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Satake H, Sasakura Y. The neuroendocrine system of Ciona intestinalis Type A, a deuterostome invertebrate and the closest relative of vertebrates. Mol Cell Endocrinol 2024; 582:112122. [PMID: 38109989 DOI: 10.1016/j.mce.2023.112122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/20/2023]
Abstract
Deuterostome invertebrates, including echinoderms, hemichordates, cephalochordates, and urochordates, exhibit common and species-specific morphological, developmental, physiological, and behavioral characteristics that are regulated by neuroendocrine and nervous systems. Over the past 15 years, omics, genetic, and/or physiological studies on deuterostome invertebrates have identified low-molecular-weight transmitters, neuropeptides and their cognate receptors, and have clarified their various biological functions. In particular, there has been increasing interest on the neuroendocrine and nervous systems of Ciona intestinalis Type A, which belongs to the subphylum Urochordata and occupies the critical phylogenetic position as the closest relative of vertebrates. During the developmental stage, gamma-aminobutylic acid, D-serine, and gonadotropin-releasing hormones regulate metamorphosis of Ciona. In adults, the neuropeptidergic mechanisms underlying ovarian follicle growth, oocyte maturation, and ovulation have been elucidated. This review article provides the most recent and fundamental knowledge of the neuroendocrine and nervous systems of Ciona, and their evolutionary aspects.
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Affiliation(s)
- Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
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Yamakawa S, Sasakura Y, Morino Y, Wada H. Detection of TALEN-mediated genome cleavage during the early embryonic stage of the starfish Patiria pectinifera. Dev Dyn 2023; 252:1471-1481. [PMID: 37431812 DOI: 10.1002/dvdy.641] [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: 12/10/2022] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Echinoderms have long been utilized as experimental materials to study the genetic control of developmental processes and their evolution. Among echinoderms, the molecular study of starfish embryos has received considerable attention across research topics such as gene regulatory network evolution and larval regeneration. Recently, experimental techniques to manipulate gene functions have been gradually established in starfish as the feasibility of genome editing methods was reported. However, it is still unclear when these techniques cause genome cleavage during the development of starfish, which is critical to understand the timeframe and applicability of the experiment during early development of starfish. RESULTS We herein reported that gene functions can be analyzed by the genome editing method TALEN in early embryos, such as the blastula of the starfish Patiria pectinifera. We injected the mRNA of TALEN targeting rar, which was previously constructed, into eggs of P. pectinifera and examined the efficiency of genome cleavage through developmental stages from 6 to 48 hours post fertilization. CONCLUSION The results will be key knowledge not only when designing TALEN-based experiments but also when assessing the results.
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Affiliation(s)
- Shumpei Yamakawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Li KL, Nakashima K, Hisata K, Satoh N. Expression and possible functions of a horizontally transferred glycosyl hydrolase gene, GH6-1, in Ciona embryogenesis. EvoDevo 2023; 14:11. [PMID: 37434168 DOI: 10.1186/s13227-023-00215-x] [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: 02/27/2023] [Accepted: 07/01/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND The Tunicata or Urochordata is the only animal group with the ability to synthesize cellulose directly and cellulose is a component of the tunic that covers the entire tunicate body. The genome of Ciona intestinalis type A contains a cellulose synthase gene, CesA, that it acquired via an ancient, horizontal gene transfer. CesA is expressed in embryonic epidermal cells and functions in cellulose production. Ciona CesA is composed of both a glycosyltransferase domain, GT2, and a glycosyl hydrolase domain, GH6, which shows a mutation at a key position and seems functionless. Interestingly, the Ciona genome contains a glycosyl hydrolase gene, GH6-1, in which the GH6 domain seems intact. This suggests expression and possible functions of GH6-1 during Ciona embryogenesis. Is GH6-1 expressed during embryogenesis? If so, in what tissues is the gene expressed? Does GH6-1 serve a function? If so, what is it? Answers to these questions may advance our understanding of evolution of this unique animal group. RESULTS Quantitative reverse transcription PCR and in situ hybridization revealed that GH6-1 is expressed in epidermis of tailbud embryos and in early swimming larvae, a pattern similar to that of CesA. Expression is downregulated at later stages and becomes undetectable in metamorphosed juveniles. The GH6-1 expression level is higher in the anterior-trunk region and caudal-tip regions of late embryos. Single-cell RNA sequencing analysis of the late tailbud stage showed that cells of three clusters with epidermal identity express GH6-1, and that some of them co-express CesA. TALEN-mediated genome editing was used to generate GH6-1 knockout Ciona larvae. Around half of TALEN-electroporated larvae showed abnormal development of adhesive papillae and altered distribution of surface cellulose. In addition, three-fourths of TALEN-electroporated animals failed to complete larval metamorphosis. CONCLUSIONS This study showed that tunicate GH6-1, a gene that originated by horizontal gene transfer of a prokaryote gene, is recruited into the ascidian genome, and that it is expressed and functions in epidermal cells of ascidian embryos. Although further research is required, this observation demonstrates that both CesA and GH6-1 are involved in tunicate cellulose metabolism, impacting tunicate morphology and ecology.
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Affiliation(s)
- Kun-Lung Li
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei City, 115, Taiwan.
| | - Keisuke Nakashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
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Sakuma T, Yamamoto T. Updated Overview of TALEN Construction Systems. Methods Mol Biol 2023; 2637:27-39. [PMID: 36773135 DOI: 10.1007/978-1-0716-3016-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Transcription activator-like effector (TALE) nuclease (TALEN) is the second-generation genome editing tool consisting of TALE protein containing customizable DNA-binding repeats and nuclease domain of FokI enzyme. Each DNA-binding repeat recognizes one base of double-strand DNA, and functional TALEN can be created by a simple modular assembly of these repeats. To easily and efficiently assemble the highly repetitive DNA-binding repeat arrays, various construction systems such as Golden Gate assembly, serial ligation, and ligation-independent cloning have been reported. In this chapter, we summarize the updated situation of these systems and publicly available reagents and protocols, enabling optimal selection of best suited systems for every researcher who wants to utilize TALENs in various research fields.
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Affiliation(s)
- Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
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Improved Genome Editing in the Ascidian Ciona with CRISPR/Cas9 and TALEN. Methods Mol Biol 2023; 2637:375-388. [PMID: 36773161 DOI: 10.1007/978-1-0716-3016-7_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The ascidian Ciona intestinalis type A (or Ciona robusta) is an important organism for elucidating the mechanisms that make the chordate body plan. CRISPR/Cas9 and TAL effector nuclease (TALEN) are widely used to quickly address genetic functions in Ciona. Our previously reported method of CRISPR/Cas9-mediated mutagenesis in this animal has inferior mutation rates compared to those of TALENs. We here describe an updated way to effectively mutate genes with CRISPR/Cas9 in Ciona. Although the construction of TALENs is much more laborious than that of CRISPR/Cas9, this technique is useful for tissue-specific knockouts that are not easy even by the optimized CRISPR/Cas9 method.
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Yamagishi M, Huang T, Hozumi A, Onuma TA, Sasakura Y, Ogasawara M. Differentiation of endostyle cells by Nkx2-1 and FoxE in the ascidian Ciona intestinalis type A: insights into shared gene regulation in glandular- and thyroid-equivalent elements of the chordate endostyle. Cell Tissue Res 2022; 390:189-205. [PMID: 36048302 DOI: 10.1007/s00441-022-03679-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
Due to similarities in iodine concentrations and peroxidase activities, the thyroid in vertebrates is considered to originate from the endostyle of invertebrate chordates even though it is a glandular (mucus-producing) organ for aquatic suspension feeding. Among chordates with an endostyle, urochordates are useful evolutionary research models for the study of vertebrate traits. The ascidian Ciona intestinalis forms an endostyle with specific components of glandular- and thyroid-related elements, and molecular markers have been identified for these components. Since we previously examined a simple endostyle in the larvacean Oikopleura dioica, the expression of the thyroid-related transcription factor genes, Ciona Nkx2-1 and FoxE, was perturbed by TALEN-mediated gene knockout in the present study to elucidate the shared and/or divergent features of a complex ascidian endostyle. The knockout of Ciona Nkx2-1 and FoxE exerted different effects on the morphology of the developing endostyle. The knockout of Nkx2-1 eliminated the expression of both glandular and thyroidal differentiation marker genes, e.g., vWFL1, vWFL2, CiEnds1, TPO, and Duox, while that of FoxE eliminated the expression of the differentiation marker genes, TPO and CiEnds1. The supporting element-related expression of Pax2/5/8a, Pax2/5/8b, FoxQ1, and β-tubulin persisted in the hypoplastic endostyles of Nkx2-1- and FoxE-knockout juveniles. Although the gene regulation of ascidian-specific CiEnds1 remains unclear, these results provide insights into the evolution of the vertebrate thyroid as well as the urochordate endostyle.
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Affiliation(s)
- Masayuki Yamagishi
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan
| | - Taoruo Huang
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima-shi, Kagoshima, 890-0065, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Michio Ogasawara
- Department of Biology, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, 263-8522, Japan.
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Sakamoto A, Hozumi A, Shiraishi A, Satake H, Horie T, Sasakura Y. The
TRP
channel
PKD2
is involved in sensing the mechanical stimulus of adhesion for initiating metamorphosis in the chordate
Ciona. Dev Growth Differ 2022; 64:395-408. [DOI: 10.1111/dgd.12801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Aya Sakamoto
- Shimoda Marine Research Center University of Tsukuba, Shimoda Shizuoka Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center University of Tsukuba, Shimoda Shizuoka Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences Kyoto Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences Kyoto Japan
| | - Takeo Horie
- Shimoda Marine Research Center University of Tsukuba, Shimoda Shizuoka Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center University of Tsukuba, Shimoda Shizuoka Japan
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Yaguchi S, Yaguchi J. Temnopleurus reevesii as a new sea urchin model in genetics. Dev Growth Differ 2021; 64:59-66. [PMID: 34923630 DOI: 10.1111/dgd.12768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
Abstract
Echinoderms, including sea urchins and starfish, have played important roles in cell, developmental and evolutionary biology research for more than a century. However, since most of them take a long time to mature sexually and their breeding seasons are limited, it has been difficult to obtain subsequent generations in the laboratory, resulting in them not being recognized as model organisms in recent genetics research. To overcome this issue, we maintained and obtained gametes from several nonmodel sea urchins in Japan and finally identified Temnopleurus reevesii as a suitable model for sea urchin genetics. Genomic and transcriptomic information was obtained for this model, and the DNA database TrBase was made publicly available. In this review, we describe how we found this species useful for biological research and show an example of CRISPR/Cas9 based knockout sea urchin.
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Affiliation(s)
- Shunsuke Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan.,PRESTO, JST, 4-1-8 Honcho, Kawaguchi, 332-0012, Japan
| | - Junko Yaguchi
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
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Kawada T, Shiraishi A, Matsubara S, Hozumi A, Horie T, Sasakura Y, Satake H. Vasopressin Promoter Transgenic and Vasopressin Gene-Edited Ascidian, Ciona intestinalis Type A ( Ciona robusta): Innervation, Gene Expression Profiles, and Phenotypes. Front Endocrinol (Lausanne) 2021; 12:668564. [PMID: 34025581 PMCID: PMC8135067 DOI: 10.3389/fendo.2021.668564] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/25/2021] [Indexed: 01/03/2023] Open
Abstract
Oxytocin (OT) and vasopressin (VP) superfamily neuropeptides are distributed in not only vertebrates but also diverse invertebrates. However, no VPergic innervation of invertebrates has ever been documented. In the ascidian, Ciona intestinalis Type A (Ciona robusta), an OT/VP superfamily peptide was identified, and the Ciona vasopressin (CiVP) induces oocyte maturation and ovulation. In the present study, we characterize the innervation and phenotypes of genetically modified Ciona: CiVP promoter-Venus transgenic and CiVP mutants. CiVP promoter-Venus transgenic Ciona demonstrated that CiVP gene was highly expressed in the cerebral ganglion and several nerves. Fluorescence was also detected in the ovary of young CiVP promoter-Venus transgenic ascidians, suggesting that the CiVP gene is also expressed temporarily in the ovary of young ascidians. Furthermore, a marked decrease of post-vitellogenic (stage III) follicles was observed in the ovary of CiVP mutants, whereas pre-vitellogenic (stage I) and vitellogenic (stage II) follicles were increased in the mutant ovary, compared with that of wildtype Ciona. Gene expression profiles showed that the expression of various genes, including genes related to ovarian follicle growth, was altered in the ovary of CiVP mutants. Altogether, these results indicated that CiVP, mainly as a neuropeptide, plays pivotal roles in diverse biological functions, including growth of early-stage ovarian follicles via regulation of the expression of a wide variety of genes. This is the first report describing a VP gene promoter-transgenic and VP gene-edited invertebrate and also on its gene expression profiles and phenotypes.
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Affiliation(s)
- Tsuyoshi Kawada
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Takeo Horie
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
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Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1236-1280. [PMID: 33893979 DOI: 10.1007/s11427-020-1915-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery. Considering the tremendous biodiversity of our planet, the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments. The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms. In this review, we review the recent work on the regulatory signaling of developmental and regeneration processes, environmental adaptation, and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila, and the emerging nonstandard model organisms including amphioxus, ascidian, ciliates, single-celled phytoplankton, and marine nematode. In addition, the challenging questions and new directions in these systems are outlined as well.
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Yamaji S, Hozumi A, Matsunobu S, Sasakura Y. Orchestration of the distinct morphogenetic movements in different tissues drives tail regression during ascidian metamorphosis. Dev Biol 2020; 465:66-78. [PMID: 32697971 DOI: 10.1016/j.ydbio.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/10/2020] [Accepted: 07/11/2020] [Indexed: 11/26/2022]
Abstract
Metamorphosis is the dramatic conversion of an animal body from larva to adult. In ascidians, tadpole-shaped, swimming larvae become sessile juveniles by losing their tail during metamorphosis. This study investigated the cellular and molecular mechanisms underlying this metamorphic event called tail regression, in the model ascidian Ciona. The ascidian tail consists of internal organs such as muscle, notochord, nerve cord, and the outer epidermal layer surrounding them. We found that the epidermis and internal organs show different regression strategies. Epidermal cells are shortened along the anterior-posterior axis and gather at the posterior region. The epidermal mass is then invaginated into the trunk by apical constriction. The internal tissues, by contrast, enter into the trunk by forming coils. During coiling, notches are introduced into the muscle cells, which likely reduces their rigidness to promote coiling. Actin filament is the major component necessary for the regression events in both the epidermis and internal tissues. The shortening and invagination of the epidermis depend on the phosphorylation of the myosin regulatory light chain (mrlc) regulated by rho-kinase (ROCK). The coiling of internal tissues does not require ROCK-dependent phosphorylation of mrlc, and they can complete coiling without epidermis, although epidermis can facilitate the coiling of internal tissues. We conclude that tail regression in ascidians consists of active morphogenetic movements in which each tissue's independent mechanism is orchestrated with the others to complete this event within the available time window.
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Affiliation(s)
- Sota Yamaji
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Shohei Matsunobu
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan.
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12
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Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer. Genes (Basel) 2020; 11:genes11080937. [PMID: 32823766 PMCID: PMC7464555 DOI: 10.3390/genes11080937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, CesA, in which a gene, probably transferred from bacteria, greatly impacted tunicate evolution. A Glycosyl Hydrolase Family 6 (GH6) hydrolase-like domain exists at the C-terminus of tunicate CesA, but not in cellulose synthases of other organisms. The recent discovery of another GH6 hydrolase-like gene (GH6-1) in tunicate genomes further raises the question of how tunicates acquired GH6. To examine the probable origin of these genes, we analyzed the phylogenetic relationship of GH6 proteins in tunicates and other organisms. Our analyses show that tunicate GH6s, the GH6-1 gene, and the GH6 part of the CesA gene, form two independent, monophyletic gene groups. We also compared their sequence signatures and exon splice sites. All tunicate species examined have shared splice sites in GH6-containing genes, implying ancient intron acquisitions. It is likely that the tunicate CesA and GH6-1 genes existed in the common ancestor of all extant tunicates.
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Hozumi A, Matsunobu S, Mita K, Treen N, Sugihara T, Horie T, Sakuma T, Yamamoto T, Shiraishi A, Hamada M, Satoh N, Sakurai K, Satake H, Sasakura Y. GABA-Induced GnRH Release Triggers Chordate Metamorphosis. Curr Biol 2020; 30:1555-1561.e4. [PMID: 32220316 DOI: 10.1016/j.cub.2020.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/14/2019] [Accepted: 02/03/2020] [Indexed: 01/13/2023]
Abstract
Metamorphosis, a widespread life history strategy in metazoans, allows dispersal and use of different ecological niches through a dramatic body change from a larval stage [1, 2]. Despite its conservation and importance, the molecular mechanisms underlying its initiation and progression have been characterized in only a few animal models. In this study, through pharmacological and gene functional analyses, we identified neurotransmitters responsible for metamorphosis of the ascidian Ciona. Ciona metamorphosis converts swimming tadpole larvae into vase-like, sessile adults. Here, we show that the neurotransmitter GABA is a key regulator of metamorphosis. We found that gonadotropin-releasing hormone (GnRH) is a downstream neuropeptide of GABA. Although GABA is generally thought of as an inhibitory neurotransmitter, we found that it positively regulates secretion of GnRH through the metabotropic GABA receptor during Ciona metamorphosis. GnRH is necessary for reproductive maturation in vertebrates, and GABA is an important excitatory regulator of GnRH in the hypothalamus during puberty [3, 4]. Our findings reveal another role of the GABA-GnRH axis in the regulation of post-embryonic development in chordates.
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Affiliation(s)
- Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka 415-0025, Japan
| | - Shohei Matsunobu
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka 415-0025, Japan
| | - Kaoru Mita
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka 415-0025, Japan
| | - Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka 415-0025, Japan
| | - Takaho Sugihara
- Department of Biology, Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Takeo Horie
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka 415-0025, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8526, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
| | - Mayuko Hamada
- Ushimado Marine Institute, Okayama University, Okayama 701-4303, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Keisuke Sakurai
- Department of Biology, Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka 415-0025, Japan.
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Sawada H, Yamamoto K, Yamaguchi A, Yamada L, Higuchi A, Nukaya H, Fukuoka M, Sakuma T, Yamamoto T, Sasakura Y, Shirae-Kurabayashi M. Three multi-allelic gene pairs are responsible for self-sterility in the ascidian Ciona intestinalis. Sci Rep 2020; 10:2514. [PMID: 32054881 PMCID: PMC7018956 DOI: 10.1038/s41598-020-59147-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
Many hermaphroditic organisms possess a self-incompatibility system to avoid inbreeding. Although the mechanisms of self-incompatibility in flowering plants are well known, little is known about the mechanisms of self-sterility in hermaphroditic marine invertebrates. Ascidians are hermaphroditic sessile marine invertebrates that release sperm and eggs into the surrounding seawater. Several species, including Ciona intestinalis type A (Ciona robusta), exhibit strict self-sterility. In a previous study, we found that the candidate genes responsible for self-sterility in Ciona reside in chromosome 2q (locus A) and chromosome 7q (locus B). Two pairs of multi-allelic genes, named s(sperm)-Themis-A and v(vitelline-coat)-Themis-A in locus A and s-Themis-B and v-Themis-B in locus B, are responsible for self-sterility. In this study, we identified a third multi-allelic gene pair, s-Themis-B2 and v-Themis-B2, within locus B that is also involved in this system. Genetic analysis revealed that the haplotypes of s/v-Themis-A, s/v-Themis-B and s/v-Themis-B2 play essential roles in self-sterility. When three haplotypes were matched between s-Themis and v-Themis, fertilization never occurred even in nonself crossing. Interestingly, gene targeting of either s/v-Themis-B/B2 or s/v-Themis-A by genome editing enabled self-fertilization. These results indicate that s/v-Themis-A, -B and -B2 are S-determinant genes responsible for self-sterility in the ascidian C. intestinalis type A.
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Affiliation(s)
- Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan.
| | - Kazunori Yamamoto
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
| | - Akira Yamaguchi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
| | - Lixy Yamada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
| | - Arata Higuchi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
| | - Haruhiko Nukaya
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
| | - Masashi Fukuoka
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8526, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Maki Shirae-Kurabayashi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, 517-0004, Japan
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15
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Tajima Y, Hozumi A, Yoshida K, Treen N, Sakuma T, Yamamoto T, Sasakura Y. Hox13 is essential for formation of a sensory organ at the terminal end of the sperm duct in Ciona. Dev Biol 2019; 458:120-131. [PMID: 31682808 DOI: 10.1016/j.ydbio.2019.10.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023]
Abstract
Species-specific traits are thought to have been acquired by natural selection. Transcription factors play central roles in the evolution of species-specific traits. Hox genes encode a set of conserved transcription factors essential for establishing the anterior-posterior body axis of animals. Changes in the expression or function of Hox genes can lead to the diversification of animal-body plans. The tunicate ascidian Ciona intestinalis Type A has an orange-colored structure at the sperm duct terminus. This orange-pigmented organ (OPO) is the characteristic that can distinguish this ascidian from other closely related species. The OPO is formed by the accumulation of orange-pigmented cells (OPCs) that are present throughout the adult body. We show that Hox13 is essential for formation of the OPO. Hox13 is expressed in the epithelium of the sperm duct and neurons surrounding the terminal openings for sperm ejection, while OPCs themselves do not express this gene. OPCs are mobile cells that can move through the body vasculature by pseudopodia, suggesting that the OPO is formed by the accumulation of OPCs guided by Hox13-positive cells. Another ascidian species, Ciona savignyi, does not have an OPO. Like Hox13 of C. intestinalis, Hox13 of C. savignyi is expressed at the terminus of its sperm duct; however, its expression domain is limited to the circular area around the openings. The genetic changes responsible for the acquisition or loss of OPO are likely to occur in the expression pattern of Hox13.
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Affiliation(s)
- Yukako Tajima
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Keita Yoshida
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan.
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16
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Igarashi K, Funakoshi M, Kato S, Moriwaki T, Kato Y, Zhang-Akiyama QM. CiApex1 has AP endonuclease activity and abrogated AP site repair disrupts early embryonic development in Ciona intestinalis. Genes Genet Syst 2019; 94:81-93. [PMID: 30930342 DOI: 10.1266/ggs.18-00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Apurinic/apyrimidinic (AP) sites are the most common form of cytotoxic DNA damage. Since AP sites inhibit DNA replication and transcription, repairing them is critical for cell growth. However, the significance of repairing AP sites during early embryonic development has not yet been clearly determined. Here, we focused on APEX1 from the ascidian Ciona intestinalis (CiApex1), a homolog of human AP endonuclease 1 (APEX1), and examined its role in early embryonic development. Recombinant CiApex1 protein complemented the drug sensitivities of an AP endonuclease-deficient Escherichia coli mutant, and exhibited Mg2+-dependent AP endonuclease activity, like human APEX1, in vitro. Next, the effects of abnormal AP site repair on embryonic development were investigated. Treatment with methyl methanesulfonate, which alkylates DNA bases and generates AP sites, induced abnormal embryonic development. This abnormal phenotype was also caused by treatment with methoxyamine, which inhibits AP endonuclease activity. Furthermore, we constructed dominant-negative CiApex1, which inhibits CiApex1 action, and found that its expression impaired embryonic growth. These results suggested that AP site repair is essential for embryonic development and CiApex1 plays an important role in AP site repair during early embryonic development in C. intestinalis.
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Affiliation(s)
- Kento Igarashi
- Laboratory of Stress Response Biology, Department of Biological Sciences, Graduate School of Science, Kyoto University.,Department of Applied Pharmacology, Graduate School of Medical and Dental Sciences, Kagoshima University
| | - Masafumi Funakoshi
- Laboratory of Stress Response Biology, Department of Biological Sciences, Graduate School of Science, Kyoto University
| | - Seiji Kato
- Laboratory of Stress Response Biology, Department of Biological Sciences, Graduate School of Science, Kyoto University
| | - Takahito Moriwaki
- Laboratory of Stress Response Biology, Department of Biological Sciences, Graduate School of Science, Kyoto University.,Department of Stem Cell Biology, Atomic Bomb Disease Institute, Nagasaki University
| | - Yuichi Kato
- Laboratory of Stress Response Biology, Department of Biological Sciences, Graduate School of Science, Kyoto University.,Engineering Biology Research Center, Kobe University
| | - Qiu-Mei Zhang-Akiyama
- Laboratory of Stress Response Biology, Department of Biological Sciences, Graduate School of Science, Kyoto University
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Dunham RA, Elaswad A, Qin Z. Gene Editing in Channel Catfish via Double Electroporation of Zinc-Finger Nucleases. Methods Mol Biol 2018; 1867:201-214. [PMID: 30155825 DOI: 10.1007/978-1-4939-8799-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The traditional approach for gene editing with zinc-finger nucleases (ZFNs) in fish has been microinjection of mRNA. Here, we develop and describe an alternative protocol in which ZFN plasmids are electroporated to channel catfish, Ictalurus punctatus, sperm, and embryos. Briefly, plasmids were propagated to supply a sufficient quantity for electroporation. Sperm cells were prepared in saline solution, electroporated with plasmids, and then used for fertilization. Embryos were incubated with the plasmids before performing electroporation just prior to first cell division. Plasmids were then transcribed and translated by embryonic cells to produce ZFNs for gene editing, resulting in mutated fry.
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Affiliation(s)
- Rex A Dunham
- School of Fisheries Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA.
| | - Ahmed Elaswad
- School of Fisheries Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Zhenkui Qin
- School of Fisheries Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, China
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18
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Elaswad A, Khalil K, Cline D, Page-McCaw P, Chen W, Michel M, Cone R, Dunham R. Microinjection of CRISPR/Cas9 Protein into Channel Catfish, Ictalurus punctatus, Embryos for Gene Editing. J Vis Exp 2018. [PMID: 29443028 DOI: 10.3791/56275] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The complete genome of the channel catfish, Ictalurus punctatus, has been sequenced, leading to greater opportunities for studying channel catfish gene function. Gene knockout has been used to study these gene functions in vivo. The clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9 (CRISPR/Cas9) system is a powerful tool used to edit genomic DNA sequences to alter gene function. While the traditional approach has been to introduce CRISPR/Cas9 mRNA into the single cell embryos through microinjection, this can be a slow and inefficient process in catfish. Here, a detailed protocol for microinjection of channel catfish embryos with CRISPR/Cas9 protein is described. Briefly, eggs and sperm were collected and then artificial fertilization performed. Fertilized eggs were transferred to a Petri dish containing Holtfreter's solution. Injection volume was calibrated and then guide RNAs/Cas9 targeting the toll/interleukin 1 receptor domain-containing adapter molecule (TICAM 1) gene and rhamnose binding lectin (RBL) gene were microinjected into the yolk of one-cell embryos. The gene knockout was successful as indels were confirmed by DNA sequencing. The predicted protein sequence alterations due to these mutations included frameshift and truncated protein due to premature stop codons.
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Affiliation(s)
- Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University; Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University;
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University; Anatomy and Embryology Department, Faculty of Veterinary Medicine, Cairo University
| | - David Cline
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University
| | - Patrick Page-McCaw
- Department of Molecular Physiology and Biophysics, Vanderbilt University
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University
| | | | - Roger Cone
- Life Science Institute, University of Michigan
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University
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19
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Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown C, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P. ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Nucleic Acids Res 2018; 46:D718-D725. [PMID: 29149270 PMCID: PMC5753386 DOI: 10.1093/nar/gkx1108] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/22/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy databases, better support for epigenomics datasets, in particular RNA-seq, ChIP-seq and SELEX-seq, and features novel interactive interfaces for existing and novel datatypes. In particular, the cross-species navigation and comparison is enhanced through a novel taxonomy section describing each represented species and through the implementation of interactive phylogenetic gene trees for 60% of tunicate genes. The gene expression section displays the results of RNA-seq experiments for the three major model species of solitary ascidians. Gene expression is controlled by the binding of transcription factors to cis-regulatory sequences. A high-resolution description of the DNA-binding specificity for 131 Ciona robusta (formerly C. intestinalis type A) transcription factors by SELEX-seq is provided and used to map candidate binding sites across the Ciona robusta and Phallusia mammillata genomes. Finally, use of a WashU Epigenome browser enhances genome navigation, while a Genomicus server was set up to explore microsynteny relationships within tunicates and with vertebrates, Amphioxus, echinoderms and hemichordates.
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Affiliation(s)
| | | | | | - Delphine Dauga
- Bioself Communication; 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Emmanuel Faure
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
- Team VORTEX, Institut de Recherche en Informatique de Toulouse, Universities Toulouse I and III, CNRS, INPT, ENSEEIHT; 2 rue Camichel, BP 7122, F-31071 Toulouse Cedex 7, France
| | | | - Alexandra Louis
- DYOGEN, IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Kazuhiro R Nitta
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Jacques Piette
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas
| | | | - Paul Simion
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Renaud Vincentelli
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Sameh Ben Aicha
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | | | | | - Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Edwin Jacox
- CRBM, Université de Montpellier, CNRS, Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
| | - Mickael Mendez
- IBDM, Aix-Marseille Université, CNRS, Campus de Luminy, Case 907; 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Rui Yokomori
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - C Titus Brown
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Christian Cambillau
- AFMB, Aix-Marseille Université, CNRS, Campus de Luminy, Case 932, 163 Avenue de Luminy, F-13288 Marseille Cedex 9, France
| | - Lionel Christiaen
- New York University, Center for Developmental Genetics, Department of Biology, 1009 Silver Center, 100 Washington Square East, New York City, NY10003, USA
| | - Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Emmanuel Douzery
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Rémi Dumollard
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Universités, Université Pierre-et-Marie-Curie, CNRS; Quai de la Darse, F-06234 Villefranche-sur-Mer Cedex, France
| | - Takehiro Kusakabe
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, 4-6-1 Shirokanedai, Minato, Tokyo 108-8639, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Billie Swalla
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI48824, USA
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS; 46 allée d’Italie, F-69364 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, Montpellier, France
- Institut de Biologie Computationnelle, Université de Montpellier, Montpellier, France
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20
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Gandhi S, Razy-Krajka F, Christiaen L, Stolfi A. CRISPR Knockouts in Ciona Embryos. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1029:141-152. [PMID: 29542087 PMCID: PMC6061950 DOI: 10.1007/978-981-10-7545-2_13] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 has emerged as a revolutionary tool for fast and efficient targeted gene knockouts and genome editing in almost any organism. The laboratory model tunicate Ciona is no exception. Here, we describe our latest protocol for the design, implementation, and evaluation of successful CRISPR/Cas9-mediated gene knockouts in somatic cells of electroporated Ciona embryos. Using commercially available reagents, publicly accessible plasmids, and free web-based software applications, any Ciona researcher can easily knock out any gene of interest in their favorite embryonic cell lineage.
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Affiliation(s)
- Shashank Gandhi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Florian Razy-Krajka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lionel Christiaen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
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21
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Abstract
Targeted mutagenesis of genes-of-interest is a powerful method of addressing the functions of genes. Genome editing techniques, such as transcriptional activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 systems, have enabled this approach in various organisms because of their ease of use. In the ascidian, Ciona intestinalis, recent studies show that TALEN-based knockout can be applied to establishing both mutant lines and tissue-specific knockout for addressing gene functions. Here, we introduce recent updates to the TALEN toolkit that facilitate detailed functional analysis of genes in ascidians.
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22
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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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23
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Nishino A. Morphology and Physiology of the Ascidian Nervous Systems and the Effectors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [PMID: 29542090 DOI: 10.1007/978-981-10-7545-2_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neurobiology in ascidians has made many advances. Ascidians have offered natural advantages to researchers, including fecundity, structural simplicity, invariant morphology, and fast and stereotyped developmental processes. The researchers have also accumulated on this animal a great deal of knowledge, genomic resources, and modern genetic techniques. A recent connectomic analysis has shown an ultimately resolved image of the larval nervous system, whereas recent applications of live imaging and optogenetics have clarified the functional organization of the juvenile nervous system. Progress in resources and techniques have provided convincing ways to deepen what we have wanted to know about the nervous systems of ascidians. Here, the research history and the current views regarding ascidian nervous systems are summarized.
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Affiliation(s)
- Atsuo Nishino
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
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24
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Transgenic Techniques for Investigating Cell Biology During Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018. [PMID: 29542088 DOI: 10.1007/978-981-10-7545-2_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ascidians are increasingly being used as a system for investigating cell biology during development. The extreme genetic and cellular simplicity of ascidian embryos in combination with superior experimental tractability make this an ideal system for in vivo analysis of dynamic cellular processes. Transgenic approaches to cellular and sub-cellular analysis of ascidian development have begun to yield new insights into the mechanisms regulating developmental signaling and morphogenesis. This chapter focuses on the targeted expression of fusion proteins in ascidian embryos and how this technique is being deployed to garner new insights into the cell biology of development.
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25
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Sasakura Y, Hozumi A. Formation of adult organs through metamorphosis in ascidians. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 7. [PMID: 29105358 DOI: 10.1002/wdev.304] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/28/2017] [Accepted: 09/11/2017] [Indexed: 02/05/2023]
Abstract
The representative characteristic of ascidians is their vertebrate-like, tadpole shape at the larval stage. Ascidians lose the tadpole shape through metamorphosis to become adults with a nonmotile, sessile body and a shape generally considered distinct from that of vertebrates. Solitary ascidians including Ciona species are extensively studied to understand the developmental mechanisms of ascidians, and to compare these mechanisms with their counterparts in vertebrates. In these ascidian species, the digestive and circulatory systems are not well developed in the larval trunk and the larvae do not take food. This is in contrast with the inner conditions of vertebrate tadpoles, which have functional organs comparable to those of adults. The adult organs and tissues of these ascidians become functional during metamorphosis that is completed quickly, suggesting that the ascidian larvae of solitary species are a transient stage of development. We here discuss how the cells and tissues in the ascidian larval body are converted into those of adults. The hearts of ascidians and vertebrates use closely related cellular and molecular mechanisms that suggest their shared origin. Hox genes of ascidians are essential for forming adult endodermal structures. To fully understand the development and evolution of chordates, a complete elucidation of the mechanisms underlying the adult tissue/organ formation of ascidians will be needed. WIREs Dev Biol 2018, 7:e304. doi: 10.1002/wdev.304 This article is categorized under: Comparative Development and Evolution > Body Plan Evolution Early Embryonic Development > Development to the Basic Body Plan.
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Affiliation(s)
- Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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26
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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.
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Affiliation(s)
| | - Cynthia L Smith
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, 04609, USA
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Gandhi S, Haeussler M, Razy-Krajka F, Christiaen L, Stolfi A. Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona. Dev Biol 2017; 425:8-20. [PMID: 28341547 PMCID: PMC5502750 DOI: 10.1016/j.ydbio.2017.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/06/2017] [Accepted: 03/05/2017] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos. We found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.
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Affiliation(s)
| | - Maximilian Haeussler
- Santa Cruz Genomics Institute, University of California, MS CBSE, Santa Cruz, USA
| | | | | | - Alberto Stolfi
- Department of Biology, New York University, New York, USA.
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28
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Germ cell regeneration-mediated, enhanced mutagenesis in the ascidian Ciona intestinalis reveals flexible germ cell formation from different somatic cells. Dev Biol 2017; 423:111-125. [DOI: 10.1016/j.ydbio.2017.01.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/12/2017] [Accepted: 01/31/2017] [Indexed: 11/22/2022]
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Abstract
Transcription activator-like effector (TALE) nuclease (TALEN) is the second-generation genome editing tool consisting of TALE protein containing customizable DNA-binding repeats and nuclease domain of FokI enzyme. Each DNA-binding repeat recognizes one base of double-strand DNA, and functional TALEN can be created by a simple modular assembly of these repeats. To easily and efficiently assemble the highly repetitive DNA-binding repeat arrays, various construction systems such as Golden Gate assembly, serial ligation, and ligation-independent cloning have been reported. In this chapter, we summarize the current situation of these systems and publically available reagents and protocols, enabling optimal selection of best suited systems for every researcher who wants to utilize TALENs in various research fields.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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Yoshida K, Nakahata A, Treen N, Sakuma T, Yamamoto T, Sasakura Y. Hox-mediated endodermal identity patterns the pharyngeal muscle formation in the chordate pharynx. Development 2017; 144:1629-1634. [DOI: 10.1242/dev.144436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/07/2017] [Indexed: 01/10/2023]
Abstract
The pharynx, possessing gill slits and the endostyle, is a characteristic of chordates that is a complex of multiple tissues well organized along the anterior-posterior (AP) axis. Although Hox genes show AP coordinated expression in the pharyngeal endoderm, tissue specific roles of these factors for establishing the regional identities within this tissue is largely unknown. Here, we show that Hox1 is essential for the establishment of AP axial identity of the endostyle, a major structure of the pharyngeal endoderm, in the ascidian Ciona intestinalis. We found that Hox1 knockout causes posterior to anterior transformation of the endostyle identity, and Hox1 represses Otx expression and anterior identity, and vice versa. Furthermore, alteration of the regional identity of the endostyle disrupts the formation of body wall muscles, suggesting that the endodermal axial identity is essential for the coordinated pharyngeal development. Our results reveal an essential role of Hox genes for establishment of the AP regional identity in the pharyngeal endoderm and crosstalk between endoderm and mesoderm for the development of chordate pharynx.
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Affiliation(s)
- Keita Yoshida
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Azusa Nakahata
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
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31
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Abstract
The ascidian Ciona intestinalis is an important model animal for studying developmental mechanisms for constructing the chordate body. Although molecular and embryological techniques for manipulating Ciona genes were developed a long time ago, recent achievements of genome editing in this animal have innovated functional analyses of genes in Ciona. Particularly, knockout of genes in the G0 generation coupled with tissue-specific expression of TALENs enables us to rapidly address gene functions that were difficult using previous methods.
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Affiliation(s)
- Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan.
| | - Keita Yoshida
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
| | - Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
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Sasakura Y, Ogura Y, Treen N, Yokomori R, Park SJ, Nakai K, Saiga H, Sakuma T, Yamamoto T, Fujiwara S, Yoshida K. Transcriptional regulation of a horizontally transferred gene from bacterium to chordate. Proc Biol Sci 2016; 283:20161712. [PMID: 28003446 PMCID: PMC5204163 DOI: 10.1098/rspb.2016.1712] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/15/2016] [Indexed: 01/21/2023] Open
Abstract
The horizontal transfer of genes between distantly related organisms is undoubtedly a major factor in the evolution of novel traits. Because genes are functionless without expression, horizontally transferred genes must acquire appropriate transcriptional regulations in their recipient organisms, although the evolutionary mechanism is not known well. The defining characteristic of tunicates is the presence of a cellulose containing tunic covering the adult and larval body surface. Cellulose synthase was acquired by horizontal gene transfer from Actinobacteria. We found that acquisition of the binding site of AP-2 transcription factor was essential for tunicate cellulose synthase to gain epidermal-specific expression. Actinobacteria have very GC-rich genomes, regions of which are capable of inducing specific expression in the tunicate epidermis as the AP-2 binds to a GC-rich region. Therefore, the actinobacterial cellulose synthase could have been potentiated to evolve its new function in the ancestor of tunicates with a higher probability than the evolution depending solely on a spontaneous event.
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Affiliation(s)
- Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Yosuke Ogura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Rui Yokomori
- The Institute of Medical Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Sung-Joon Park
- The Institute of Medical Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Kenta Nakai
- The Institute of Medical Sciences, University of Tokyo, Tokyo 108-8639, Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Shigeki Fujiwara
- Department of Applied Science, Kochi University, 2-5-1, Akebono-cho, Kochi-shi, Kochi 780-8520, Japan
| | - Keita Yoshida
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
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33
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Diving into marine genomics with CRISPR/Cas9 systems. Mar Genomics 2016; 30:55-65. [DOI: 10.1016/j.margen.2016.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 12/12/2022]
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34
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Stanley EC, Azzinaro PA, Vierra DA, Howlett NG, Irvine SQ. The Simple Chordate Ciona intestinalis Has a Reduced Complement of Genes Associated with Fanconi Anemia. Evol Bioinform Online 2016; 12:133-48. [PMID: 27279728 PMCID: PMC4898443 DOI: 10.4137/ebo.s37920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/10/2016] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Fanconi anemia (FA) is a human genetic disease characterized by congenital defects, bone marrow failure, and increased cancer risk. FA is associated with mutation in one of 24 genes. The protein products of these genes function cooperatively in the FA pathway to orchestrate the repair of DNA interstrand cross-links. Few model organisms exist for the study of FA. Seeking a model organism with a simpler version of the FA pathway, we searched the genome of the simple chordate Ciona intestinalis for homologs of the human FA-associated proteins. BLAST searches, sequence alignments, hydropathy comparisons, maximum likelihood phylogenetic analysis, and structural modeling were used to infer the likelihood of homology between C. intestinalis and human FA proteins. Our analysis indicates that C. intestinalis indeed has a simpler and potentially functional FA pathway. The C. intestinalis genome was searched for candidates for homology to 24 human FA and FA-associated proteins. Support was found for the existence of homologs for 13 of these 24 human genes in C. intestinalis. Members of each of the three commonly recognized FA gene functional groups were found. In group I, we identified homologs of FANCE, FANCL, FANCM, and UBE2T/FANCT. Both members of group II, FANCD2 and FANCI, have homologs in C. intestinalis. In group III, we found evidence for homologs of FANCJ, FANCO, FANCQ/ERCC4, FANCR/RAD51, and FANCS/BRCA1, as well as the FA-associated proteins ERCC1 and FAN1. Evidence was very weak for the existence of homologs in C. intestinalis for any other recognized FA genes. This work supports the notion that C. intestinalis, as a close relative of vertebrates, but having a much reduced complement of FA genes, offers a means of studying the function of certain FA proteins in a simpler pathway than that of vertebrate cells.
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Affiliation(s)
- Edward C Stanley
- Integrative and Evolutionary Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA
| | - Paul A Azzinaro
- Cell and Molecular Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA
| | - David A Vierra
- Cell and Molecular Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA
| | - Niall G Howlett
- Cell and Molecular Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA.; Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI, USA
| | - Steven Q Irvine
- Integrative and Evolutionary Biology Graduate Specialization, University of Rhode Island, Kingston, RI, USA.; Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
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35
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Rocha-Martins M, Cavalheiro GR, Matos-Rodrigues GE, Martins RAP. From Gene Targeting to Genome Editing: Transgenic animals applications and beyond. AN ACAD BRAS CIENC 2016; 87:1323-48. [PMID: 26397828 DOI: 10.1590/0001-3765201520140710] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Genome modification technologies are powerful tools for molecular biology and related areas. Advances in animal transgenesis and genome editing technologies during the past three decades allowed systematic interrogation of gene function that can help model how the genome influences cellular physiology. Genetic engineering via homologous recombination (HR) has been the standard method to modify genomic sequences. Nevertheless, nuclease-guided genome editing methods that were developed recently, such as ZFN, TALEN and CRISPR/Cas, opened new perspectives for biomedical research. Here, we present a brief historical perspective of genome modification methods, focusing on transgenic mice models. Moreover, we describe how new techniques were discovered and improved, present the paradigm shifts and discuss their limitations and applications for biomedical research as well as possible future directions.
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Affiliation(s)
- Maurício Rocha-Martins
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BR
| | - Gabriel R Cavalheiro
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BR
| | | | - Rodrigo A P Martins
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, BR
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36
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Li W, Ou G. The application of somatic CRISPR-Cas9 to conditional genome editing in Caenorhabditis elegans. Genesis 2016; 54:170-81. [PMID: 26934570 DOI: 10.1002/dvg.22932] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/20/2022]
Abstract
Forward and reverse genetic approaches have been well developed in the nematode Caenorhabditis elegans; however, efficient genetic tools to generate conditional gene mutations are still in high demand. Recently, the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) system for genome modification has provided an additional tool for C. elegans researchers to achieve simple and efficient conditional targeted mutagenesis. Here, we review recent advances in the somatic expression of Cas9 endonuclease for conditional gene editing. We present some practical considerations for improving the efficiency and reducing the off-target effects of somatic CRISPR-Cas9 and highlight a strategy to analyze somatic mutation at single-cell resolution. Finally, we outline future applications and consider challenges for this emerging genome editing platform that will need to be addressed in the future.
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Affiliation(s)
- Wei Li
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Guangshuo Ou
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
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37
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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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38
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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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39
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Abstract
Among various strategies for constructing customized transcription activator-like effector nucleases (TALENs), the Golden Gate assembly is the most widely used and most characterized method. The principle of Golden Gate assembly involves cycling reactions of digestion and ligation of multiple plasmids in a single tube, resulting in PCR-, fragmentation-, and purification-free concatemerization of DNA-binding repeats. Here, we describe the protocols for Golden Gate assembly-based TALEN construction using the Platinum Gate TALEN Kit, which allows generation of highly active Platinum TALENs.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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Shi X, He BL, Ma ACH, Leung AYH. Fishing the targets of myeloid malignancies in the era of next generation sequencing. Blood Rev 2015; 30:119-30. [PMID: 26443083 DOI: 10.1016/j.blre.2015.09.001] [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: 07/17/2015] [Revised: 08/15/2015] [Accepted: 09/04/2015] [Indexed: 11/29/2022]
Abstract
Recent advent in next generation sequencing (NGS) and bioinformatics has generated an unprecedented amount of genetic information in myeloidmalignancies. This information may shed lights to the pathogenesis, diagnosis and prognostication of these diseases and provide potential targets for therapeutic intervention. However, the rapid emergence of genetic information will quickly outpace their functional validation by conventional laboratory platforms. Foundational knowledge about zebrafish hematopoiesis accumulated over the past two decades and novel genomeediting technologies and research strategies in thismodel organismhavemade it a unique and timely research tool for the study of human blood diseases. Recent studies modeling human myeloid malignancies in zebrafish have also highlighted the technical feasibility and clinical relevance of thesemodels. Careful validation of experimental protocols and standardization among laboratorieswill further enhance the application of zebrafish in the scientific communities and provide important insights to the personalized treatment ofmyeloid malignancies.
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Affiliation(s)
- Xiangguo Shi
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
| | - Bai-Liang He
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
| | - Alvin C H Ma
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
| | - Anskar Y H Leung
- Division of Haematology, Medical Oncology and Bone Marrow Transplantation, Department of Medicine, LKS Faculty Medicine, The University of Hong Kong.
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41
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Ueki T, Yamaguchi N, Romaidi, Isago Y, Tanahashi H. Vanadium accumulation in ascidians: A system overview. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Hozumi A, Horie T, Sasakura Y. Neuronal map reveals the highly regionalized pattern of the juvenile central nervous system of the ascidian Ciona intestinalis. Dev Dyn 2015; 244:1375-93. [PMID: 26250096 DOI: 10.1002/dvdy.24317] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/28/2015] [Accepted: 08/02/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The dorsally located central nervous system (CNS) is an important hallmark of chordates. Among chordates, tunicate ascidians change their CNS remarkably by means of a metamorphosis from a highly regionalized larval CNS to an oval-shaped juvenile CNS without prominent morphological features. The neuronal organization of the CNS of ascidian tadpole larvae has been well described, but that in the CNS of postmetamorphosis juveniles has not been characterized well. RESULTS We investigated the number of neural cells, the number and position of differentiated neurons, and their axonal trajectories in the juvenile CNS of the ascidian Ciona intestinalis. The cell bodies of cholinergic, glutamatergic, and GABAergic/glycinergic neurons exhibited different localization patterns along the anterior-posterior axis in the juvenile CNS. Cholinergic neurons extended their axons toward the oral, atrial and body wall muscles and pharyngeal gill to regulate muscle contraction and ciliary movement. CONCLUSIONS Unlike its featureless shape, the juvenile CNS is highly patterned along the anterior-posterior axis. This patterning may be necessary for exerting multiple roles in the regulation of adult tissues distributed throughout the body. This basic information of the juvenile CNS of Ciona will allow in-depth studies of molecular mechanisms underlying the reconstruction of the CNS during ascidian metamorphosis.
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Affiliation(s)
- Akiko Hozumi
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Takeo Horie
- Japan Science and Technology Agency, PRESTO, Honcho, Kawaguchi, Saitama, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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Kawai N, Ogura Y, Ikuta T, Saiga H, Hamada M, Sakuma T, Yamamoto T, Satoh N, Sasakura Y. Hox10-regulated endodermal cell migration is essential for development of the ascidian intestine. Dev Biol 2015; 403:43-56. [PMID: 25888074 DOI: 10.1016/j.ydbio.2015.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/25/2015] [Indexed: 11/17/2022]
Abstract
Hox cluster genes play crucial roles in development of the metazoan antero-posterior axis. Functions of Hox genes in patterning the central nervous system and limb buds are well known. They are also expressed in chordate endodermal tissues, where their roles in endodermal development are still poorly understood. In the invertebrate chordate, Ciona intestinalis, endodermal tissues are in a premature state during the larval stage, and they differentiate into the digestive tract during metamorphosis. In this study, we showed that disruption of a Hox gene, Ci-Hox10, prevented intestinal formation. Ci-Hox10-knock-down larvae displayed defective migration of endodermal strand cells. Formation of a protrusion, which is important for cell migration, was disrupted in these cells. The collagen type IX gene is a downstream target of Ci-Hox10, and is negatively regulated by Ci-Hox10 and a matrix metalloproteinase ortholog, prior to endodermal cell migration. Inhibition of this regulation prevented cellular migration. These results suggest that Ci-Hox10 regulates endodermal strand cell migration by forming a protrusion and by reconstructing the extracellular matrix.
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Affiliation(s)
- Narudo Kawai
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan.
| | - Yosuke Ogura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Tetsuro Ikuta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiohji, Tokyo 192-0397, Japan; Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiohji, Tokyo 192-0397, Japan
| | - Mayuko Hamada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
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44
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Regulation and evolution of cardiopharyngeal cell identity and behavior: insights from simple chordates. Curr Opin Genet Dev 2015; 32:119-28. [PMID: 25819888 DOI: 10.1016/j.gde.2015.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 01/08/2023]
Abstract
The vertebrate heart arises from distinct first and second heart fields. The latter also share a common origin with branchiomeric muscles in the pharyngeal mesoderm and transcription regulators, such as Nkx2-5, Tbx1 and Islet1. Despite significant progress, the complexity of vertebrate embryos has hindered the identification of multipotent cardiopharyngeal progenitors. Here, we summarize recent insights in cardiopharyngeal development gained from ascidian models, among the closest relatives to vertebrates. In a simplified cellular context, progressive fate specification of the ascidian cardiopharyngeal precursors presents striking similarities with their vertebrate counterparts. Multipotent cardiopharyngeal progenitors are primed to activate both the early cardiac and pharyngeal muscles programs, which segregate following asymmetric cells divisions as a result of regulatory cross-antagonisms involving Tbx1 and Nkx2-5 homologs. Activation of Ebf in pharyngeal muscle founder cells triggers both Myogenic Regulatory Factor-associated differentiation and Notch-mediated maintenance of an undifferentiated state in distinct precursors. Cross-species comparisons revealed the deep conservation of the cardiopharyngeal developmental sequence in spite of extreme genome sequence divergence, gene network rewiring and specific morphogenetic differences. Finally, analyses are beginning to uncover the influence of surrounding tissues in determining cardiopharyngeal cell identity and behavior. Thus, ascidian embryos offer a unique opportunity to study gene regulation and cell behaviors at the cellular level throughout cardiopharyngeal morphogenesis and evolution.
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45
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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.
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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
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Veeman M, Reeves W. Quantitative and in toto imaging in ascidians: working toward an image-centric systems biology of chordate morphogenesis. Genesis 2015; 53:143-59. [PMID: 25262824 PMCID: PMC4378666 DOI: 10.1002/dvg.22828] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/20/2014] [Accepted: 09/25/2014] [Indexed: 12/16/2022]
Abstract
Developmental biology relies heavily on microscopy to image the finely controlled cell behaviors that drive embryonic development. Most embryos are large enough that a field of view with the resolution and magnification needed to resolve single cells will not span more than a small region of the embryo. Ascidian embryos, however, are sufficiently small that they can be imaged in toto with fine subcellular detail using conventional microscopes and objectives. Unlike other model organisms with particularly small embryos, ascidians have a chordate embryonic body plan that includes a notochord, hollow dorsal neural tube, heart primordium and numerous other anatomical details conserved with the vertebrates. Here we compare the size and anatomy of ascidian embryos with those of more traditional model organisms, and relate these features to the capabilities of both conventional and exotic imaging methods. We review the emergence of Ciona and related ascidian species as model organisms for a new era of image-based developmental systems biology. We conclude by discussing some important challenges in ascidian imaging and image analysis that remain to be solved.
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Affiliation(s)
- Michael Veeman
- Division of Biology, Kansas State University, Manhattan KS, USA
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan KS, USA
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47
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Stolfi A, Gandhi S, Salek F, Christiaen L. Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9. Development 2014; 141:4115-20. [PMID: 25336740 DOI: 10.1242/dev.114488] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has ushered in a new era of targeted genetic manipulations. Here, we report the use of CRISPR/Cas9 to induce double-stranded breaks in the genome of the sea squirt Ciona intestinalis. We use electroporation to deliver CRISPR/Cas9 components for tissue-specific disruption of the Ebf (Collier/Olf/EBF) gene in hundreds of synchronized Ciona embryos. Phenotyping of transfected embryos in the 'F0' generation revealed that endogenous Ebf function is required for specification of Islet-expressing motor ganglion neurons and atrial siphon muscles. We demonstrate that CRISPR/Cas9 is sufficiently effective and specific to generate large numbers of embryos carrying mutations in a targeted gene of interest, which should allow for rapid screening of gene function in Ciona.
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Affiliation(s)
- Alberto Stolfi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Shashank Gandhi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Farhana Salek
- 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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48
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Xu J, Wang Y, Li Z, Ling L, Zeng B, James AA, Tan A, Huang Y. Transcription activator-like effector nuclease (TALEN)-mediated female-specific sterility in the silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2014; 23:800-7. [PMID: 25125145 PMCID: PMC4412852 DOI: 10.1111/imb.12125] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Engineering sex-specific sterility is critical for developing transgene-based sterile insect technology. Targeted genome engineering achieved by customized zinc-finger nuclease, transcription activator-like effector nuclease (TALEN) or clustered, regularly interspaced, short palindromic repeats/Cas9 systems has been exploited extensively in a variety of model organisms; however, screening mutated individuals without a detectable phenotype is still challenging. In addition, genetically recessive mutations only detectable in homozygotes make the experiments time-consuming. In the present study, we model a novel genetic system in the silkworm, Bombyx mori, that results in female-specific sterility by combining transgenesis with TALEN technologies. This system induces sex-specific sterility at a high efficiency by targeting the female-specific exon of the B. mori doublesex (Bmdsx) gene, which has sex-specific splicing isoforms regulating somatic sexual development. Transgenic animals co-expressing TALEN left and right arms targeting the female-specific Bmdsx exon resulted in somatic mutations and female mutants lost fecundity because of lack of egg storage and abnormal external genitalia. The wild-type sexual dimorphism of abdominal segment was not evident in mutant females. In contrast, there were no deleterious effects in mutant male moths. The current somatic TALEN technologies provide a promising approach for future insect functional genetics, thus providing the basis for the development of attractive genetic alternatives for insect population management.
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Affiliation(s)
- Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueqiang Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqian Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Ling
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baosheng Zeng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Anthony A. James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California, Irvine, CA 92697-3900
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Correspondence: Y.P. Huang, ; Tel: 86-2154924046; Fax: 86- 2154924014; AJ.. Tan, ; Tel: 86-2154924046; Fax: 86- 2154924014
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Correspondence: Y.P. Huang, ; Tel: 86-2154924046; Fax: 86- 2154924014; AJ.. Tan, ; Tel: 86-2154924046; Fax: 86- 2154924014
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49
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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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50
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Gilles AF, Averof M. Functional genetics for all: engineered nucleases, CRISPR and the gene editing revolution. EvoDevo 2014; 5:43. [PMID: 25699168 PMCID: PMC4332929 DOI: 10.1186/2041-9139-5-43] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 10/03/2014] [Indexed: 12/26/2022] Open
Abstract
Developmental biology, as all experimental science, is empowered by technological advances. The availability of genetic tools in some species - designated as model organisms - has driven their use as major platforms for understanding development, physiology and behavior. Extending these tools to a wider range of species determines whether (and how) we can experimentally approach developmental diversity and evolution. During the last two decades, comparative developmental biology (evo-devo) was marked by the introduction of gene knockdown and deep sequencing technologies that are applicable to a wide range of species. These approaches allowed us to test the developmental role of specific genes in diverse species, to study biological processes that are not accessible in established models and, in some cases, to conduct genome-wide screens that overcome the limitations of the candidate gene approach. The recent discovery of CRISPR/Cas as a means of precise alterations into the genome promises to revolutionize developmental genetics. In this review we describe the development of gene editing tools, from zinc-finger nucleases to TALENs and CRISPR, and examine their application in gene targeting, their limitations and the opportunities they present for evo-devo. We outline their use in gene knock-out and knock-in approaches, and in manipulating gene functions by directing molecular effectors to specific sites in the genome. The ease-of-use and efficiency of CRISPR in diverse species provide an opportunity to close the technology gap that exists between established model organisms and emerging genetically-tractable species.
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Affiliation(s)
- Anna F Gilles
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon, 69364 France ; BMIC graduate programme and Université Claude Bernard - Lyon 1, Lyon, France
| | - Michalis Averof
- Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon, 69364 France ; Centre National de la Recherche Scientifique (CNRS), Lyon, France
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