under control of human cytomegalovirus immediate early promoter upon any chromosomal integration, whereas rvGTgfp contains a splicing acceptor and expresses GFP only upon gene trapping (GT) via intronic in-frame integration and spliced to endogenous active genes. We show that rvLegfp and rvLcherry produce a transduction efficiency of 11~23% in medaka and zebrafish stem cell lines, which is as 30~67% efficient as the positive control in NIH/3T3. Upon co-infection with rvGTgfp and rvLcherry, GFP-positive cells were much fewer than Cherry-positive cells, consistent with rareness of productive gene trapping events versus random integration. Importantly, rvGTgfp infection in the medaka haploid embryonic stem (ES) cell line HX1 generated GTgfp insertion on all 24 chromosomes of the haploid genome. Similar to the mammalian haploid cells, these insertion events were presented predominantly in intergenic regions and introns but rarely in exons. RV-transduced HX1 retained the ES cell properties such as stable growth, embryoid body formation and pluripotency gene expression. Therefore, RV is proficient for gene transfer and IM in fish stem cells. Our results open new avenue for genome-wide IM in medaka haploid ES cells in culture.
Collapse
Affiliation(s)
- Qizhi Liu
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yunzhi Wang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Fan Lin
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Lei Zhang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yan Li
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ruowen Ge
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Yunhan Hong
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * E-mail:
| |
Collapse
|
8
|
Aluru N, Karchner SI, Franks DG, Nacci D, Champlin D, Hahn ME. Targeted mutagenesis of aryl hydrocarbon receptor 2a and 2b genes in Atlantic killifish (Fundulus heteroclitus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 158:192-201. [PMID: 25481785 PMCID: PMC4272816 DOI: 10.1016/j.aquatox.2014.11.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Understanding molecular mechanisms of toxicity is facilitated by experimental manipulations, such as disruption of function by gene targeting, that are especially challenging in non-standard model species with limited genomic resources. While loss-of-function approaches have included gene knock-down using morpholino-modified oligonucleotides and random mutagenesis using mutagens or retroviruses, more recent approaches include targeted mutagenesis using zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology. These latter methods provide more accessible opportunities to explore gene function in non-traditional model species. To facilitate evaluation of toxic mechanisms for important categories of aryl hydrocarbon pollutants, whose actions are known to be receptor mediated, we used ZFN and CRISPR-Cas9 approaches to generate aryl hydrocarbon receptor 2a (AHR2a) and AHR2b gene mutations in Atlantic killifish (Fundulus heteroclitus) embryos. This killifish is a particularly valuable non-traditional model, with multiple paralogs of AHR whose functions are not well characterized. In addition, some populations of this species have evolved resistance to toxicants such as halogenated aromatic hydrocarbons. AHR-null killifish will be valuable for characterizing the role of the individual AHR paralogs in evolved resistance, as well as in normal development. We first used five-finger ZFNs targeting exons 1 and 3 of AHR2a. Subsequently, CRISPR-Cas9 guide RNAs were designed to target regions in exon 2 and 3 of AHR2a and AHR2b. We successfully induced frameshift mutations in AHR2a exon 3 with ZFN and CRISPR-Cas9 guide RNAs, with mutation frequencies of 10% and 16%, respectively. In AHR2b, mutations were induced using CRISPR-Cas9 guide RNAs targeting sites in both exon 2 (17%) and exon 3 (63%). We screened AHR2b exon 2 CRISPR-Cas9-injected embryos for off-target effects in AHR paralogs. No mutations were observed in closely related AHR genes (AHR1a, AHR1b, AHR2a, AHRR) in the CRISPR-Cas9-injected embryos. Overall, our results demonstrate that targeted genome-editing methods are efficient in inducing mutations at specific loci in embryos of a non-traditional model species, without detectable off-target effects in paralogous genes.
Collapse
Affiliation(s)
- Neelakanteswar Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA.
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Diana G Franks
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Diane Nacci
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Denise Champlin
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| |
Collapse
|
9
|
Li M, Zhao H, Wei J, Zhang J, Hong Y. Medaka vasa gene has an exonic enhancer for germline expression. Gene 2015; 555:403-8. [DOI: 10.1016/j.gene.2014.11.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/04/2014] [Accepted: 11/15/2014] [Indexed: 11/26/2022]
|