1
|
Drago L, Pennati A, Rothbächer U, Ashita R, Hashimoto S, Saito R, Fujiwara S, Ballarin L. Stress granule-related genes during embryogenesis of an invertebrate chordate. Front Cell Dev Biol 2024; 12:1414759. [PMID: 39149517 PMCID: PMC11324471 DOI: 10.3389/fcell.2024.1414759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/20/2024] [Indexed: 08/17/2024] Open
Abstract
Controlling global protein synthesis through the assembly of stress granules represents a strategy adopted by eukaryotic cells to face various stress conditions. TIA 1-related nucleolysin (TIAR), tristetraprolin (TTP), and Ras-GTPase-activating protein SH3-domain-binding protein (G3BP) are key components of stress granules, allowing the regulation of mRNA stability, and thus controlling not only stress responses but also cell proliferation and differentiation. In this study, we aimed at investigating the roles of tiar, ttp, and g3bp during embryogenesis of the solitary ascidian Ciona robusta under both physiological and stress conditions. We carried out CRISPR/Cas9 to evaluate the effects of gene knockout on normal embryonic development, and gene reporter assay to study the time and tissue specificity of gene transcription, together with whole-mount in situ hybridization and quantitative real time PCR. To induce acute stress conditions, we used iron and cadmium as "essential" and "non-essential" metals, respectively. Our results highlight, for the first time, the importance of tiar, ttp, and g3bp in controlling the development of mesendodermal tissue derivatives during embryogenesis of an invertebrate chordate.
Collapse
Affiliation(s)
- Laura Drago
- Department of Biology, University of Padova, Padua, Italy
| | | | - Ute Rothbächer
- Institute of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Ryuji Ashita
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | - Seika Hashimoto
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | - Ryota Saito
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | - Shigeki Fujiwara
- Department of Chemistry and Biotechnology, University of Kochi, Kochi, Japan
| | | |
Collapse
|
2
|
Pennati A, Jakobi M, Zeng F, Ciampa L, Rothbächer U. Optimizing CRISPR/Cas9 approaches in the polymorphic tunicate Ciona intestinalis. Dev Biol 2024; 510:31-39. [PMID: 38490564 DOI: 10.1016/j.ydbio.2024.03.003] [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: 12/29/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
CRISPR/Cas9 became a powerful tool for genetic engineering and in vivo knockout also in the invertebrate chordate Ciona intestinalis. Ciona (ascidians, tunicates) is an important model organism because it shares developmental features with the vertebrates, considered the sister group of tunicates, and offers outstanding experimental advantages: a compact genome and an invariant developmental cell lineage that, combined with electroporation mediated transgenesis allows for precise and cell type specific targeting in vivo. A high polymorphism and the mosaic expression of electroporated constructs, however, often hamper the efficient CRISPR knockout, and an optimization in Ciona is desirable. Furthermore, seasonality and artificial maintenance settings can profit from in vitro approaches that would save on animals. Here we present improvements for the CRISPR/Cas9 protocol in silico, in vitro and in vivo. Firstly, in designing sgRNAs, prior sequencing of target genomic regions from experimental animals and alignment with reference genomes of C. robusta and C. intestinalis render a correction possible of subspecies polymorphisms. Ideally, the screening for efficient and non-polymorphic sgRNAs will generate a database compatible for worldwide Ciona populations. Secondly, we challenged in vitro assays for sgRNA validation towards reduced in vivo experimentation and report their suitability but also overefficiency concerning mismatch tolerance. Thirdly, when comparing Cas9 with Cas9:Geminin, thought to synchronize editing and homology-direct repair, we could indeed increase the in vivo efficiency and notably the access to an early expressed gene. Finally, for in vivo CRISPR, genotyping by next generation sequencing (NGS) ex vivo streamlined the definition of efficient single guides. Double CRISPR then generates large deletions and reliable phenotypic excision effects. Overall, while these improvements render CRISPR more efficient in Ciona, they are useful when newly establishing the technique and very transferable to CRISPR in other organisms.
Collapse
Affiliation(s)
- Alessandro Pennati
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Miloš Jakobi
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Fan Zeng
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Luca Ciampa
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Ute Rothbächer
- Institute of Zoology, University of Innsbruck, 6020, Innsbruck, Austria; Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020, Innsbruck, Austria.
| |
Collapse
|
3
|
Gallo A, Penna YM, Russo M, Rosapane M, Tosti E, Russo GL. An organic extract from ascidian Ciona robusta induces cytotoxic autophagy in human malignant cell lines. Front Chem 2024; 12:1322558. [PMID: 38389727 PMCID: PMC10881676 DOI: 10.3389/fchem.2024.1322558] [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: 10/16/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
The last decades have seen an increase in the isolation and characterization of anticancer compounds derived from marine organisms, especially invertebrates, and their use in clinical trials. In this regard, ascidians, which are included in the subphylum Tunicata, represent successful examples with two drugs, Aplidine© and Yondelis© that reached the market as orphan drugs against several malignancies. Here, we report that an organic extract prepared from homogenized tissues of the Mediterranean ascidian Ciona robusta inhibited cell proliferation in HT-29, HepG2, and U2OS human cells with the former being the most sensitive to the extract (EC50 = 250 μg/mL). We demonstrated that the ascidian organic extract was not cytotoxic on HT-29 cells that were induced to differentiate with sodium butyrate, suggesting a preference for the mixture for the malignant phenotype. Finally, we report that cell death induced by the organic extract was mediated by the activation of a process of cytotoxic autophagy as a result of the increased expression of the LC3-II marker and number of autophagic vacuoles, which almost doubled in the treated HT-29 cells. In summary, although the detailed chemical composition of the Ciona robusta extract is still undetermined, our data suggest the presence of bioactive compounds possessing anticancer activity.
Collapse
Affiliation(s)
- Alessandra Gallo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - Maria Russo
- National Research Council, Institute of Food Sciences, Avellino, Italy
| | - Marco Rosapane
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Research Council, Institute of Food Sciences, Avellino, Italy
| | - Elisabetta Tosti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Gian Luigi Russo
- National Research Council, Institute of Food Sciences, Avellino, Italy
| |
Collapse
|
4
|
Chen Y, Ni P, Fu R, Murphy KJ, Wyeth RC, Bishop CD, Huang X, Li S, Zhan A. (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2772. [PMID: 36316814 DOI: 10.1002/eap.2772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.
Collapse
Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kieran J Murphy
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Cory D Bishop
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
5
|
Onai T, Adachi N, Urakubo H, Sugahara F, Aramaki T, Matsumoto M, Ohno N. Ultrastructure of the lamprey head mesoderm reveals evolution of the vertebrate head. iScience 2023; 26:108338. [PMID: 38187188 PMCID: PMC10767164 DOI: 10.1016/j.isci.2023.108338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 01/09/2024] Open
Abstract
The cranial muscle is a critical component in the vertebrate head for a predatory lifestyle. However, its evolutionary origin and possible segmental nature during embryogenesis have been controversial. In jawed vertebrates, the presence of pre-otic segments similar to trunk somites has been claimed based on developmental observations. However, evaluating such arguments has been hampered by the paucity of research on jawless vertebrates. Here, we discovered different cellular arrangements in the head mesoderm in lamprey embryos (Lethenteron camtschaticum) using serial block-face scanning electron and laser scanning microscopies. These cell populations were morphologically and molecularly different from somites. Furthermore, genetic comparison among deuterostomes revealed that mesodermal gene expression domains were segregated antero-posteriorly in vertebrates, whereas such segregation was not recognized in invertebrate deuterostome embryos. These findings indicate that the vertebrate head mesoderm evolved from the anteroposterior repatterning of an ancient mesoderm and developmentally diversified before the split of jawless and jawed vertebrates.
Collapse
Affiliation(s)
- Takayuki Onai
- Department of Anatomy, University of Fukui, School of Medical Sciences, 23-3, Matsuokashimoaizuki, Eiheiji, Yoshida, Fukui, Japan
- Life Science Innovation Center, University of Fukui, 23-3, Matsuokashimoaizuki, Eiheiji, Yoshida, Fukui, Japan
| | - Noritaka Adachi
- Aix-Marseille Université, IBDM, CNRS UMR 7288, Campus De Luminy Case 907, 13288 Marseille Cedex 9, France
| | - Hidetoshi Urakubo
- Section of Electron Microscopy, National Institute for Physiological Sciences, 38, Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
| | - Fumiaki Sugahara
- Division of Biology, Hyogo Medical University, 1-1, Mukogawa, Nishinomiya, Hyogo, Japan
| | - Toshihiro Aramaki
- Graduate School of Frontier Biosciences, Osaka University, 1-1, Yamadaoka, Suita, Osaka, Japan
| | - Mami Matsumoto
- Section of Electron Microscopy, Supportive Center for Brain Research, National Institute for Physiological Sciences, 38, Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
- Department of Developmental and Regenerative Biology, Nagoya City University Graduate School of Medical Sciences, 1, Kawasumi, Mizuho, Nagoya, Aichi, Japan
| | - Nobuhiko Ohno
- Department of Anatomy, Division of Histology and Cell Biology, School of Medicine, Jichi Medical University, 3311-1, Yakushiji, Shimotsuke, Tochigi, Japan
- Division of Ultrastructural Research, National Institute for Physiological Sciences, 38, Nishigonaka, Myodaiji, Okazaki, Aichi, Japan
| |
Collapse
|
6
|
Beyer J, Song Y, Lillicrap A, Rodríguez-Satizábal S, Chatzigeorgiou M. Ciona spp. and ascidians as bioindicator organisms for evaluating effects of endocrine disrupting chemicals: A discussion paper. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106170. [PMID: 37708617 DOI: 10.1016/j.marenvres.2023.106170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023]
Abstract
In context of testing, screening and monitoring of endocrine-disrupting (ED) type of environmental pollutants, tunicates could possibly represent a particularly interesting group of bioindicator organisms. These primitive chordates are already important model organisms within developmental and genomics research due to their central position in evolution and close relationship to vertebrates. The solitary ascidians, such as the genus Ciona spp. (vase tunicates), could possibly be extra feasible as ED bioindicators. They have a free-swimming, tadpole-like larval stage that develops extremely quickly (<20 h under favorable conditions), has a short life cycle (typically 2-3 months), are relatively easy to maintain in laboratory culture, have fully sequenced genomes, and transgenic embryos with 3D course data of the embryo ontogeny are available. In this article, we discuss possible roles of Ciona spp. (and other solitary ascidians) as ecotoxicological bioindicator organisms in general but perhaps especially for effect studies of contaminants with presumed endocrine disrupting modes of action.
Collapse
Affiliation(s)
- Jonny Beyer
- Norwegian Institute for Water Research (NIVA), Økernveien 94, NO-0579, Oslo, Norway.
| | - You Song
- Norwegian Institute for Water Research (NIVA), Økernveien 94, NO-0579, Oslo, Norway
| | - Adam Lillicrap
- Norwegian Institute for Water Research (NIVA), Økernveien 94, NO-0579, Oslo, Norway
| | | | | |
Collapse
|
7
|
Liu D, Lum KK, Treen N, Núñez CT, Yang J, Howard T, Levine M, Cristea I. IFI16 phase separation via multi-phosphorylation drives innate immune signaling. Nucleic Acids Res 2023; 51:6819-6840. [PMID: 37283074 PMCID: PMC10359621 DOI: 10.1093/nar/gkad449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/11/2023] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
The interferon inducible protein 16 (IFI16) is a prominent sensor of nuclear pathogenic DNA, initiating innate immune signaling and suppressing viral transcription. However, little is known about mechanisms that initiate IFI16 antiviral functions or its regulation within the host DNA-filled nucleus. Here, we provide in vitro and in vivo evidence to establish that IFI16 undergoes liquid-liquid phase separation (LLPS) nucleated by DNA. IFI16 binding to viral DNA initiates LLPS and induction of cytokines during herpes simplex virus type 1 (HSV-1) infection. Multiple phosphorylation sites within an intrinsically disordered region (IDR) function combinatorially to activate IFI16 LLPS, facilitating filamentation. Regulated by CDK2 and GSK3β, IDR phosphorylation provides a toggle between active and inactive IFI16 and the decoupling of IFI16-mediated cytokine expression from repression of viral transcription. These findings show how IFI16 switch-like phase transitions are achieved with temporal resolution for immune signaling and, more broadly, the multi-layered regulation of nuclear DNA sensors.
Collapse
Affiliation(s)
- Dawei Liu
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Krystal K Lum
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Corazón T Núñez
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jinhang Yang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Timothy R Howard
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael Levine
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
8
|
Ferran JL, Irimia M, Puelles L. Is There a Prechordal Region and an Acroterminal Domain in Amphioxus? BRAIN, BEHAVIOR AND EVOLUTION 2022; 96:334-352. [PMID: 35034027 DOI: 10.1159/000521966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022]
Abstract
This essay re-examines the singular case of the supposedly unique rostrally elongated notochord described classically in amphioxus. We start from our previous observations in hpf 21 larvae [Albuixech-Crespo et al.: PLoS Biol. 2017;15(4):e2001573] indicating that the brain vesicle has rostrally a rather standard hypothalamic molecular configuration. This correlates with the notochord across a possible rostromedian acroterminal hypothalamic domain. The notochord shows some molecular differences that specifically characterize its pre-acroterminal extension beyond its normal rostral end under the mamillary region. We explored an alternative interpretation that the putative extension of this notochord actually represents a variant form of the prechordal plate in amphioxus, some of whose cells would adopt the notochordal typology, but would lack notochordal patterning properties, and might have some (but not all) prechordal ones instead. We survey in detail the classic and recent literature on gastrulation, prechordal plate, and notochord formation in amphioxus, compare the observed patterns with those of some other vertebrates of interest, and re-examine the literature on differential gene expression patterns in this rostralmost area of the head. We noted that previous literature failed to identify the amphioxus prechordal primordia at appropriate stages. Under this interpretation, a consistent picture can be drawn for cephalochordates, tunicates, and vertebrates. Moreover, there is little evidence for an intrinsic capacity of the early notochord to grow rostralwards (it normally elongates caudalwards). Altogether, we conclude that the hypothesis of a prechordal nature of the elongated amphioxus notochord is consistent with the evidence presented.
Collapse
Affiliation(s)
- José Luis Ferran
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute of Biomedical Research of Murcia - IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute of Biomedical Research of Murcia - IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| |
Collapse
|
9
|
Morphological Study and 3D Reconstruction of the Larva of the Ascidian Halocynthia roretzi. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse10010011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The swimming larva represents the dispersal phase of ascidians, marine invertebrates belonging to tunicates. Due to its adhesive papillae, the larva searches the substrate, adheres to it, and undergoes metamorphosis, thereby becoming a sessile filter feeding animal. The larva anatomy has been described in detail in a few species, revealing a different degree of adult structure differentiation, called adultation. In the solitary ascidian Halocynthia roretzi, a species reared for commercial purposes, embryogenesis has been described in detail, but information on the larval anatomy is still lacking. Here, we describe it using a comparative approach, utilizing 3D reconstruction, as well as histological/TEM observations, with attention to its papillae. The larva is comparable to those of other solitary ascidians, such as Ciona intestinalis. However, it displays a higher level of adultation for the presence of the atrium, opened outside by means of the atrial siphon, and the peribranchial chambers. It does not reach the level of complexity of the larva of Botryllus schlosseri, a phylogenetically close colonial ascidian. Our study reveals that the papillae of H. roretzi, previously described as simple and conform, exhibit dynamic changes during settlement. This opens up new considerations on papillae morphology and evolution and deserves to be further investigated.
Collapse
|
10
|
Nourizadeh S, Kassmer S, Rodriguez D, Hiebert LS, De Tomaso AW. Whole body regeneration and developmental competition in two botryllid ascidians. EvoDevo 2021; 12:15. [PMID: 34911568 PMCID: PMC8675491 DOI: 10.1186/s13227-021-00185-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Botryllid ascidians are a group of marine invertebrate chordates that are colonial and grow by repeated rounds of asexual reproduction to form a colony of individual bodies, called zooids, linked by a common vascular network. Two distinct processes are responsible for zooid regeneration. In the first, called blastogenesis, new zooids arise from a region of multipotent epithelium from a pre-existing zooid. In the second, called whole body regeneration (WBR), mobile cells in the vasculature coalesce and are the source of the new zooid. In some botryllid species, blastogenesis and WBR occur concurrently, while in others, blastogenesis is used exclusively for growth, while WBR only occurs following injury or exiting periods of dormancy. In species such as Botrylloides diegensis, injury induced WBR is triggered by the surgical isolation of a small piece of vasculature. However, Botryllus schlosseri has unique requirements that must be met for successful injury induced WBR. Our goal was to understand why there would be different requirements between these two species. RESULTS While WBR in B. diegensis was robust, we found that in B. schlosseri, new zooid growth following injury is unlikely due to circulatory cells, but instead a result of ectopic development of tissues leftover from the blastogenic process. These tissues could be whole, damaged, or partially resorbed developing zooids, and we defined the minimal amount of vascular biomass to support ectopic regeneration. We did find a common theme between the two species: a competitive process exists which results in only a single zooid reaching maturity following injury. We utilized this phenomenon and found that competition is reversible and mediated by circulating factors and/or cells. CONCLUSIONS We propose that WBR does not occur in B. schlosseri and that the unique requirements defined in other studies only serve to increase the chances of ectopic development. This is likely a response to injury as we have discovered a vascular-based reversible competitive mechanism which ensures that only a single zooid completes development. This competition has been described in other species, but the unique response of B. schlosseri to injury provides a new model to study resource allocation and competition within an individual.
Collapse
Affiliation(s)
- Shane Nourizadeh
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, 93106, USA.
| | - Susannah Kassmer
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, 93106, USA
| | - Delany Rodriguez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, 93106, USA
| | - Laurel S Hiebert
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, 93106, USA
| | - Anthony W De Tomaso
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, 93106, USA
| |
Collapse
|
11
|
Winkley KM, Reeves WM, Veeman MT. Single-cell analysis of cell fate bifurcation in the chordate Ciona. BMC Biol 2021; 19:180. [PMID: 34465302 PMCID: PMC8408944 DOI: 10.1186/s12915-021-01122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. RESULTS AND CONCLUSIONS We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a "broad-hourglass" model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.
Collapse
Affiliation(s)
- Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
12
|
Gordon T, Upadhyay AK, Manni L, Huchon D, Shenkar N. And Then There Were Three…: Extreme Regeneration Ability of the Solitary Chordate Polycarpa mytiligera. Front Cell Dev Biol 2021; 9:652466. [PMID: 33937252 PMCID: PMC8083962 DOI: 10.3389/fcell.2021.652466] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Extensive regenerative ability is a common trait of animals capable of asexual development. The current study reveals the extraordinary regeneration abilities of the solitary ascidian Polycarpa mytiligera. Dissection of a single individual into separate fragments along two body axes resulted in the complete regeneration of each fragment into an independent, functional individual. The ability of a solitary ascidian, incapable of asexual development, to achieve bidirectional regeneration and fully regenerate all body structures and organs is described here for the first time. Amputation initiated cell proliferation in proximity to the amputation line. Phylogenetic analysis demonstrated the close affinity of P. mytiligera to colonial species. This evolutionary proximity suggests the ability for regeneration as an exaptation feature for colonial lifestyle. P. mytiligera’s exceptional regenerative abilities and phylogenetic position highlight its potential to serve as a new comparative system for studies seeking to uncover the evolution of regeneration and coloniality among the chordates.
Collapse
Affiliation(s)
- Tal Gordon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Arnav Kumar Upadhyay
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Lucia Manni
- Department of Biology, University of Padua, Padua, Italy
| | - Dorothée Huchon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv, Israel
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
13
|
Brandi V, Polticelli F. In Silico Analysis of Huntingtin Homologs in Lower Eukaryotes. Int J Mol Sci 2021; 22:3214. [PMID: 33809947 PMCID: PMC8004120 DOI: 10.3390/ijms22063214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022] Open
Abstract
Huntington's disease is a rare neurodegenerative and autosomal dominant disorder. HD is caused by a mutation in the gene coding for huntingtin (Htt). The result is the production of a mutant Htt with an abnormally long polyglutamine repeat that leads to pathological Htt aggregates. Although the structure of human Htt has been determined, albeit at low resolution, its functions and how they are performed are largely unknown. Moreover, there is little information on the structure and function of Htt in other organisms. The comparison of Htt homologs can help to understand if there is a functional conservation of domains in the evolution of Htt in eukaryotes. In this work, through a computational approach, Htt homologs from lower eukaryotes have been analysed, identifying ordered domains and modelling their structure. Based on the structural models, a putative function for most of the domains has been predicted. A putative C. elegans Htt-like protein has also been analysed following the same approach. The results obtained support the notion that this protein is a orthologue of human Htt.
Collapse
Affiliation(s)
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy;
- National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy
| |
Collapse
|
14
|
Reeves WM, Shimai K, Winkley KM, Veeman MT. Brachyury controls Ciona notochord fate as part of a feed-forward network. Development 2021; 148:dev195230. [PMID: 33419874 PMCID: PMC7875503 DOI: 10.1242/dev.195230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022]
Abstract
The notochord is a defining feature of the chordates. The transcription factor Brachyury (Bra) is a key regulator of notochord fate but here we show that it is not a unitary master regulator in the model chordate Ciona Ectopic Bra expression only partially reprograms other cell types to a notochord-like transcriptional profile and a subset of notochord-enriched genes is unaffected by CRISPR Bra disruption. We identify Foxa.a and Mnx as potential co-regulators, and find that combinatorial cocktails are more effective at reprogramming other cell types than Bra alone. We reassess the network relationships between Bra, Foxa.a and other components of the notochord gene regulatory network, and find that Foxa.a expression in the notochord is regulated by vegetal FGF signaling. It is a direct activator of Bra expression and has a binding motif that is significantly enriched in the regulatory regions of notochord-enriched genes. These and other results indicate that Bra and Foxa.a act together in a regulatory network dominated by positive feed-forward interactions, with neither being a classically defined master regulator.
Collapse
Affiliation(s)
- Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Kotaro Shimai
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
15
|
Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging. Sci Rep 2020; 10:20829. [PMID: 33257720 PMCID: PMC7709464 DOI: 10.1038/s41598-020-77585-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/12/2020] [Indexed: 12/01/2022] Open
Abstract
The transparency of animals is an important biological feature. Ascidian eggs have various degrees of transparency, but this characteristic has not yet been measured quantitatively and comprehensively. In this study, we established a method for evaluating the transparency of eggs to first characterize the transparency of ascidian eggs across different species and to infer a phylogenetic relationship among multiple taxa in the class Ascidiacea. We measured the transmittance of 199 eggs from 21 individuals using a hyperspectral camera. The spectrum of the visual range of wavelengths (400–760 nm) varied among individuals and we calculated each average transmittance of the visual range as bio-transparency. When combined with phylogenetic analysis based on the nuclear 18S rRNA and the mitochondrial cytochrome c oxidase subunit I gene sequences, the bio-transparencies of 13 species were derived from four different families: Ascidiidae, Cionidae, Pyuridae, and Styelidae. The bio-transparency varied 10–90% and likely evolved independently in each family. Ascidiella aspersa showed extremely high (88.0 ± 1.6%) bio-transparency in eggs that was maintained in the “invisible” larva. In addition, it was indicated that species of the Ascidiidae family may have a phylogenetic constraint of egg transparency.
Collapse
|
16
|
Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate. Genes (Basel) 2020; 11:genes11111262. [PMID: 33114624 PMCID: PMC7693978 DOI: 10.3390/genes11111262] [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: 09/19/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Tunicates are marine invertebrates whose tadpole-like larvae feature a highly simplified version of the chordate body plan. Similar to their distant vertebrate relatives, tunicate larvae develop a regionalized central nervous system and form distinct neural structures, which include a rostral sensory vesicle, a motor ganglion, and a caudal nerve cord. The sensory vesicle contains a photoreceptive complex and a statocyst, and based on the comparable expression patterns of evolutionarily conserved marker genes, it is believed to include proto-hypothalamic and proto-retinal territories. The evolutionarily conserved molecular fingerprints of these landmarks of the vertebrate brain consist of genes encoding for different transcription factors, and of the gene batteries that they control, and include several members of the bHLH family. Here we review the complement of bHLH genes present in the streamlined genome of the tunicate Ciona robusta and their current classification, and summarize recent studies on proneural bHLH transcription factors and their expression territories. We discuss the possible roles of bHLH genes in establishing the molecular compartmentalization of the enticing nervous system of this unassuming chordate.
Collapse
|
17
|
Demeter A, Romero-Mulero MC, Csabai L, Ölbei M, Sudhakar P, Haerty W, Korcsmáros T. ULK1 and ULK2 are less redundant than previously thought: computational analysis uncovers distinct regulation and functions of these autophagy induction proteins. Sci Rep 2020; 10:10940. [PMID: 32616830 PMCID: PMC7331686 DOI: 10.1038/s41598-020-67780-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/15/2020] [Indexed: 01/17/2023] Open
Abstract
Macroautophagy, the degradation of cytoplasmic content by lysosomal fusion, is an evolutionary conserved process promoting homeostasis and intracellular defence. Macroautophagy is initiated primarily by a complex containing ULK1 or ULK2 (two paralogs of the yeast Atg1 protein). To understand the differences between ULK1 and ULK2, we compared the human ULK1 and ULK2 proteins and their regulation. Despite the similarity in their enzymatic domain, we found that ULK1 and ULK2 have major differences in their autophagy-related interactors and their post-translational and transcriptional regulators. We identified 18 ULK1-specific and 7 ULK2-specific protein motifs serving as different interaction interfaces. We found that interactors of ULK1 and ULK2 all have different tissue-specific expressions partially contributing to diverse and ULK-specific interaction networks in various tissues. We identified three ULK1-specific and one ULK2-specific transcription factor binding sites, and eight sites shared by the regulatory region of both genes. Importantly, we found that both their post-translational and transcriptional regulators are involved in distinct biological processes-suggesting separate functions for ULK1 and ULK2. Unravelling differences between ULK1 and ULK2 could lead to a better understanding of how ULK-type specific dysregulation affects autophagy and other cellular processes that have been implicated in diseases such as inflammatory bowel disease and cancer.
Collapse
Affiliation(s)
- Amanda Demeter
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mari Carmen Romero-Mulero
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- Faculty of Biology, University of Seville, 41012, Seville, Spain
| | - Luca Csabai
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- Eötvös Loránd University, Budapest, 1117, Hungary
| | - Márton Ölbei
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Tamás Korcsmáros
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
| |
Collapse
|
18
|
Gordon T, Roth L, Caicci F, Manni L, Shenkar N. Spawning induction, development and culturing of the solitary ascidian Polycarpa mytiligera, an emerging model for regeneration studies. Front Zool 2020; 17:19. [PMID: 32536959 PMCID: PMC7288498 DOI: 10.1186/s12983-020-00365-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/21/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Ascidians (phylum Chordata, class Ascidiacea) represent the closest living invertebrate relatives of the vertebrates and constitute an important model for studying the evolution of chordate development. The solitary ascidian Polycarpa mytiligera exhibits a robust regeneration ability, unique among solitary chordates, thus offering a promising new model for regeneration studies. Understanding its reproductive development and establishing land-based culturing methods is pivotal for utilizing this species for experimental studies. Its reproduction cycle, spawning behavior, and developmental processes were therefore studied in both the field and the lab, and methods were developed for its culture in both open and closed water systems. RESULTS Field surveys revealed that P. mytiligera's natural recruitment period starts in summer (June) and ends in winter (December) when seawater temperature decreases. Laboratory experiments revealed that low temperature (21 °C) has a negative effect on its fertilization and development. Although spontaneous spawning events occur only between June and December, we were able to induce spawning under controlled conditions year-round by means of gradual changes in the environmental conditions. Spawning events, followed by larval development and metamorphosis, took place in ascidians maintained in either artificial or natural seawater facilities. P. mytiligera's fast developmental process indicated its resemblance to other oviparous species, with the larvae initiating settlement and metamorphosis at about 12 h post-hatching, and reaching the juvenile stage 3 days later. CONCLUSIONS Polycarpa mytiligera can be induced to spawn in captivity year-round, independent of the natural reproduction season. The significant advantages of P. mytiligera as a model system for regenerative studies, combined with the detailed developmental data and culturing methods presented here, will contribute to future research addressing developmental and evolutionary questions, and promote the use of this species as an applicable model system for experimental studies.
Collapse
Affiliation(s)
- Tal Gordon
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| | - Lachan Roth
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| | - Federico Caicci
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Lucia Manni
- Department of Biology, University of Padova, 35121 Padova, Italy
| | - Noa Shenkar
- George S. Wise Faculty of Life Sciences, School of Zoology, Tel-Aviv University, 6997801 Tel-Aviv, Israel
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, 6997801 Tel-Aviv, Israel
| |
Collapse
|
19
|
DeBiasse MB, Colgan WN, Harris L, Davidson B, Ryan JF. Inferring Tunicate Relationships and the Evolution of the Tunicate Hox Cluster with the Genome of Corella inflata. Genome Biol Evol 2020; 12:948-964. [PMID: 32211845 PMCID: PMC7337526 DOI: 10.1093/gbe/evaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 12/21/2022] Open
Abstract
Tunicates, the closest living relatives of vertebrates, have served as a foundational model of early embryonic development for decades. Comparative studies of tunicate phylogeny and genome evolution provide a critical framework for analyzing chordate diversification and the emergence of vertebrates. Toward this goal, we sequenced the genome of Corella inflata (Ascidiacea, Phlebobranchia), so named for the capacity to brood self-fertilized embryos in a modified, "inflated" atrial chamber. Combining the new genome sequence for Co. inflata with publicly available tunicate data, we estimated a tunicate species phylogeny, reconstructed the ancestral Hox gene cluster at important nodes in the tunicate tree, and compared patterns of gene loss between Co. inflata and Ciona robusta, the prevailing tunicate model species. Our maximum-likelihood and Bayesian trees estimated from a concatenated 210-gene matrix were largely concordant and showed that Aplousobranchia was nested within a paraphyletic Phlebobranchia. We demonstrated that this relationship is not an artifact due to compositional heterogeneity, as had been suggested by previous studies. In addition, within Thaliacea, we recovered Doliolida as sister to the clade containing Salpida and Pyrosomatida. The Co. inflata genome provides increased resolution of the ancestral Hox clusters of key tunicate nodes, therefore expanding our understanding of the evolution of this cluster and its potential impact on tunicate morphological diversity. Our analyses of other gene families revealed that several cardiovascular associated genes (e.g., BMP10, SCL2A12, and PDE2a) absent from Ci. robusta, are present in Co. inflata. Taken together, our results help clarify tunicate relationships and the genomic content of key ancestral nodes within this phylogeny, providing critical insights into tunicate evolution.
Collapse
Affiliation(s)
- Melissa B DeBiasse
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| | - William N Colgan
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Lincoln Harris
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida
- Department of Biology, University of Florida, Gainesville
| |
Collapse
|
20
|
Liu B, Satou Y. The genetic program to specify ectodermal cells in ascidian embryos. Dev Growth Differ 2020; 62:301-310. [PMID: 32130723 DOI: 10.1111/dgd.12660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 12/18/2022]
Abstract
The ascidian belongs to the sister group of vertebrates and shares many features with them. The gene regulatory network (GRN) controlling gene expression in ascidian embryonic development leading to the tadpole larva has revealed evolutionarily conserved gene circuits between ascidians and vertebrates. These conserved mechanisms are indeed useful to infer the original developmental programs of the ancestral chordates. Simultaneously, these studies have revealed which gene circuits are missing in the ascidian GRN; these gene circuits may have been acquired in the vertebrate lineage. In particular, the GRN responsible for gene expression in ectodermal cells of ascidian embryos has revealed the genetic programs that regulate the regionalization of the brain, formation of palps derived from placode-like cells, and differentiation of sensory neurons derived from neural crest-like cells. We here discuss how these studies have given insights into the evolution of these traits.
Collapse
Affiliation(s)
- Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
21
|
Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. Exploring miR-9 Involvement in Ciona intestinalis Neural Development Using Peptide Nucleic Acids. Int J Mol Sci 2020; 21:ijms21062001. [PMID: 32183450 PMCID: PMC7139483 DOI: 10.3390/ijms21062001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/16/2022] Open
Abstract
The microRNAs are small RNAs that regulate gene expression at the post-transcriptional level and can be involved in the onset of neurodegenerative diseases and cancer. They are emerging as possible targets for antisense-based therapy, even though the in vivo stability of miRNA analogues is still questioned. We tested the ability of peptide nucleic acids, a novel class of nucleic acid mimics, to downregulate miR-9 in vivo in an invertebrate model organism, the ascidian Ciona intestinalis, by microinjection of antisense molecules in the eggs. It is known that miR-9 is a well-conserved microRNA in bilaterians and we found that it is expressed in epidermal sensory neurons of the tail in the larva of C. intestinalis. Larvae developed from injected eggs showed a reduced differentiation of tail neurons, confirming the possibility to use peptide nucleic acid PNA to downregulate miRNA in a whole organism. By identifying putative targets of miR-9, we discuss the role of this miRNA in the development of the peripheral nervous system of ascidians.
Collapse
Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy;
- Correspondence: (S.C.); (S.C.); Tel.: +39-0250314147 (S.C.); +39-0103538051 (S.C.)
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16132 Genova, Italy
- Correspondence: (S.C.); (S.C.); Tel.: +39-0250314147 (S.C.); +39-0103538051 (S.C.)
| | - Giorgio Scarì
- Department of Biosciences, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Emanuela Licandro
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy;
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy; (S.M.); (R.M.); (R.P.)
| |
Collapse
|
22
|
Di Gregorio A. The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates. Curr Top Dev Biol 2020; 139:325-374. [PMID: 32450965 DOI: 10.1016/bs.ctdb.2020.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The notochord is a structure required for support and patterning of all chordate embryos, from sea squirts to humans. An increasing amount of information on notochord development and on the molecular strategies that ensure its proper morphogenesis has been gleaned through studies in the sea squirt Ciona. This invertebrate chordate offers a fortunate combination of experimental advantages, ranging from translucent, fast-developing embryos to a compact genome and impressive biomolecular resources. These assets have enabled the rapid identification of numerous notochord genes and cis-regulatory regions, and provide a rather unique opportunity to reconstruct the gene regulatory network that controls the formation of this developmental and evolutionary chordate landmark. This chapter summarizes the morphogenetic milestones that punctuate notochord formation in Ciona, their molecular effectors, and the current knowledge of the gene regulatory network that ensures the accurate spatial and temporal orchestration of these processes.
Collapse
Affiliation(s)
- Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, United States.
| |
Collapse
|
23
|
Sordino P, D'Aniello S, Pelletier E, Wincker P, Nittoli V, Stemmann L, Mazzocchi MG, Lombard F, Iudicone D, Caputi L. Into the bloom: Molecular response of pelagic tunicates to fluctuating food availability. Mol Ecol 2019; 29:292-307. [PMID: 31793138 DOI: 10.1111/mec.15321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 01/07/2023]
Abstract
The planktonic tunicates appendicularians and thaliaceans are highly efficient filter feeders on a wide range of prey size including bacteria and have shorter generation times than any other marine grazers. These traits allow some tunicate species to reach high population densities and ensure their success in a favourable environment. However, there are still few studies focusing on which genes and gene pathways are associated with responses of pelagic tunicates to environmental variability. Herein, we present the effect of food availability increase on tunicate community and gene expression at the Marquesas Islands (South-East Pacific Ocean). By using data from the Tara Oceans expedition, we show that changes in phytoplankton density and composition trigger the success of a dominant larvacean species (an undescribed appendicularian). Transcriptional signature to the autotroph bloom suggests key functions in specific physiological processes, i.e., energy metabolism, muscle contraction, membrane trafficking, and proteostasis. The relative abundance of reverse transcription-related Pfams was lower at bloom conditions, suggesting a link with adaptive genetic diversity in tunicates in natural ecosystems. Downstream of the bloom, pelagic tunicates were outcompeted by copepods. Our work represents the first metaomics study of the biological effects of phytoplankton bloom on a key zooplankton taxon.
Collapse
Affiliation(s)
| | | | - Eric Pelletier
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | - Patrick Wincker
- CEA - Institut Francois Jacob, Genoscope, Evry, France.,CNRS, UMR, Evry, France.,Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France
| | | | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | | | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, Paris, France.,CNRS, UMR 7093, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, Sorbonne Université, Villefranche-sur-Mer, France
| | | | | |
Collapse
|
24
|
Mercurio S, Cauteruccio S, Manenti R, Candiani S, Scarì G, Licandro E, Pennati R. miR-7 Knockdown by Peptide Nucleic Acids in the Ascidian Ciona intestinalis. Int J Mol Sci 2019; 20:ijms20205127. [PMID: 31623150 PMCID: PMC6829576 DOI: 10.3390/ijms20205127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Peptide Nucleic Acids (PNAs) are synthetic mimics of natural oligonucleotides, which bind complementary DNA/RNA strands with high sequence specificity. They display numerous advantages, but in vivo applications are still rare. One of the main drawbacks of PNAs application is the poor cellular uptake that could be overcome by using experimental models, in which microinjection techniques allow direct delivery of molecules into eggs. Thus, in this communication, we investigated PNAs efficiency in miR-7 downregulation and compared its effects with those obtained with the commercially available antisense molecule, Antagomir (Dharmacon) in the ascidian Ciona intestinalis. Ascidians are marine invertebrates closely related to vertebrates, in which PNA techniques have not been applied yet. Our results suggested that anti-miR-7 PNAs were able to reach their specific targets in the developing ascidian embryos with high efficiency, as the same effects were obtained with both PNA and Antagomir. To the best of our knowledge, this is the first evidence that unmodified PNAs can be applied in in vivo knockdown strategies when directly injected into eggs.
Collapse
Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Silvia Cauteruccio
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Simona Candiani
- Department of Earth Science, Environment and Life, Università degli Studi di Genova, 16126 Genova, Italy.
| | - Giorgio Scarì
- Department of Biosciences, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Emanuela Licandro
- Department of Chemistry, Università degli Studi di Milano, 20133 Milano, Italy.
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133 Milano, Italy.
| |
Collapse
|
25
|
Automated behavioural analysis reveals the basic behavioural repertoire of the urochordate Ciona intestinalis. Sci Rep 2019; 9:2416. [PMID: 30787329 PMCID: PMC6382837 DOI: 10.1038/s41598-019-38791-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
Quantitative analysis of animal behaviour in model organisms is becoming an increasingly essential approach for tackling the great challenge of understanding how activity in the brain gives rise to behaviour. Here we used automated image-based tracking to extract behavioural features from an organism of great importance in understanding the evolution of chordates, the free-swimming larval form of the tunicate Ciona intestinalis, which has a compact and fully mapped nervous system composed of only 231 neurons. We analysed hundreds of videos of larvae and we extracted basic geometric and physical descriptors of larval behaviour. Importantly, we used machine learning methods to create an objective ontology of behaviours for C. intestinalis larvae. We identified eleven behavioural modes using agglomerative clustering. Using our pipeline for quantitative behavioural analysis, we demonstrate that C. intestinalis larvae exhibit sensory arousal and thigmotaxis. Notably, the anxiotropic drug modafinil modulates thigmotactic behaviour. Furthermore, we tested the robustness of the larval behavioural repertoire by comparing different rearing conditions, ages and group sizes. This study shows that C. intestinalis larval behaviour can be broken down to a set of stereotyped behaviours that are used to different extents in a context-dependent manner.
Collapse
|
26
|
Kugler JE, Wu Y, Katikala L, Passamaneck YJ, Addy J, Caballero N, Oda-Ishii I, Maguire JE, Li R, Di Gregorio A. Positioning a multifunctional basic helix-loop-helix transcription factor within the Ciona notochord gene regulatory network. Dev Biol 2019; 448:119-135. [PMID: 30661645 DOI: 10.1016/j.ydbio.2019.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/27/2018] [Accepted: 01/01/2019] [Indexed: 11/26/2022]
Abstract
In a multitude of organisms, transcription factors of the basic helix-loop-helix (bHLH) family control the expression of genes required for organ development and tissue differentiation. The functions of different bHLH transcription factors in the specification of nervous system and paraxial mesoderm have been widely investigated in various model systems. Conversely, the knowledge of the role of these regulators in the development of the axial mesoderm, the embryonic territory that gives rise to the notochord, and the identities of their target genes, remain still fragmentary. Here we investigated the transcriptional regulation and target genes of Bhlh-tun1, a bHLH transcription factor expressed in the developing Ciona notochord as well as in additional embryonic territories that contribute to the formation of both larval and adult structures. We describe its possible role in notochord formation, its relationship with the key notochord transcription factor Brachyury, and suggest molecular mechanisms through which Bhlh-tun1 controls the spatial and temporal expression of its effectors.
Collapse
Affiliation(s)
- Jamie E Kugler
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Yushi Wu
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Lavanya Katikala
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Yale J Passamaneck
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Jermyn Addy
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Natalia Caballero
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Izumi Oda-Ishii
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Julie E Maguire
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Raymond Li
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - 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.
| |
Collapse
|
27
|
Messinetti S, Mercurio S, Pennati R. Bisphenol A affects neural development of the ascidian Ciona robusta. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2018; 331:5-16. [PMID: 30218549 DOI: 10.1002/jez.2230] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 08/06/2018] [Accepted: 08/21/2018] [Indexed: 11/06/2022]
Abstract
Bisphenol A (BPA) is an organic pollutant derived from plastic degradation that has numerous and variable adverse effects on human health and wildlife. In particular, it has been reported that BPA can alter reproductive processes and nervous system development in vertebrates. Considering BPA presence in marine environment and the scant data available on its interaction with nervous system development, we analyzed the effect of BPA exposure on sperm viability, fertilization, embryogenesis, and neural differentiation of the ascidian Ciona robusta. Ascidians are members of the Phylum Tunicata, the sister group of Vertebrata, sharing with them fundamental developmental processes. Our results showed that first cell division was altered starting from 5 µM concentration. Lethal concentration (LC 50 ) was estimated to be 5.2 µM. Larvae developed from treated embryos showed specific malformations to the pigment cells even at 0.1 µM, corresponding to the highest environmental concentration reported so far. Moreover, GABAergic and dopaminergic neurons proved to be target organs of BPA teratogenic action, in accordance with similar results reported in vertebrate animal models. Overall, our results suggest that BPA can exert its effects on nervous system acting on different pathways and underline that C. robusta is a valuable invertebrate animal model for preliminary screenings of effects of pollutants on vertebrates.
Collapse
Affiliation(s)
- Silvia Messinetti
- Department of Environmental Science and Policy, Università degli Studi di Milano, Italy
| | - Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, Italy
| | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, Italy
| |
Collapse
|
28
|
Pennati R, Manenti R, Stillitano A, Ficetola GF, Scarì G, Mercurio S, Menegola E. Teratogenic potential of nanoencapsulated vitamin A evaluated on an alternative model organism, the tunicate Ciona intestinalis. Int J Food Sci Nutr 2018; 69:805-813. [PMID: 29336191 DOI: 10.1080/09637486.2017.1418843] [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: 10/18/2022]
Abstract
Nano-encapsulation is a technology used to pack substances in order to enhance their stability and bioavailability, but this packing may interact with living systems, causing unexpected toxicity. Vitamin A (vit A) is a substance that has received attention, because in developed countries, the increasing availability of supplements is leading to its excessive intake. This study aims to compare teratogenic effects caused by exposure to the traditional formulation of vit A versus nano-encapsulated vit A. We used ascidian embryos as an alternative model. Ascidians are marine organisms closely related to vertebrates that share with them a body plan and developmental programme, including the morphogenetic role of retinoic acid (RA). Our data showed that the adverse effects of exposure to the same concentration of the two formulations were different, suggesting that the nano-encapsulation increased the bioavailability of the molecule, which could be better absorbed and metabolised to RA, the effective teratogenic substance.
Collapse
Affiliation(s)
- Roberta Pennati
- a Department of Environmental Science and Policy , University of Milan , Milan , Italy
| | - Raoul Manenti
- a Department of Environmental Science and Policy , University of Milan , Milan , Italy
| | - Antonella Stillitano
- a Department of Environmental Science and Policy , University of Milan , Milan , Italy
| | | | - Giorgio Scarì
- b Department of Biosciences , University of Milan , Milan , Italy
| | - Silvia Mercurio
- a Department of Environmental Science and Policy , University of Milan , Milan , Italy
| | - Elena Menegola
- a Department of Environmental Science and Policy , University of Milan , Milan , Italy
| |
Collapse
|
29
|
|
30
|
Maguire JE, Pandey A, Wu Y, Di Gregorio A. Investigating Evolutionarily Conserved Molecular Mechanisms Controlling Gene Expression in the Notochord. TRANSGENIC ASCIDIANS 2018. [DOI: 10.1007/978-981-10-7545-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
31
|
Battistoni M, Mercurio S, Ficetola GF, Metruccio FC, Menegola E, Pennati R. The Ascidian Embryo Teratogenicity assay in Ciona intestinalis as a new teratological screening to test the mixture effect of the co-exposure to ethanol and fluconazole. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 57:76-85. [PMID: 29223040 DOI: 10.1016/j.etap.2017.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work was to evaluate the Ascidian Embryo Teratogenicity assay (AET) as new alternative invertebrate model to test the developmental effects of the co-exposure to ethanol and fluconazole. Ciona intestinalis embryos were exposed to the azolic fungicide fluconazole, (FLUCO, 7.8-250μM), to ethanol (Eth, 0.01-0.5%) and to their mixture (0.01% Eth+FLUCO 7.8-250μM) from neurula to larval stage. At the end of the exposure period, larvae were morphologically evaluated and benchmark analysis performed by using the PROAST modelling software. Both compounds were teratogenic in a concentration-related manner, particularly affecting the pigmented organs. The co-exposure to Eth enhanced the effects of FLUCO, the additive hypothesis was not rejected by the modelling. The results demonstrated that AET could be considered a good vertebrate-free alternative model for toxicological investigation in embryos.
Collapse
Affiliation(s)
- Maria Battistoni
- Department of Environmental Sciences and Policy, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| | - Silvia Mercurio
- Department of Environmental Sciences and Policy, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| | - Gentile Francesco Ficetola
- Department of Environmental Sciences and Policy, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| | - Francesca Cristiana Metruccio
- International Centre for Pesticides and Health Risk Prevention (ICPS), University Hospital Luigi Sacco, via G.B. Grassi 74, 20157 Milan, Italy
| | - Elena Menegola
- Department of Environmental Sciences and Policy, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy.
| | - Roberta Pennati
- Department of Environmental Sciences and Policy, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy
| |
Collapse
|
32
|
Reeves WM, Wu Y, Harder MJ, Veeman MT. Functional and evolutionary insights from the Ciona notochord transcriptome. Development 2017; 144:3375-3387. [PMID: 28928284 DOI: 10.1242/dev.156174] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022]
Abstract
The notochord of the ascidian Ciona consists of only 40 cells, and is a longstanding model for studying organogenesis in a small, simple embryo. Here, we perform RNAseq on flow-sorted notochord cells from multiple stages to define a comprehensive Ciona notochord transcriptome. We identify 1364 genes with enriched expression and extensively validate the results by in situ hybridization. These genes are highly enriched for Gene Ontology terms related to the extracellular matrix, cell adhesion and cytoskeleton. Orthologs of 112 of the Ciona notochord genes have known notochord expression in vertebrates, more than twice as many as predicted by chance alone. This set of putative effector genes with notochord expression conserved from tunicates to vertebrates will be invaluable for testing hypotheses about notochord evolution. The full set of Ciona notochord genes provides a foundation for systems-level studies of notochord gene regulation and morphogenesis. We find only modest overlap between this set of notochord-enriched transcripts and the genes upregulated by ectopic expression of the key notochord transcription factor Brachyury, indicating that Brachyury is not a notochord master regulator gene as strictly defined.
Collapse
Affiliation(s)
- Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Yuye Wu
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Matthew J Harder
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
33
|
Sharma N, Khurana N, Muthuraman A. Lower vertebrate and invertebrate models of Alzheimer's disease - A review. Eur J Pharmacol 2017; 815:312-323. [PMID: 28943103 DOI: 10.1016/j.ejphar.2017.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/20/2017] [Accepted: 09/13/2017] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease is a common neurodegenerative disorder which is characterized by the presence of beta- amyloid protein and neurofibrillary tangles (NFTs) in the brain. Till now, various higher vertebrate models have been in use to study the pathophysiology of this disease. But, these models possess some limitations like ethical restrictions, high cost, difficult maintenance of large quantity and lesser reproducibility. Besides, various lower chordate animals like Danio rerio, Drosophila melanogaster, Caenorhabditis elegans and Ciona intestinalis have been proved to be an important model for the in vivo determination of targets of drugs with least limitations. In this article, we reviewed different studies conducted on theses models for the better understanding of the pathophysiology of AD and their subsequent application as a potential tool in the preclinical evaluation of new drugs.
Collapse
Affiliation(s)
- Neha Sharma
- Department of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Navneet Khurana
- Department of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Arunachalam Muthuraman
- Department of Pharmacology, Akal College of Pharmacy and Technical Education, Mastuana Sahib, Sangrur, Punjab, India; Department of Pharmacology, JSS College of Pharmacy, Jagadguru Sri Shivarathreeshwara University, Mysuru 570015, Karnataka, India.
| |
Collapse
|
34
|
Konrad MW. Blood circulation in the ascidian tunicate Corella inflata (Corellidae). PeerJ 2016; 4:e2771. [PMID: 27994977 PMCID: PMC5160921 DOI: 10.7717/peerj.2771] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 11/08/2016] [Indexed: 01/20/2023] Open
Abstract
The body of the ascidian tunicate Corella inflata is relatively transparent. Thus, the circulatory system can be visualized by injecting high molecular weight fluorescein labeled dextran into the heart or the large vessels at the ends of the heart without surgery to remove the body wall. In addition, after staining with neutral red, the movement of blood cells can be easily followed to further characterize the circulatory system. The heart is two gently curved concentric tubes extending across the width of the animal. The inner myocardial tube has a partial constriction approximately in the middle. As in other tunicates, the heart is peristaltic and periodically reverses direction. During the branchial phase blood leaves the anterior end of the heart by two asymmetric vessels that connect to the two sides of the branchial basket. Blood then flows in both transverse directions through a complex system of ducts in the basket into large ventral and dorsal vessels which carry blood back to the visceral organs in the posterior of the animal. During the visceral phase blood leaves the posterior end of the heart in two vessels that repeatedly bifurcate and fan into the stomach and gonads. Blood velocity, determined by following individual cells in video frames, is high and pulsatory near the heart. A double peak in velocity at the maximum may be due to the constriction in the middle of the heart tube. Blood velocity progressively decreases with distance from the heart. In peripheral regions with vessels of small diameter blood cells frequently collide with vessel walls and cell motion is erratic. The estimated volume of blood flow during each directional phase is greater than the total volume of the animal. Circulating blood cells are confined to vessels or ducts in the visible parts of the animal and retention of high molecular weight dextran in the vessels is comparable to that seen in vertebrates. These are characteristics of a closed circulatory system.
Collapse
|
35
|
Abstract
Ascidians are invertebrate chordates with a biphasic life cycle characterized by a dual body plan that displays simplified versions of chordate structures, such as a premetamorphic 40-cell notochord topped by a dorsal nerve cord and postmetamorphic pharyngeal slits. These relatively simple chordates are characterized by rapid development, compact genomes and ease of transgenesis, and thus provide the opportunity to rapidly characterize the genomic organization, developmental function, and transcriptional regulation of evolutionarily conserved gene families. This review summarizes the current knowledge on members of the T-box family of transcription factors in Ciona and other ascidians. In both chordate and nonchordate animals, these genes control a variety of morphogenetic processes, and their mutations are responsible for malformations and developmental defects in organisms ranging from flies to humans. In ascidians, T-box transcription factors are required for the formation and specialization of essential structures, including notochord, muscle, heart, and differentiated neurons. In recent years, the experimental advantages offered by ascidian embryos have allowed the rapid accumulation of a wealth of information on the molecular mechanisms that regulate the expression of T-box genes. These studies have also elucidated the strategies employed by these transcription factors to orchestrate the appropriate spatial and temporal deployment of the numerous target genes that they control.
Collapse
Affiliation(s)
- A Di Gregorio
- New York University College of Dentistry, New York, NY, United States.
| |
Collapse
|
36
|
Segade F, Cota C, Famiglietti A, Cha A, Davidson B. Fibronectin contributes to notochord intercalation in the invertebrate chordate, Ciona intestinalis. EvoDevo 2016; 7:21. [PMID: 27583126 PMCID: PMC5006582 DOI: 10.1186/s13227-016-0056-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/13/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genomic analysis has upended chordate phylogeny, placing the tunicates as the sister group to the vertebrates. This taxonomic rearrangement raises questions about the emergence of a tunicate/vertebrate ancestor. RESULTS Characterization of developmental genes uniquely shared by tunicates and vertebrates is one promising approach for deciphering developmental shifts underlying acquisition of novel, ancestral traits. The matrix glycoprotein Fibronectin (FN) has long been considered a vertebrate-specific gene, playing a major instructive role in vertebrate embryonic development. However, the recent computational prediction of an orthologous "vertebrate-like" Fn gene in the genome of a tunicate, Ciona savignyi, challenges this viewpoint suggesting that Fn may have arisen in the shared tunicate/vertebrate ancestor. Here we verify the presence of a tunicate Fn ortholog. Transgenic reporter analysis was used to characterize a Ciona Fn enhancer driving expression in the notochord. Targeted knockdown in the notochord lineage indicates that FN is required for proper convergent extension. CONCLUSIONS These findings suggest that acquisition of Fn was associated with altered notochord morphogenesis in the vertebrate/tunicate ancestor.
Collapse
Affiliation(s)
- Fernando Segade
- Department of Anatomy and Cell Biology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA 19104 USA
| | - Christina Cota
- Department of Biology, Swarthmore College, 500 College Ave., Swarthmore, PA 19081 USA
| | - Amber Famiglietti
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anna Cha
- Department of Systems Biology, Harvard Medical School, Boston, MA USA
| | - Brad Davidson
- Department of Biology, Swarthmore College, 500 College Ave., Swarthmore, PA 19081 USA
| |
Collapse
|
37
|
José-Edwards DS, Oda-Ishii I, Kugler JE, Passamaneck YJ, Katikala L, Nibu Y, Di Gregorio A. Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord. PLoS Genet 2015; 11:e1005730. [PMID: 26684323 PMCID: PMC4684326 DOI: 10.1371/journal.pgen.1005730] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022] Open
Abstract
A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs), and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC) microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.
Collapse
Affiliation(s)
- Diana S. José-Edwards
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Izumi Oda-Ishii
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Jamie E. Kugler
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Yale J. Passamaneck
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Lavanya Katikala
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Yutaka Nibu
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Anna Di Gregorio
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
38
|
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.
Collapse
Affiliation(s)
- Michael Veeman
- Division of Biology, Kansas State University, Manhattan KS, USA
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan KS, USA
| |
Collapse
|
39
|
Carlson M, Reeves W, Veeman M. Stochasticity and stereotypy in the Ciona notochord. Dev Biol 2014; 397:248-56. [PMID: 25459659 DOI: 10.1016/j.ydbio.2014.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/17/2014] [Accepted: 11/13/2014] [Indexed: 12/21/2022]
Abstract
Fate mapping with single cell resolution has typically been confined to embryos with completely stereotyped development. The lineages giving rise to the 40 cells of the Ciona notochord are invariant, but the intercalation of those cells into a single-file column is not. Here we use genetic labeling methods to fate map the Ciona notochord with both high resolution and large sample sizes. We find that the ordering of notochord cells into a single column is not random, but instead shows a distinctive signature characteristic of mediolaterally-biased intercalation. We find that patterns of cell intercalation in the notochord are somewhat stochastic but far more stereotyped than previously believed. Cell behaviors vary by lineage, with the secondary notochord lineage being much more constrained than the primary lineage. Within the primary lineage, patterns of intercalation reflect the geometry of the intercalating tissue. We identify the latest point at which notochord morphogenesis is largely stereotyped, which is shortly before the onset of mediolateral intercalation and immediately after the final cell divisions in the primary lineage. These divisions are consistently oriented along the AP axis. Our results indicate that the interplay between stereotyped and stochastic cell behaviors in morphogenesis can only be assessed by fate mapping experiments that have both cellular resolution and large sample sizes.
Collapse
Affiliation(s)
- Maia Carlson
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States.
| |
Collapse
|
40
|
Thompson JM, Di Gregorio A. Insulin-like genes in ascidians: findings in Ciona and hypotheses on the evolutionary origins of the pancreas. Genesis 2014; 53:82-104. [PMID: 25378051 DOI: 10.1002/dvg.22832] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 10/13/2014] [Accepted: 10/16/2014] [Indexed: 12/22/2022]
Abstract
Insulin plays an extensively characterized role in the control of sugar metabolism, growth and homeostasis in a wide range of organisms. In vertebrate chordates, insulin is mainly produced by the beta cells of the endocrine pancreas, while in non-chordate animals insulin-producing cells are mainly found in the nervous system and/or scattered along the digestive tract. However, recent studies have indicated the notochord, the defining feature of the chordate phylum, as an additional site of expression of insulin-like peptides. Here we show that two of the three insulin-like genes identified in Ciona intestinalis, an invertebrate chordate with a dual life cycle, are first expressed in the developing notochord during embryogenesis and transition to distinct areas of the adult digestive tract after metamorphosis. In addition, we present data suggesting that the transcription factor Ciona Brachyury is involved in the control of notochord expression of at least one of these genes, Ciona insulin-like 2. Finally, we review the information currently available on insulin-producing cells in ascidians and on pancreas-related transcription factors that might control their expression.
Collapse
Affiliation(s)
- Jordan M Thompson
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York
| | | |
Collapse
|
41
|
Exploiting the extraordinary genetic polymorphism of ciona for developmental genetics with whole genome sequencing. Genetics 2014; 197:49-59. [PMID: 24532781 DOI: 10.1534/genetics.114.161778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca(2+) channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.
Collapse
|
42
|
Reeves W, Thayer R, Veeman M. Anterior-posterior regionalized gene expression in the Ciona notochord. Dev Dyn 2013; 243:612-620. [PMID: 24288133 DOI: 10.1002/dvdy.24101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND In the simple ascidian chordate Ciona, the signaling pathways and gene regulatory networks giving rise to initial notochord induction are largely understood and the mechanisms of notochord morphogenesis are being systematically elucidated. The notochord has generally been thought of as a non-compartmentalized or regionalized organ that is not finely patterned at the level of gene expression. Quantitative imaging methods have recently shown, however, that notochord cell size, shape, and behavior vary consistently along the anterior-posterior (AP) axis. RESULTS Here we screen candidate genes by whole mount in situ hybridization for potential AP asymmetry. We identify 4 genes that show non-uniform expression in the notochord. Ezrin/radixin/moesin (ERM) is expressed more strongly in the secondary notochord lineage than the primary. CTGF is expressed stochastically in a subset of notochord cells. A novel calmodulin-like gene (BCamL) is expressed more strongly at both the anterior and posterior tips of the notochord. A TGF-β ortholog is expressed in a gradient from posterior to anterior. The asymmetries in ERM, BCamL, and TGF-β expression are evident even before the notochord cells have intercalated into a single-file column. CONCLUSIONS We conclude that the Ciona notochord is not a homogeneous tissue but instead shows distinct patterns of regionalized gene expression.
Collapse
Affiliation(s)
- Wendy Reeves
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Rachel Thayer
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Michael Veeman
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| |
Collapse
|
43
|
Parallel evolution of chordate cis-regulatory code for development. PLoS Genet 2013; 9:e1003904. [PMID: 24282393 PMCID: PMC3836708 DOI: 10.1371/journal.pgen.1003904] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/09/2013] [Indexed: 12/17/2022] Open
Abstract
Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations. Vertebrates share many aspects of early development with our closest chordate ancestors, the tunicates. However, whilst the repertoire of genes that orchestrate development is essentially the same in the two lineages, the genomic code that regulates these genes appears to be very different, even though it is highly conserved within vertebrates themselves. Using comparative genomics, we have identified a parallel developmental code in tunicates and confirmed that this code, despite a lack of sequence conservation, associates with a similar repertoire of genes. However, the organisation of the code spatially is very different in the two lineages, strongly suggesting that most of it arose independently in vertebrates and tunicates, and in most cases lacking any direct sequence ancestry. We have assayed elements of the tunicate code, and found that at least some of them can regulate gene expression in zebrafish embryos. Our results suggest that regulatory code has arisen independently in different animal lineages but possesses some common functionality because its evolution has been driven by a similar cohort of developmental transcription factors. Our work helps illuminate how complex, stable gene regulatory networks evolve and become fixed within lineages.
Collapse
|
44
|
Katikala L, Aihara H, Passamaneck YJ, Gazdoiu S, José-Edwards DS, Kugler JE, Oda-Ishii I, Imai JH, Nibu Y, Di Gregorio A. Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord. PLoS Biol 2013; 11:e1001697. [PMID: 24204212 PMCID: PMC3812116 DOI: 10.1371/journal.pbio.1001697] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 09/19/2013] [Indexed: 11/18/2022] Open
Abstract
During notochord formation in chordate embryos, the transcription factor Brachyury employs different regulatory strategies to ensure the sequential activation of downstream genes and thereby the deployment of a specific developmental program at the right time and place. The appearance of the notochord represented a milestone in Deuterostome evolution. The notochord is necessary for the development of the chordate body plan and for the formation of the vertebral column and numerous organs. It is known that the transcription factor Brachyury is required for notochord formation in all chordates, and that it controls transcription of a large number of target genes. However, studies of the structure of the cis-regulatory modules (CRMs) through which this control is exerted are complicated in vertebrates by the genomic complexity and the pan-mesodermal expression territory of Brachyury. We used the ascidian Ciona, in which the single-copy Brachyury is notochord-specific and CRMs are easily identifiable, to carry out a systematic characterization of Brachyury-downstream notochord CRMs. We found that Ciona Brachyury (Ci-Bra) controls most of its targets directly, through non-palindromic binding sites that function either synergistically or individually to activate early- and middle-onset genes, respectively, while late-onset target CRMs are controlled indirectly, via transcriptional intermediaries. These results illustrate how a transcriptional regulator can efficiently shape a shallow gene regulatory network into a multi-tiered transcriptional output, and provide insights into the mechanisms that establish temporal read-outs of gene expression in a fast-developing chordate embryo. Transcription factors control where and when gene expression is switched on by binding to specific stretches of DNA known as cis-regulatory modules (CRMs). In this study, we investigated the architecture and composition of CRMs that direct gene expression in the notochord—a transient rod-like structure found in all embryos that belong to the phylum chordata, which includes humans. Here we used the sea squirt Ciona, a simple chordate, and analyzed how the transcription factor Brachyury ensures the appropriate deployment of its target genes at specific times during the sequential steps of notochord formation. We compared CRMs found in different notochord genes downstream of Brachyury, expecting to find genes associated with greater numbers of Brachyury binding sites to be expressed at higher levels. To our surprise, we found instead that a higher number of functional Brachyury binding sites is typical of CRMs associated with genes that are expressed early in notochord development, while single-site CRMs are characteristic of genes that are turned on during the intermediate stages of this process. Finally, CRMs associated with genes expressed late in notochord development do not contain functional Brachyury binding sites but are controlled by Brachyury indirectly, through the action of intermediary transcription factors. These differences explain how a transcription factor that is present at all stages in a certain cell type can generate a sequential transcriptional output of gene expression.
Collapse
Affiliation(s)
- Lavanya Katikala
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Hitoshi Aihara
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Yale J. Passamaneck
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Stefan Gazdoiu
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Diana S. José-Edwards
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Jamie E. Kugler
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Izumi Oda-Ishii
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Janice H. Imai
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Yutaka Nibu
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail: (YN); (ADG)
| | - Anna Di Gregorio
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail: (YN); (ADG)
| |
Collapse
|
45
|
José-Edwards DS, Oda-Ishii I, Nibu Y, Di Gregorio A. Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development. Development 2013; 140:2422-33. [PMID: 23674602 DOI: 10.1242/dev.094227] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
T-box genes are potent regulators of mesoderm development in many metazoans. In chordate embryos, the T-box transcription factor Brachyury (Bra) is required for specification and differentiation of the notochord. In some chordates, including the ascidian Ciona, members of the Tbx2 subfamily of T-box genes are also expressed in this tissue; however, their regulatory relationships with Bra and their contributions to the development of the notochord remain uncharacterized. We determined that the notochord expression of Ciona Tbx2/3 (Ci-Tbx2/3) requires Ci-Bra, and identified a Ci-Tbx2/3 notochord CRM that necessitates multiple Ci-Bra binding sites for its activity. Expression of mutant forms of Ci-Tbx2/3 in the developing notochord revealed a role for this transcription factor primarily in convergent extension. Through microarray screens, we uncovered numerous Ci-Tbx2/3 targets, some of which overlap with known Ci-Bra-downstream notochord genes. Among the Ci-Tbx2/3 notochord targets are evolutionarily conserved genes, including caspases, lineage-specific genes, such as Noto4, and newly identified genes, such as MLKL. This work sheds light on a large section of the notochord regulatory circuitry controlled by T-box factors, and reveals new components of the complement of genes required for the proper formation of this structure.
Collapse
Affiliation(s)
- Diana S José-Edwards
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, Box 60, New York, NY 10065, USA
| | | | | | | |
Collapse
|
46
|
From notochord formation to hereditary chordoma: the many roles of Brachyury. BIOMED RESEARCH INTERNATIONAL 2013; 2013:826435. [PMID: 23662285 PMCID: PMC3626178 DOI: 10.1155/2013/826435] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/22/2013] [Indexed: 12/25/2022]
Abstract
Chordoma is a rare, but often malignant, bone cancer that preferentially affects the axial skeleton and the skull base. These tumors are both sporadic and hereditary and appear to occur more frequently after the fourth decade of life; however, modern technologies have increased the detection of pediatric chordomas. Chordomas originate from remnants of the notochord, the main embryonic axial structure that precedes the backbone, and share with notochord cells both histological features and the expression of characteristic genes. One such gene is Brachyury, which encodes for a sequence-specific transcription factor. Known for decades as a main regulator of notochord formation, Brachyury has recently gained interest as a biomarker and causative agent of chordoma, and therefore as a promising therapeutic target. Here, we review the main characteristics of chordoma, the molecular markers, and the clinical approaches currently available for the early detection and possible treatment of this cancer. In particular, we report on the current knowledge of the role of Brachyury and of its possible mechanisms of action in both notochord formation and chordoma etiogenesis.
Collapse
|
47
|
Saxena S, Dupont S, Meghah V, Lakshmi MGM, Singh SK, Swamy CVB, Idris MM. Proteome map of the neural complex of the tunicate Ciona intestinalis, the closest living relative to vertebrates. Proteomics 2013; 13:860-5. [PMID: 23300126 DOI: 10.1002/pmic.201200148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 11/13/2012] [Accepted: 11/28/2012] [Indexed: 11/07/2022]
Abstract
Ciona intestinalis (the common sea squirt) is the closest living chordate relative to vertebrates with cosmopolitan presence worldwide. It has a relatively simple nervous system and development, making it a widely studied alternative model system in neuroscience and developmental biology. The use of Ciona as a model organism has increased significantly after the draft genome was published. In this study, we describe the first proteome map of the neural complex of C. intestinalis. A total of 544 proteins were identified based on 1DE and 2DE FTMS/ITMSMS analyses. Proteins were annotated against the Ciona database and analyzed to predict their molecular functions, roles in biological processes, and position in constructed network pathways. The identified Ciona neural complex proteome was found to map onto vertebrate nervous system pathways, including cytoskeleton remodeling neurofilaments, cell adhesion through the histamine receptor signaling pathway, γ-aminobutyric acid-A receptor life cycle neurophysiological process, glycolysis, and amino acid metabolism. The proteome map of the Ciona neural complex is the first step toward a better understanding of several important processes, including the evolution and regeneration capacity of the Ciona nervous system.
Collapse
Affiliation(s)
- Sandeep Saxena
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, Andhra Pradesh, India
| | | | | | | | | | | | | |
Collapse
|
48
|
Xavier-Neto J, Trueba SS, Stolfi A, Souza HM, Sobreira TJP, Schubert M, Castillo HA. An unauthorized biography of the second heart field and a pioneer/scaffold model for cardiac development. Curr Top Dev Biol 2012; 100:67-105. [PMID: 22449841 DOI: 10.1016/b978-0-12-387786-4.00003-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The identification of subpharyngeal cardiac precursors has had a strong influence on the way we think about early cardiac development. From this discovery was born the concept of multiple heart fields. Early support for the concept came from gene expression, genetic retrospective fate mapping, and gene targeting studies, which collectively suggested the existence of a second heart field (SHF) on the basis of specific Islet-1 (Isl-1) expression, presence of two cardiac ancestral lineages, and compatible cardiac knockout phenotypes, respectively. A decade after the original studies, support for the SHF concept is dwindling. This is because in all bilaterian models studied, Isl expression in heart progenitors is not SHF-specific, because lineage data are best explained by alternative models including an older, truly ancestral, lineage of cardiac pioneers with unrestricted contribution to all cardiac segments and, finally, because the inflow-to-outflow segmental nature of the early vertebrate peristaltic heart has been reaffirmed with novel, less invasive, methodologies. Altogether, the paradigms derived from the discovery of subpharyngeal cardiac progenitors helped us shift from relatively simple models, which rely predominantly either on patterning, gene expression patterns or lineages, to a much more sophisticated body of knowledge in which all these parameters must be accounted. Thus, it is well possible that due consideration of the key elements contained in the inflow/outflow, pioneer/scaffold, ballooning, and SHF hypotheses may provide us with a unified framework of the early stages of cardiac development. Here, we advance into this direction by suggesting an intuitive model of early heart development based on the concept of an inflow/outflow scaffold erected by cardiac pioneers, one that is required to assemble all the subsequent cell contribution that emigrates from cardiac progenitor areas.
Collapse
Affiliation(s)
- José Xavier-Neto
- Brazilian National Laboratory for Biosciences, Brazilian Association for Synchrotron Light Technology, Rua Giuseppe Máximo Scolfaro, Campinas, São Paulo, Brazil
| | | | | | | | | | | | | |
Collapse
|
49
|
Wagner E, Levine M. FGF signaling establishes the anterior border of the Ciona neural tube. Development 2012; 139:2351-9. [PMID: 22627287 DOI: 10.1242/dev.078485] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Ciona tadpole is constructed from simple, well-defined cell lineages governed by provisional gene networks that have been defined via extensive gene disruption assays. Here, we examine the patterning of the anterior neural plate, which produces placodal derivatives such as the adhesive palps and stomodeum, as well as the sensory vesicle (simple brain) of the Ciona tadpole. Evidence is presented that the doublesex-related gene DMRT is expressed throughout the anterior neural plate of neurulating embryos. It leads to the activation of FoxC and ZicL in the palp placode and anterior neural tube, respectively. This differential expression depends on FGF signaling, which inhibits FoxC expression in the anterior neural tube. Inhibition of FGF signaling leads to expanded expression of FoxC, the loss of ZicL, and truncation of the anterior neural tube.
Collapse
Affiliation(s)
- Eileen Wagner
- Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | | |
Collapse
|
50
|
Abstract
Noggin, along with other secreted bone morphogenetic protein (BMP) inhibitors, plays a crucial role in neural induction and neural tube patterning as well as in somitogenesis, cardiac morphogenesis and formation of the skeleton in vertebrates. The BMP signalling pathway is one of the seven fundamental pathways that drive embryonic development and pattern formation in animals. Understanding its evolutionary origin and role in pattern formation is, therefore, important to evolutionary developmental biology (evo-devo). We have studied the evolutionary origin of BMP-Noggin antagonism in hydra, which is a powerful diploblastic model to study evolution of pattern-forming mechanisms because of the unusual cellular dynamics during its pattern formation and its remarkable ability to regenerate. We cloned and characterized the noggin gene from hydra and found it to exhibit considerable similarity with its orthologues at the amino acid level. Microinjection of hydra Noggin mRNA led to duplication of the dorsoventral axis in Xenopus embryos, demonstrating its functional conservation across the taxa. Our data, along with those of others, indicate that the evolutionarily conserved antagonism between BMP and its inhibitors predates bilateral divergence. This article reviews the various roles of Noggin in different organisms and some of our recent work on hydra Noggin in the context of evolution of developmental signalling pathways.
Collapse
Affiliation(s)
- Kalpana Chandramore
- Division of Animal Sciences, Agharkar Research Institute, Pune 411 004, India
| | | |
Collapse
|