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Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024; 15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [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: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.
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Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Diana S José-Edwards
- Post-Baccalaureate Premedical Program, Washington University, St. Louis, MO, 63130, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
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2
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Di Gregorio A. The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates. Curr Top Dev Biol 2020; 139:325-374. [PMID: 32450965 DOI: 10.1016/bs.ctdb.2020.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The notochord is a structure required for support and patterning of all chordate embryos, from sea squirts to humans. An increasing amount of information on notochord development and on the molecular strategies that ensure its proper morphogenesis has been gleaned through studies in the sea squirt Ciona. This invertebrate chordate offers a fortunate combination of experimental advantages, ranging from translucent, fast-developing embryos to a compact genome and impressive biomolecular resources. These assets have enabled the rapid identification of numerous notochord genes and cis-regulatory regions, and provide a rather unique opportunity to reconstruct the gene regulatory network that controls the formation of this developmental and evolutionary chordate landmark. This chapter summarizes the morphogenetic milestones that punctuate notochord formation in Ciona, their molecular effectors, and the current knowledge of the gene regulatory network that ensures the accurate spatial and temporal orchestration of these processes.
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Affiliation(s)
- Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, United States.
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3
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Pickett CJ, Zeller RW. Efficient genome editing using CRISPR-Cas-mediated homology directed repair in the ascidian Ciona robusta. Genesis 2018; 56:e23260. [PMID: 30375719 DOI: 10.1002/dvg.23260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/21/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
Eliminating or silencing a gene's level of activity is one of the classic approaches developmental biologists employ to determine a gene's function. A recently developed method of gene perturbation called CRISPR-Cas, which was derived from a prokaryotic adaptive immune system, has been adapted for use in eukaryotic cells. This technology has been established in several model organisms as a powerful and efficient tool for knocking out or knocking down the function of a gene of interest. It has been recently shown that CRISPR-Cas functions with fidelity and efficiency in Ciona robusta. Here, we show that in C. robusta CRISPR-Cas mediated genomic knock-ins can be efficiently generated. Electroporating a tissue-specific transgene driving Cas9 and a U6-driven gRNA transgene together with a fluorescent protein-containing homology directed repair (FP-HDR) template results in gene-specific patterns of fluorescence consistent with a targeted genomic insertion. Using the Tyrosinase locus to optimize reagents, we first characterize a new Pol III promoter for expressing gRNAs from the Ciona savignyi H1 gene, and then adapt technology that flanks gRNAs by ribozymes allowing cell-specific expression from Pol II promoters. Next, we examine homology arm-length efficiencies of FP-HDR templates. Reagents were then developed for targeting Brachyury and Pou4 that resulted in expected patterns of fluorescence, and sequenced PCR amplicons derived from single embryos validated predicted genomic insertions. Finally, using two differentially colored FP-HDR templates, we show that biallelic FP-HDR template insertion can be detected in live embryos of the F0 generation.
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Affiliation(s)
- C J Pickett
- Department of Biology, San Diego State University, San Diego, California
| | - Robert W Zeller
- Department of Biology, San Diego State University, San Diego, California.,Coastal and Marine Institute, San Diego State University, San Diego, California.,Center for Applied and Experimental Genomics, San Diego State University, San Diego, California
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4
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Tominaga H, Satoh N, Ueno N, Takahashi H. Enhancer activities of amphioxus Brachyury genes in embryos of the ascidian, Ciona intestinalis. Genesis 2018; 56:e23240. [PMID: 30113767 DOI: 10.1002/dvg.23240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/09/2018] [Accepted: 07/14/2018] [Indexed: 12/22/2022]
Abstract
The notochord and somites are distinctive chordate structures. The T-box transcription factor gene, Brachyury, is expressed in notochord and plays a pivotal role in its formation. In the cephalochordate, Branchiostoma floridae, Brachyury is duplicated into BfBra1 and BfBra2, which are expressed in the somite-formation region as well. In a series of experiments to elucidate the regulatory machinery of chordate Brachyury expression, we carried out a lacZ reporter assay of BfBra in embryos of the urochordate, Ciona intestinalis. Vista analyses suggest the presence of conserved non-coding sequences, not only in the 5'-upstream, but also in the 3'-downstream and in introns of BfBra. We found that: (1) 5'-upstream sequences of both BfBra1 and BfBra2 promote lacZ expression in muscle cells, (2) 3'-downstream sequences have enhancer activity that promotes lacZ expression in notochord cells, and (3) introns of BfBra2 and BfBra1 exhibit lacZ expression preferentially in muscle and notochord cells. These results suggest shared cephalochordate Brachyury enhancer machinery that also works in urochordates. We discuss the results in relation to evolutionary modification of Brachyury expression in formation of chordate-specific organs characteristic of each lineage.
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Affiliation(s)
- Hitoshi Tominaga
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Hiroki Takahashi
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
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5
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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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Tolkin T, Christiaen L. Rewiring of an ancestral Tbx1/10-Ebf-Mrf network for pharyngeal muscle specification in distinct embryonic lineages. Development 2017; 143:3852-3862. [PMID: 27802138 DOI: 10.1242/dev.136267] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/30/2016] [Indexed: 01/01/2023]
Abstract
Skeletal muscles arise from diverse embryonic origins in vertebrates, yet converge on extensively shared regulatory programs that require muscle regulatory factor (MRF)-family genes. Myogenesis in the tail of the simple chordate Ciona exhibits a similar reliance on its single MRF-family gene, and diverse mechanisms activate Ci-Mrf Here, we show that myogenesis in the atrial siphon muscles (ASMs) and oral siphon muscles (OSMs), which control the exhalant and inhalant siphons, respectively, also requires Mrf We characterize the ontogeny of OSM progenitors and compare the molecular basis of Mrf activation in OSM versus ASM. In both muscle types, Ebf and Tbx1/10 are expressed and function upstream of Mrf However, we demonstrate that regulatory relationships between Tbx1/10, Ebf and Mrf differ between the OSM and ASM lineages. We propose that Tbx1, Ebf and Mrf homologs form an ancient conserved regulatory state for pharyngeal muscle specification, whereas their regulatory relationships might be more evolutionarily variable.
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Affiliation(s)
- Theadora Tolkin
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
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Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A, Fujiwara S, Gineste M, Lowe EK, Piette J, Racioppi C, Ristoratore F, Sasakura Y, Takatori N, Brown TC, Delsuc F, Douzery E, Gissi C, McDougall A, Nishida H, Sawada H, Swalla BJ, Yasuo H, Lemaire P. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res 2016; 44:D808-18. [PMID: 26420834 PMCID: PMC4702943 DOI: 10.1093/nar/gkv966] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/14/2015] [Indexed: 11/24/2022] Open
Abstract
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
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Affiliation(s)
- Matija Brozovic
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Cyril Martin
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Christelle Dantec
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Delphine Dauga
- Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France Bioself Communication, 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Mickaël Mendez
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Paul Simion
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Madeline Percher
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Baptiste Laporte
- Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France
| | - Céline Scornavacca
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Shigeki Fujiwara
- Department of Applied Science, Kochi University, Kochi-shi, Kochi 780-8520, Japan
| | - Mathieu Gineste
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Filomena Ristoratore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Naohito Takatori
- Developmental Biology Laboratory, Department of Biological Sciences, School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiooji, Tokyo 192-0397, Japan Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Titus C Brown
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Emmanuel Douzery
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Carmela Gissi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Alex McDougall
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba 517-0004, Japan
| | - Billie J Swalla
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Hitoyoshi Yasuo
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France
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8
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José-Edwards DS, Oda-Ishii I, Kugler JE, Passamaneck YJ, Katikala L, Nibu Y, Di Gregorio A. Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet 2015; 11:e1005730. [PMID: 26684323 PMCID: PMC4684326 DOI: 10.1371/journal.pgen.1005730] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022] Open
Abstract
A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.
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Affiliation(s)
- Diana S. José-Edwards
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Izumi Oda-Ishii
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Jamie E. Kugler
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Yale J. Passamaneck
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Lavanya Katikala
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Yutaka Nibu
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Anna Di Gregorio
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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9
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Kourakis MJ, Smith WC. An organismal perspective on C. intestinalis development, origins and diversification. eLife 2015; 4. [PMID: 25807088 PMCID: PMC4373457 DOI: 10.7554/elife.06024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/10/2015] [Indexed: 11/13/2022] Open
Abstract
The ascidian Ciona intestinalis, commonly known as a 'sea squirt', has become an important model for embryological studies, offering a simple blueprint for chordate development. As a model organism, it offers the following: a small, compact genome; a free swimming larva with only about 2600 cells; and an embryogenesis that unfolds according to a predictable program of cell division. Moreover, recent phylogenies reveal that C. intestinalis occupies a privileged branch in the tree of life: it is our nearest invertebrate relative. Here, we provide an organismal perspective of C. intestinalis, highlighting aspects of its life history and habitat-from its brief journey as a larva to its radical metamorphosis into adult form-and relate these features to its utility as a laboratory model.
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Affiliation(s)
- Matthew J Kourakis
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
| | - William C Smith
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States
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10
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Vassalli QA, Anishchenko E, Caputi L, Sordino P, D'Aniello S, Locascio A. Regulatory elements retained during chordate evolution: Coming across tunicates. Genesis 2014; 53:66-81. [DOI: 10.1002/dvg.22838] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/06/2014] [Accepted: 11/11/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Quirino Attilio Vassalli
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Evgeniya Anishchenko
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Luigi Caputi
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Paolo Sordino
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
- CNR ISAFOM, Institute for Agricultural and Forest Systems in the Mediterranean, Unitá organizzativa di supporto; Catania Italy
| | - Salvatore D'Aniello
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
| | - Annamaria Locascio
- Cellular and Developmental Biology Laboratory; Stazione Zoologica Anton Dohrn; Villa Comunale Naples Italy
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11
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Irvine SQ. Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. Curr Genomics 2013; 14:56-67. [PMID: 23997651 PMCID: PMC3580780 DOI: 10.2174/138920213804999192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/30/2012] [Accepted: 01/01/2013] [Indexed: 01/31/2023] Open
Abstract
The ascidian (sea squirt) C. intestinalis has become an important model organism for the study of cis-regulation. This is largely due to the technology that has been developed for assessing cis-regulatory activity through the use of transient reporter transgenes introduced into fertilized eggs. This technique allows the rapid and inexpensive testing of endogenous or altered DNA for regulatory activity in vivo. This review examines evidence that C. intestinaliscis-regulatory elements are located more closely to coding regions than in other model organisms. I go on to compare the organization of cis-regulatory elements and conserved non-coding sequences in Ciona, mammals, and other deuterostomes for three representative C.intestinalis genes, Pax6, FoxAa, and the DlxA-B cluster, along with homologs in the other species. These comparisons point out some of the similarities and differences between cis-regulatory elements and their study in the various model organisms. Finally, I provide illustrations of how C. intestinalis lends itself to detailed study of the structure of cis-regulatory elements, which have led, and promise to continue to lead, to important insights into the fundamentals of transcriptional regulation.
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Affiliation(s)
- Steven Q Irvine
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
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