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Popsuj S, Cohen L, Ward S, Lewis A, Yoshida S, Herrera RA, Cota CD, Stolfi A. CRISPR/Cas9 protocols for disrupting gene function in the non-vertebrate chordate Ciona. Integr Comp Biol 2024:icae108. [PMID: 38982335 DOI: 10.1093/icb/icae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024] Open
Abstract
The evolutionary origins of chordates and their diversification into the three major subphyla of tunicates, vertebrates, and cephalochordates pose myriad questions about the genetic and developmental mechanisms underlying this radiation. Studies in non-vertebrate chordates have refined our model of what the ancestral chordate may have looked like, and have revealed the pre-vertebrate origins of key cellular and developmental traits. Work in the major tunicate laboratory model Ciona has benefitted greatly from the emergence of CRISPR/Cas9 techniques for targeted gene disruption. Here we review some of the important findings made possible by CRISPR in Ciona, and present our latest protocols and recommended practices for plasmid-based, tissue-specific CRISPR/Cas9-mediated mutagenesis.
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Affiliation(s)
- Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lindsey Cohen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Sydney Ward
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Agnes Scott College, Decatur, GA, 30030, USA
| | - Arabella Lewis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Agnes Scott College, Decatur, GA, 30030, USA
| | | | | | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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Frese AN, Mariossi A, Levine MS, Wühr M. Quantitative proteome dynamics across embryogenesis in a model chordate. iScience 2024; 27:109355. [PMID: 38510129 PMCID: PMC10951915 DOI: 10.1016/j.isci.2024.109355] [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: 08/14/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
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Affiliation(s)
- Alexander N. Frese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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Smith HM, Khairallah SM, Nguyen AH, Newman-Smith E, Smith WC. Misregulation of cell adhesion molecules in the Ciona neural tube closure mutant bugeye. Dev Biol 2021; 480:14-24. [PMID: 34407458 DOI: 10.1016/j.ydbio.2021.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/16/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
Neural tube closure (NTC) is a complex multi-step morphogenetic process that transforms the flat neural plate found on the surface of the post-gastrulation embryo into the hollow and subsurface central nervous system (CNS). Errors in this process underlie some of the most prevalent human birth defects, and occur in about 1 out of every 1000 births. Previously, we discovered a mutant in the basal chordate Ciona savignyi (named bugeye) that revealed a novel role for a T-Type Calcium Channel (Cav3) in this process. Moreover, the requirement for CAV3s in Xenopus NTC suggests a conserved function among the chordates. Loss of CAV3 leads to defects restricted to anterior NTC, with the brain apparently fully developed, but protruding from the head. Here we report first on a new Cav3 mutant in the related species C. robusta. RNAseq analysis of both C. robusta and C. savignyi bugeye mutants reveals misregulation of a number of transcripts including ones that are involved in cell-cell recognition and adhesion. Two in particular, Selectin and Fibronectin leucine-rich repeat transmembrane, which are aberrantly upregulated in the mutant, are expressed in the closing neural tube, and when disrupted by CRISPR gene editing lead to the open brain phenotype displayed in bugeye mutants. We speculate that these molecules play a transient role in tissue separation and adhesion during NTC and failure to downregulate them leads to an open neural tube.
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Affiliation(s)
- Haley M Smith
- Department of Molecular, Cellular and Developmental Biology, USA
| | | | - Ann Hong Nguyen
- Department of Molecular, Cellular and Developmental Biology, USA
| | | | - William C Smith
- Department of Molecular, Cellular and Developmental Biology, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.
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Nydam ML, Yanckello LM, Bialik SB, Giesbrecht KB, Nation GK, Peak JL. Introgression in two species of broadcast spawning marine invertebrate. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Lemaire P, Piette J. Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley. Open Biol 2016; 5:150053. [PMID: 26085517 PMCID: PMC4632506 DOI: 10.1098/rsob.150053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology. We also briefly comment on the more philosophical reflections of Huxley on individuality. In the second part, we stress the originality and relevance of past and future studies of tunicates in the resolution of major biological issues. In particular, we focus on the complex relationship between genotype and phenotype and the phenomenon of developmental system drift. We propose that more than 150 years after Huxley's papers, tunicate embryos are still worth studying in their own right, independently of their evolutionary proximity to vertebrates, as they provide original and crucial insights into the process of animal evolution. Tunicates are still at the forefront of biological research.
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Affiliation(s)
- Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire. UMR 5237, Centre National de la Recherche Scientifique, Université de Montpellier, 1919 Route de Mende, 34293, Montpellier cedex 5, France
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Morales Diaz H, Mejares E, Newman-Smith E, Smith WC. ACAM, a novel member of the neural IgCAM family, mediates anterior neural tube closure in a primitive chordate. Dev Biol 2016; 409:288-296. [PMID: 26542009 DOI: 10.1016/j.ydbio.2015.10.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 01/18/2023]
Abstract
The neural IgCAM family of cell adhesion molecules, which includes NCAM and related molecules, has evolved via gene duplication and alternative splicing to allow for a wide range of isoforms with distinct functions and homophilic binding properties. A search for neural IgCAMs in ascidians (Ciona intestinalis, Ciona savignyi, and Phallusia mammillata) has identified a novel set of truncated family members that, unlike the known members, lack fibronectin III domains and consist of only repeated Ig domains. Within the tunicates this form appears to be unique to the ascidians, and it was designated ACAM, for Ascidian Cell Adhesion Molecule. In C. intestinalis ACAM is expressed in the developing neural plate and neural tube, with strongest expression in the anterior sensory vesicle precursor. Unlike the two other conventional neural IgCAMs in C. intestinalis, which are expressed maternally and throughout the morula and blastula stages, ACAM expression initiates at the gastrula stage. Moreover, C. intestinalis ACAM is a target of the homeodomain transcription factor OTX, which plays an essential role in the development of the anterior central nervous system. Morpholino (MO) knockdown shows that ACAM is required for neural tube closure. In MO-injected embryos neural tube closure was normal caudally, but the anterior neuropore remained open. A similar phenotype was seen with overexpression of a secreted version of ACAM. The presence of ACAM in ascidians highlights the diversity of this gene family in morphogenesis and neurodevelopment.
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Affiliation(s)
- Heidi Morales Diaz
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - Emil Mejares
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - Erin Newman-Smith
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - William C Smith
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States.
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Abdul-Wajid S, Morales-Diaz H, Khairallah SM, Smith WC. T-type Calcium Channel Regulation of Neural Tube Closure and EphrinA/EPHA Expression. Cell Rep 2015; 13:829-839. [PMID: 26489462 DOI: 10.1016/j.celrep.2015.09.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 08/06/2015] [Accepted: 09/11/2015] [Indexed: 10/22/2022] Open
Abstract
A major class of human birth defects arise from aberrations during neural tube closure (NTC). We report on a NTC signaling pathway requiring T-type calcium channels (TTCCs) that is conserved between primitive chordates (Ciona) and Xenopus. With loss of TTCCs, there is a failure to seal the anterior neural folds. Accompanying loss of TTCCs is an upregulation of EphrinA effectors. Ephrin signaling is known to be important in NTC, and ephrins can affect both cell adhesion and repulsion. In Ciona, ephrinA-d expression is downregulated at the end of neurulation, whereas, with loss of TTCC, ephrinA-d remains elevated. Accordingly, overexpression of ephrinA-d phenocopied TTCC loss of function, while overexpression of a dominant-negative Ephrin receptor was able to rescue NTC in a Ciona TTCC mutant. We hypothesize that signaling through TTCCs is necessary for proper anterior NTC through downregulation of ephrins, and possibly elimination of a repulsive signal.
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Affiliation(s)
- Sarah Abdul-Wajid
- Department of Molecular, Cell and Developmental Biology, and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Heidi Morales-Diaz
- Department of Molecular, Cell and Developmental Biology, and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Stephanie M Khairallah
- Department of Molecular, Cell and Developmental Biology, and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - William C Smith
- Department of Molecular, Cell and Developmental Biology, and Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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Crocetta F, Marino R, Cirino P, Macina A, Staiano L, Esposito R, Pezzotti MR, Racioppi C, Toscano F, De Felice E, Locascio A, Ristoratore F, Spagnuolo A, Zanetti L, Branno M, Sordino P. Mutation studies in ascidians: a review. Genesis 2014; 53:160-9. [PMID: 25395385 DOI: 10.1002/dvg.22837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022]
Abstract
Historically, mutations have had a significant impact on the study of developmental processes and phenotypic evolution. Lesions in DNA are created by artificial methods or detected by natural genetic variation. Random mutations are then ascribed to genetic change by direct sequencing or positional cloning. Tunicate species of the ascidian genus Ciona represent nearly fully realized model systems in which gene function can be investigated in depth. Additionally, tunicates are valuable organisms for the study of naturally occurring mutations due to the capability to exploit genetic variation down to the molecular level. Here, we summarize the available information about how mutations are studied in ascidians with examples of insights that have resulted from these applications. We also describe notions and methodologies that might be useful for the implementation of easy and tight procedures for mutations studies in Ciona.
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Affiliation(s)
- Fabio Crocetta
- Laboratory of Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
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