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Drago L, Pennati A, Rothbächer U, Ashita R, Hashimoto S, Saito R, Fujiwara S, Ballarin L. Stress granule-related genes during embryogenesis of an invertebrate chordate. Front Cell Dev Biol 2024; 12:1414759. [PMID: 39149517 PMCID: PMC11324471 DOI: 10.3389/fcell.2024.1414759] [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: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 08/17/2024] Open
Abstract
Controlling global protein synthesis through the assembly of stress granules represents a strategy adopted by eukaryotic cells to face various stress conditions. TIA 1-related nucleolysin (TIAR), tristetraprolin (TTP), and Ras-GTPase-activating protein SH3-domain-binding protein (G3BP) are key components of stress granules, allowing the regulation of mRNA stability, and thus controlling not only stress responses but also cell proliferation and differentiation. In this study, we aimed at investigating the roles of tiar, ttp, and g3bp during embryogenesis of the solitary ascidian Ciona robusta under both physiological and stress conditions. We carried out CRISPR/Cas9 to evaluate the effects of gene knockout on normal embryonic development, and gene reporter assay to study the time and tissue specificity of gene transcription, together with whole-mount in situ hybridization and quantitative real time PCR. To induce acute stress conditions, we used iron and cadmium as "essential" and "non-essential" metals, respectively. Our results highlight, for the first time, the importance of tiar, ttp, and g3bp in controlling the development of mesendodermal tissue derivatives during embryogenesis of an invertebrate chordate.
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Affiliation(s)
- Laura Drago
- Department of Biology, University of Padova, Padua, Italy
| | | | - Ute Rothbächer
- Institute of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Ryuji Ashita
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | - Seika Hashimoto
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | - Ryota Saito
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | - Shigeki Fujiwara
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
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Rothbächer U. Ascidian gene regulation and bioadhesion. Genesis 2023; 61:e23572. [PMID: 38009987 PMCID: PMC10909405 DOI: 10.1002/dvg.23572] [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: 08/31/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/29/2023]
Affiliation(s)
- Ute Rothbächer
- Research unit Evolutionary Developmental BiologyInstitute of Zoology, University InnsbruckAustria
- Detachement CNRSMarseilleFrance
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Targeted mutagenesis in the olive flounder (Paralichthys olivaceus) using the CRISPR/Cas9 system with electroporation. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00677-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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4
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Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. Exploring miR-9 Involvement in Ciona intestinalis Neural Development Using Peptide Nucleic Acids. Int J Mol Sci 2020; 21:ijms21062001. [PMID: 32183450 PMCID: PMC7139483 DOI: 10.3390/ijms21062001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/16/2022] Open
Abstract
The microRNAs are small RNAs that regulate gene expression at the post-transcriptional level and can be involved in the onset of neurodegenerative diseases and cancer. They are emerging as possible targets for antisense-based therapy, even though the in vivo stability of miRNA analogues is still questioned. We tested the ability of peptide nucleic acids, a novel class of nucleic acid mimics, to downregulate miR-9 in vivo in an invertebrate model organism, the ascidian Ciona intestinalis, by microinjection of antisense molecules in the eggs. It is known that miR-9 is a well-conserved microRNA in bilaterians and we found that it is expressed in epidermal sensory neurons of the tail in the larva of C. intestinalis. Larvae developed from injected eggs showed a reduced differentiation of tail neurons, confirming the possibility to use peptide nucleic acid PNA to downregulate miRNA in a whole organism. By identifying putative targets of miR-9, we discuss the role of this miRNA in the development of the peripheral nervous system of ascidians.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy;
- Correspondence: (S.C.); (S.C.); Tel.: +39-0250314147 (S.C.); +39-0103538051 (S.C.)
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16132 Genova, Italy
- Correspondence: (S.C.); (S.C.); Tel.: +39-0250314147 (S.C.); +39-0103538051 (S.C.)
| | - Giorgio Scarì
- Department of Biosciences, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Emanuela Licandro
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
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Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. miR-7 Knockdown by Peptide Nucleic Acids in the Ascidian Ciona intestinalis. Int J Mol Sci 2019; 20:ijms20205127. [PMID: 31623150 PMCID: PMC6829576 DOI: 10.3390/ijms20205127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Peptide Nucleic Acids (PNAs) are synthetic mimics of natural oligonucleotides, which bind complementary DNA/RNA strands with high sequence specificity. They display numerous advantages, but in vivo applications are still rare. One of the main drawbacks of PNAs application is the poor cellular uptake that could be overcome by using experimental models, in which microinjection techniques allow direct delivery of molecules into eggs. Thus, in this communication, we investigated PNAs efficiency in miR-7 downregulation and compared its effects with those obtained with the commercially available antisense molecule, Antagomir (Dharmacon) in the ascidian Ciona intestinalis. Ascidians are marine invertebrates closely related to vertebrates, in which PNA techniques have not been applied yet. Our results suggested that anti-miR-7 PNAs were able to reach their specific targets in the developing ascidian embryos with high efficiency, as the same effects were obtained with both PNA and Antagomir. To the best of our knowledge, this is the first evidence that unmodified PNAs can be applied in in vivo knockdown strategies when directly injected into eggs.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16126 Genova, Italy.
| | - Giorgio Scarì
- Department of Biosciences, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Emanuela Licandro
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
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Zeng F, Wunderer J, Salvenmoser W, Ederth T, Rothbächer U. Identifying adhesive components in a model tunicate. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190197. [PMID: 31495315 DOI: 10.1098/rstb.2019.0197] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Tunicates populate a great variety of marine underwater substrates worldwide and represent a significant concern in marine shipping and aquaculture. Adhesives are secreted from the anterior papillae of their swimming larvae, which attach and metamorphose into permanently adhering, filter-feeding adults. We recently described the cellular composition of the sensory adhesive organ of the model tunicate Ciona intestinalis in great detail. Notably, the adhesive secretions of collocytes accumulate at the tip of the organ and contain glycoproteins. Here, we further explore the components of adhesive secretions and have screened for additional specificities that may influence adhesion or cohesion of the Ciona glue, including other carbohydrate moieties, catechols and substrate properties. We found a distinct set of sugar residues in the glue recognized by specific lectins with little overlap to other known marine adhesives. Surprisingly, we also detect catechol residues that likely originate from an adjacent cellular reservoir, the test cells. Furthermore, we provide information on substrate preferences where hydrophobicity outperforms charge in the attachment. Finally, we can influence the settlement process by the addition of hydrophilic heparin. The further analysis of tunicate adhesive strategies should provide a valuable knowledge source in designing physiological adhesives or green antifoulants. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.
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Affiliation(s)
- Fan Zeng
- Department of Evolutionary Developmental Biology, Institute of Zoology, University Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Julia Wunderer
- Department of Evolutionary Developmental Biology, Institute of Zoology, University Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Willi Salvenmoser
- Department of Evolutionary Developmental Biology, Institute of Zoology, University Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Thomas Ederth
- Division of Molecular Physics, Department of Physics, Chemistry and Biology (IFM), Linköping University, 581 83 Linköping, Sweden
| | - Ute Rothbächer
- Department of Evolutionary Developmental Biology, Institute of Zoology, University Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
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Zeng F, Wunderer J, Salvenmoser W, Hess MW, Ladurner P, Rothbächer U. Papillae revisited and the nature of the adhesive secreting collocytes. Dev Biol 2019; 448:183-198. [DOI: 10.1016/j.ydbio.2018.11.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 11/26/2022]
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Karabulut A, He S, Chen CY, McKinney SA, Gibson MC. Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone, Nematostella vectensis. Dev Biol 2019; 448:7-15. [PMID: 30641041 DOI: 10.1016/j.ydbio.2019.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/18/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
Abstract
A mechanistic understanding of evolutionary developmental biology requires the development of novel techniques for the manipulation of gene function in phylogenetically diverse organismal systems. Recently, gene-specific knockdown by microinjection of short hairpin RNA (shRNA) was applied in the sea anemone Nematostella vectensis, demonstrating that the shRNA approach can be used for efficient and robust sequence-specific knockdown of a gene of interest. However, the time- and labor-intensive process of microinjection limits access to this technique and its application in large scale experiments. To address this issue, here we present an electroporation protocol for shRNA delivery into Nematostella eggs. This method leverages the speed and simplicity of electroporation, enabling users to manipulate gene expression in hundreds of eggs or embryos within minutes. We provide a detailed description of the experimental procedure, including reagents, electroporation conditions, preparation of Nematostella eggs, and follow-up care of experimental animals. Finally, we demonstrate the knockdown of several endogenous and exogenous genes with known phenotypes and discuss the potential applications of this method.
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Affiliation(s)
- Ahmet Karabulut
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Shuonan He
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Cheng-Yi Chen
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Sean A McKinney
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Matthew C Gibson
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA; Dept. Anatomy and Cell Biology, University of Kansas School of Medicine, Kansas City, KS 66160 USA.
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Shimai K, Kusakabe TG. The Use of cis-Regulatory DNAs as Molecular Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [DOI: 10.1007/978-981-10-7545-2_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Zeller RW. Electroporation in Ascidians: History, Theory and Protocols. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [PMID: 29542079 DOI: 10.1007/978-981-10-7545-2_5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Embryonic development depends on the orchestration of hundreds of regulatory and structural genes to initiate expression at the proper time, in the correct spatial domain(s), and in the amounts required for cells and tissues to become specified, determined, and ultimately to differentiate into a multicellular embryo. One of the key approaches to studying embryonic development is the generation of transgenic animals in which recombinant DNA molecules are transiently or stably introduced into embryos to alter gene expression, to manipulate gene function or to serve as reporters for specific cell types or subcellular compartments. In some model systems, such as the mouse, well-defined approaches for generating transgenic animals have been developed. In other systems, particularly non-model systems, a key challenge is to find a way of introducing molecules or other reagents into cells that produces large numbers of embryos with a minimal effect on normal development. A variety of methods have been developed, including the use of viral vectors, microinjection, and electroporation. Here, I describe how electroporation was adapted to generate transgenic embryos in the ascidian, a nontraditional invertebrate chordate model that is particularly well-suited for studying gene regulatory activity during development. I present a review of the electroporation process, describe how electroporation was first implemented in the ascidian, and provide a series of protocols describing the electroporation process, as implemented in our laboratory.
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Affiliation(s)
- Robert W Zeller
- Center for Applied and Experimental Genomics, Department of Biology, San Diego State University, San Diego, CA, USA.
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