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Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583753. [PMID: 38559144 PMCID: PMC10979880 DOI: 10.1101/2024.03.06.583753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is only expressed in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. While in vertebrates Myogenic Regulatory Factors (MRFs) like MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF/MyoD and Early B-Cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models.
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Affiliation(s)
| | - Zheng Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Renjie Shang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pengpeng Bi
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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2
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Long J, Mariossi A, Cao C, Mo Z, Thompson JW, Levine MS, Lemaire LA. Cereblon influences the timing of muscle differentiation in Ciona tadpoles. Proc Natl Acad Sci U S A 2023; 120:e2309989120. [PMID: 37856545 PMCID: PMC10614628 DOI: 10.1073/pnas.2309989120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/09/2023] [Indexed: 10/21/2023] Open
Abstract
Thalidomide has a dark history as a teratogen, but in recent years, its derivates have been shown to function as potent chemotherapeutic agents. These drugs bind cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, and modify its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ Ciona, a simple invertebrate chordate, to identify endogenous Crbn targets. In Ciona, Crbn is specifically expressed in developing muscles during tail elongation before they acquire contractile activity. Crbn expression is activated by Mrf, the ortholog of MYOD1, a transcription factor important for muscle differentiation. CRISPR/Cas9-mediated mutations of Crbn lead to precocious onset of muscle contractions. By contrast, overexpression of Crbn delays contractions and is associated with decreased expression of contractile protein genes such as troponin. This reduction is possibly due to reduced Mrf protein levels without altering Mrf mRNA levels. Our findings suggest that Mrf and Crbn form a negative feedback loop to control the precision of muscle differentiation during tail elongation.
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Affiliation(s)
- Juanjuan Long
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | | | | | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Laurence A. Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Biology, Saint Louis University, St. Louis, MO63103
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3
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Yu D, Iwamura Y, Satou Y, Oda-Ishii I. Tbx15/18/22 shares a binding site with Tbx6-r.b to maintain expression of a muscle structural gene in ascidian late embryos. Dev Biol 2021; 483:1-12. [PMID: 34963554 DOI: 10.1016/j.ydbio.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 12/25/2022]
Abstract
The ascidian larval tail contains muscle cells for swimming. Most of these muscle cells differentiate autonomously. The genetic program behind this autonomy has been studied extensively and the genetic cascade from maternal factors to initiation of expression of a muscle structural gene, Myl.c, has been uncovered; Myl.c expression is directed initially by transcription factor Tbx6-r.b at the 64-cell stage and then by the combined actions of Tbx6-r.b and Mrf from the gastrula to early tailbud stages. In the present study, we showed that transcription of Myl.c continued in late tailbud embryos and larvae, although a fusion protein of Tbx6-r.b and GFP was hardly detectable in late tailbud embryos. A knockdown experiment, reporter assay, and in vitro binding assay indicated that an essential cis-regulatory element of Myl.c that bound Tbx6-r.b in early embryos bound Tbx15/18/22 in late embryos to maintain expression of Myl.c. We also found that Tbx15/18/22 was controlled by Mrf, which constitutes a regulatory loop with Tbx6-r.b. Therefore, our data indicated that Tbx15/18/22 was activated initially under control of this regulatory loop as in the case of Myl.c, and then Tbx15/18/22 maintained the expression of Myl.c after Tbx6-r.b had disappeared. RNA-sequencing of Tbx15/18/22 morphant embryos revealed that many muscle structural genes were regulated similarly by Tbx15/18/22. Thus, the present study revealed the mechanisms of maintenance of transcription of muscle structural genes in late embryos in which Tbx15/18/22 takes the place of Tbx6-r.b.
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Affiliation(s)
- Deli Yu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yuri Iwamura
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
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4
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Matsuo K, Tamura R, Hotta K, Okada M, Takeuchi A, Wu Y, Hashimoto K, Takano H, Momose A, Nishino A. Bilaterally Asymmetric Helical Myofibrils in Ascidian Tadpole Larvae. Front Cell Dev Biol 2021; 9:800455. [PMID: 34950666 PMCID: PMC8688927 DOI: 10.3389/fcell.2021.800455] [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: 10/23/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
The locomotor system is highly bilateral at the macroscopic level. Homochirality of biological molecules is fully compatible with the bilateral body. However, whether and how single-handed cells contribute to the bilateral locomotor system is obscure. Here, exploiting the small number of cells in the swimming tadpole larva of the ascidian Ciona, we analyzed morphology of the tail at cellular and subcellular scales. Quantitative phase-contrast X-ray tomographic microscopy revealed a high-density midline structure ventral to the notochord in the tail. Muscle cell nuclei on each side of the notochord were roughly bilaterally aligned. However, fluorescence microscopy detected left-right asymmetry of myofibril inclination relative to the longitudinal axis of the tail. Zernike phase-contrast X-ray tomographic microscopy revealed the presence of left-handed helices of myofibrils in muscle cells on both sides. Therefore, the locomotor system of ascidian larvae harbors symmetry-breaking left-handed helical cells, while maintaining bilaterally symmetrical cell alignment. These results suggest that bilateral animals can override cellular homochirality to generate the bilateral locomotor systems at the supracellular scale.
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Affiliation(s)
- Koichi Matsuo
- Laboratory of Cell and Tissue Biology, Keio University School of Medicine, Tokyo, Japan
| | - Ryota Tamura
- Department of Neurosurgery, Keio University School of Medicine, Tokyo, Japan
| | - Kohji Hotta
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Mayu Okada
- Laboratory of Cell and Tissue Biology, Keio University School of Medicine, Tokyo, Japan
| | - Akihisa Takeuchi
- Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Japan
| | - Yanlin Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Koh Hashimoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Hidekazu Takano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Atsushi Momose
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Atsuo Nishino
- Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
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5
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Kobayashi K, Maeda K, Tokuoka M, Mochizuki A, Satou Y. Using linkage logic theory to control dynamics of a gene regulatory network of a chordate embryo. Sci Rep 2021; 11:4001. [PMID: 33597570 PMCID: PMC7889898 DOI: 10.1038/s41598-021-83045-y] [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: 07/24/2020] [Accepted: 01/28/2021] [Indexed: 11/09/2022] Open
Abstract
Linkage logic theory provides a mathematical criterion to control network dynamics by manipulating activities of a subset of network nodes, which are collectively called a feedback vertex set (FVS). Because many biological functions emerge from dynamics of biological networks, this theory provides a promising tool for controlling biological functions. By manipulating the activity of FVS molecules identified in a gene regulatory network (GRN) for fate specification of seven tissues in ascidian embryos, we previously succeeded in reproducing six of the seven cell types. Simultaneously, we discovered that the experimentally reconstituted GRN lacked information sufficient to reproduce muscle cells. Here, we utilized linkage logic theory as a tool to find missing edges in the GRN. Then, we identified a FVS from an updated version of the GRN and confirmed that manipulating the activity of this FVS was sufficient to induce all seven cell types, even in a multi-cellular environment. Thus, linkage logic theory provides tools to find missing edges in experimentally reconstituted networks, to determine whether reconstituted networks contain sufficient information to fulfil expected functions, and to reprogram cell fate.
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Affiliation(s)
- Kenji Kobayashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Kazuki Maeda
- Faculty of Informatics, The University of Fukuchiyama, 3370 Hori, Fukuchiyama, Kyoto, 620-0886, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan
| | - Atsushi Mochizuki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo, Kyoto, 606-8507, Japan.
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, 606-8502, Japan.
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Mercurio S, Messinetti S, Manenti R, Ficetola GF, Pennati R. Embryotoxicity characterization of the flame retardant tris(1-chloro-2-propyl)phosphate (TCPP) in the invertebrate chordate Ciona intestinalis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2021; 335:339-347. [PMID: 33503327 DOI: 10.1002/jez.2446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/27/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022]
Abstract
Tris(1-chloro-2-propyl)phosphate (TCPP) is the most common chlorinated organophosphorus flame retardant in seawater. Due to its chemical features and abundance, TCPP has been classified as a high hazard, and restrictions of use have been set in multiple countries. Despite TCPP being highly present in the marine environment, only a few studies have explored the TCPP impact on the development of marine invertebrates. Ascidians are important invertebrate members of benthic marine communities and reliable model systems for ecotoxicological research. The aim of this study was to assess the adverse effects of TCPP exposure on the embryogenesis of the ascidian Ciona intestinalis. Our results showed that this pollutant affected both muscles and nervous system development. Malformations appeared similar to those reported in other animal models for other flame retardants, suggesting that these molecules could share a common mechanism of action and induce a mixture effect when simultaneously present in the aquatic environment even at sub-teratogenic concentrations.
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Affiliation(s)
- Silvia Mercurio
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Silvia Messinetti
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - Raoul Manenti
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | | | - Roberta Pennati
- Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
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Zullo L, Bozzo M, Daya A, Di Clemente A, Mancini FP, Megighian A, Nesher N, Röttinger E, Shomrat T, Tiozzo S, Zullo A, Candiani S. The Diversity of Muscles and Their Regenerative Potential across Animals. Cells 2020; 9:cells9091925. [PMID: 32825163 PMCID: PMC7563492 DOI: 10.3390/cells9091925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Cells with contractile functions are present in almost all metazoans, and so are the related processes of muscle homeostasis and regeneration. Regeneration itself is a complex process unevenly spread across metazoans that ranges from full-body regeneration to partial reconstruction of damaged organs or body tissues, including muscles. The cellular and molecular mechanisms involved in regenerative processes can be homologous, co-opted, and/or evolved independently. By comparing the mechanisms of muscle homeostasis and regeneration throughout the diversity of animal body-plans and life cycles, it is possible to identify conserved and divergent cellular and molecular mechanisms underlying muscle plasticity. In this review we aim at providing an overview of muscle regeneration studies in metazoans, highlighting the major regenerative strategies and molecular pathways involved. By gathering these findings, we wish to advocate a comparative and evolutionary approach to prompt a wider use of “non-canonical” animal models for molecular and even pharmacological studies in the field of muscle regeneration.
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Affiliation(s)
- Letizia Zullo
- Istituto Italiano di Tecnologia, Center for Micro-BioRobotics & Center for Synaptic Neuroscience and Technology (NSYN), 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
- Correspondence: (L.Z.); (A.Z.)
| | - Matteo Bozzo
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genova, Viale Benedetto XV 5, 16132 Genova, Italy; (M.B.); (S.C.)
| | - Alon Daya
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Alessio Di Clemente
- Istituto Italiano di Tecnologia, Center for Micro-BioRobotics & Center for Synaptic Neuroscience and Technology (NSYN), 16132 Genova, Italy;
- Department of Experimental Medicine, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | | | - Aram Megighian
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Nir Nesher
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Eric Röttinger
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, CNRS, INSERM, 06107 Nice, France;
| | - Tal Shomrat
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Stefano Tiozzo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Paris, France;
| | - Alberto Zullo
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy;
- Correspondence: (L.Z.); (A.Z.)
| | - Simona Candiani
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genova, Viale Benedetto XV 5, 16132 Genova, Italy; (M.B.); (S.C.)
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8
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Fiuza UM, Negishi T, Rouan A, Yasuo H, Lemaire P. A Nodal/Eph signalling relay drives the transition from apical constriction to apico-basal shortening in ascidian endoderm invagination. Development 2020; 147:dev.186965. [DOI: 10.1242/dev.186965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/02/2020] [Indexed: 01/13/2023]
Abstract
Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin network. First, endoderm precursors constrict their apex. Second, they shorten apico-basally, while retaining small apical surfaces, thereby causing invagination. The mechanisms that prevent endoderm cell division, trigger the transition between step 1 and step 2, and drive apico-basal shortening have remained elusive. Here, we demonstrate a conserved role for Nodal and Eph signalling during invagination in two distantly related ascidian species, Phallusia mammillata and Ciona intestinalis. Specifically, we show that the transition to step 2 is triggered by Nodal relayed by Eph signalling. Additionally, our results indicate that Eph signalling lengthens the endodermal cell cycle, independently of Nodal. Finally, we find that both Nodal and Eph signals are dispensable for endoderm fate specification. These results illustrate commonalities as well as differences in the action of Nodal during ascidian and vertebrate gastrulation.
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Affiliation(s)
- Ulla-Maj Fiuza
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | - Takefumi Negishi
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, CNRS, Sorbonne Universités, 06230 Villefranche-sur-Mer, France
| | - Alice Rouan
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, CNRS, Sorbonne Universités, 06230 Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, CNRS, Sorbonne Universités, 06230 Villefranche-sur-Mer, France
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9
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Satou Y. A gene regulatory network for cell fate specification in Ciona embryos. Curr Top Dev Biol 2020; 139:1-33. [DOI: 10.1016/bs.ctdb.2020.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Lewandowski D, Dubińska-Magiera M, Migocka-Patrzałek M, Niedbalska-Tarnowska J, Haczkiewicz-Leśniak K, Dzięgiel P, Daczewska M. Everybody wants to move-Evolutionary implications of trunk muscle differentiation in vertebrate species. Semin Cell Dev Biol 2019; 104:3-13. [PMID: 31759871 DOI: 10.1016/j.semcdb.2019.10.009] [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: 06/07/2019] [Accepted: 10/17/2019] [Indexed: 10/25/2022]
Abstract
In our review we have completed current knowledge on myotomal myogenesis in model and non-model vertebrate species (fishes, amphibians, reptiles, birds and mammals) at morphological and molecular levels. Data obtained from these studies reveal distinct similarities and differences between amniote and anamniote species. Based on the available data, we decided to present evolutionary implications in vertebrate trunk muscle development. Despite the fact that in all vertebrates muscle fibres are multinucleated, the pathways leading to them vary between vertebrate taxa. In fishes during early myogenesis myoblasts differentiate into multinucleated lamellae or multinucleate myotubes. In amphibians, myoblasts fuse to form multinucleated myotubes or, bypassing fusion, directly differentiate into mononucleated myotubes. Furthermore, mononucleated myotubes were also observed during primary myogenesis in amniotes. The mononucleated state of myogenic cells could be considered as an old phylogenetic, plesiomorphic feature, whereas direct multinuclearity of myotubes has a synapomorphic character. On the other hand, the explanation of this phenomenon could also be linked to the environmental conditions in which animals develop. The similarities observed in vertebrate myogenesis might result from a conservative myogenic programme governed by the Pax3/Pax7 and myogenic regulatory factor (MRF) network, whereas differences in anamniotes and amniotes are established by spatiotemporal pattern expression of MRFs during muscle differentiation and/or environmental conditions.
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Affiliation(s)
- Damian Lewandowski
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wrocław, Poland.
| | - Magda Dubińska-Magiera
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Marta Migocka-Patrzałek
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Joanna Niedbalska-Tarnowska
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wrocław, Poland; Laboratory of Molecular and Cellular Immunology, Department of Tumor Immunology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wrocław, Poland
| | | | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Chałubińskiego 6a, 50-368 Wrocław, Poland; Department of Physiotherapy, University School of Physical Education, Paderewskiego 35, 51-612 Wrocław, Poland
| | - Małgorzata Daczewska
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, Sienkiewicza 21, 50-335 Wrocław, Poland
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11
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Racioppi C, Wiechecki KA, Christiaen L. Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices. eLife 2019; 8:49921. [PMID: 31746740 PMCID: PMC6952182 DOI: 10.7554/elife.49921] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022] Open
Abstract
During embryogenesis, chromatin accessibility profiles control lineage-specific gene expression by modulating transcription, thus impacting multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. We found that multiple cis-regulatory elements, with distinct chromatin accessibility profiles and motif compositions, are required to activate Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that these 'combined enhancers' foster spatially and temporally accurate fate choices, by increasing the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity.
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Affiliation(s)
- Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Keira A Wiechecki
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
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12
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Razy-Krajka F, Stolfi A. Regulation and evolution of muscle development in tunicates. EvoDevo 2019; 10:13. [PMID: 31249657 PMCID: PMC6589888 DOI: 10.1186/s13227-019-0125-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/08/2019] [Indexed: 12/16/2022] Open
Abstract
For more than a century, studies on tunicate muscle formation have revealed many principles of cell fate specification, gene regulation, morphogenesis, and evolution. Here, we review the key studies that have probed the development of all the various muscle cell types in a wide variety of tunicate species. We seize this occasion to explore the implications and questions raised by these findings in the broader context of muscle evolution in chordates.
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Affiliation(s)
- Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
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13
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Ratcliffe LE, Asiedu EK, Pickett CJ, Warburton MA, Izzi SA, Meedel TH. The Ciona myogenic regulatory factor functions as a typical MRF but possesses a novel N-terminus that is essential for activity. Dev Biol 2019; 448:210-225. [PMID: 30365920 PMCID: PMC6478573 DOI: 10.1016/j.ydbio.2018.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/28/2018] [Accepted: 10/16/2018] [Indexed: 11/26/2022]
Abstract
Electroporation-based assays were used to test whether the myogenic regulatory factor (MRF) of Ciona intestinalis (CiMRF) interferes with endogenous developmental programs, and to evaluate the importance of its unusual N-terminus for muscle development. We found that CiMRF suppresses both notochord and endoderm development when it is expressed in these tissues by a mechanism that may involve activation of muscle-specific microRNAs. Because these results add to a large body of evidence demonstrating the exceptionally high degree of functional conservation among MRFs, we were surprised to discover that non-ascidian MRFs were not myogenic in Ciona unless they formed part of a chimeric protein containing the CiMRF N-terminus. Equally surprising, we found that despite their widely differing primary sequences, the N-termini of MRFs of other ascidian species could form chimeric MRFs that were also myogenic in Ciona. This domain did not rescue the activity of a Brachyury protein whose transcriptional activation domain had been deleted, and so does not appear to constitute such a domain. Our results indicate that ascidians have previously unrecognized and potentially novel requirements for MRF-directed myogenesis. Moreover, they provide the first example of a domain that is essential to the core function of an important family of gene regulatory proteins, one that, to date, has been found in only a single branch of the family.
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Affiliation(s)
- Lindsay E Ratcliffe
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Emmanuel K Asiedu
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - C J Pickett
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Megan A Warburton
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Stephanie A Izzi
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
| | - Thomas H Meedel
- Department of Biology, Rhode Island College, 600 Mt. Pleasant Ave., Providence, RI 02908, USA.
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Yu D, Oda-Ishii I, Kubo A, Satou Y. The regulatory pathway from genes directly activated by maternal factors to muscle structural genes in ascidian embryos. Development 2019; 146:dev.173104. [PMID: 30674480 DOI: 10.1242/dev.173104] [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: 10/22/2018] [Accepted: 01/14/2019] [Indexed: 10/27/2022]
Abstract
Striated muscle cells in the tail of ascidian tadpole larvae differentiate cell-autonomously. Although several key regulatory factors have been identified, the genetic regulatory pathway is not fully understood; comprehensive understanding of the regulatory pathway is essential for accurate modeling in order to deduce principles for gene regulatory network dynamics, and for comparative analysis on how ascidians have evolved the cell-autonomous gene regulatory mechanism. Here, we reveal regulatory interactions among three key regulatory factors, Zic-r.b, Tbx6-r.b and Mrf, and elucidate the mechanism by which these factors activate muscle structural genes. We reveal a cross-regulatory circuit among these regulatory factors, which maintains the expression of Tbx6-r.b and Mrf during gastrulation. Although these two factors combinatorially activate muscle structural genes in late-stage embryos, muscle structural genes are activated mainly by Tbx6-r.b before gastrulation. Time points when expression of muscle structural genes become first detectable are strongly correlated with the degree of Tbx6-r.b occupancy. Thus, the genetic pathway, starting with Tbx6-r.b and Zic-r.b, which are activated by maternal factors, and ending with expression of muscle structural genes, has been revealed.
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Affiliation(s)
- Deli Yu
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Atsushi Kubo
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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15
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Kobayashi K, Maeda K, Tokuoka M, Mochizuki A, Satou Y. Controlling Cell Fate Specification System by Key Genes Determined from Network Structure. iScience 2018; 4:281-293. [PMID: 30240747 PMCID: PMC6147236 DOI: 10.1016/j.isci.2018.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/19/2018] [Accepted: 05/07/2018] [Indexed: 11/25/2022] Open
Abstract
Network structures describing regulation between biomolecules have been determined in many biological systems. Dynamics of molecular activities based on such networks are considered to be the origin of many biological functions. Recently, it has been proved mathematically that key nodes for controlling dynamics in networks are identified from network structure alone. Here, we applied this theory to a gene regulatory network for the cell fate specification of seven tissues in the ascidian embryo and found that this network, which consisted of 92 factors, had five key molecules. By controlling the activities of these key molecules, the specific gene expression of six of seven tissues observed in the embryo was successfully reproduced. Since this method is applicable to all nonlinear dynamic systems, we propose this method as a tool for controlling gene regulatory networks and reprogramming cell fates.
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Affiliation(s)
- Kenji Kobayashi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuki Maeda
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Department of Mathematical Sciences, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Atsushi Mochizuki
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Theoretical Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo, Kyoto 606-8507, Japan.
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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16
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Gene regulatory networks and cell lineages that underlie the formation of skeletal muscle. Proc Natl Acad Sci U S A 2018; 114:5830-5837. [PMID: 28584083 DOI: 10.1073/pnas.1610605114] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Skeletal muscle in vertebrates is formed by two major routes, as illustrated by the mouse embryo. Somites give rise to myogenic progenitors that form all of the muscles of the trunk and limbs. The behavior of these cells and their entry into the myogenic program is controlled by gene regulatory networks, where paired box gene 3 (Pax3) plays a predominant role. Head and some neck muscles do not derive from somites, but mainly form from mesoderm in the pharyngeal region. Entry into the myogenic program also depends on the myogenic determination factor (MyoD) family of genes, but Pax3 is not expressed in these myogenic progenitors, where different gene regulatory networks function, with T-box factor 1 (Tbx1) and paired-like homeodomain factor 2 (Pitx2) as key upstream genes. The regulatory genes that underlie the formation of these muscles are also important players in cardiogenesis, expressed in the second heart field, which is a major source of myocardium and of the pharyngeal arch mesoderm that gives rise to skeletal muscles. The demonstration that both types of striated muscle derive from common progenitors comes from clonal analyses that have established a lineage tree for parts of the myocardium and different head and neck muscles. Evolutionary conservation of the two routes to skeletal muscle in vertebrates extends to chordates, to trunk muscles in the cephlochordate Amphioxus and to muscles derived from cardiopharyngeal mesoderm in the urochordate Ciona, where a related gene regulatory network determines cardiac or skeletal muscle cell fates. In conclusion, Eric Davidson's visionary contribution to our understanding of gene regulatory networks and their evolution is acknowledged.
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Tolkin T, Christiaen L. Rewiring of an ancestral Tbx1/10-Ebf-Mrf network for pharyngeal muscle specification in distinct embryonic lineages. Development 2017; 143:3852-3862. [PMID: 27802138 DOI: 10.1242/dev.136267] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/30/2016] [Indexed: 01/01/2023]
Abstract
Skeletal muscles arise from diverse embryonic origins in vertebrates, yet converge on extensively shared regulatory programs that require muscle regulatory factor (MRF)-family genes. Myogenesis in the tail of the simple chordate Ciona exhibits a similar reliance on its single MRF-family gene, and diverse mechanisms activate Ci-Mrf Here, we show that myogenesis in the atrial siphon muscles (ASMs) and oral siphon muscles (OSMs), which control the exhalant and inhalant siphons, respectively, also requires Mrf We characterize the ontogeny of OSM progenitors and compare the molecular basis of Mrf activation in OSM versus ASM. In both muscle types, Ebf and Tbx1/10 are expressed and function upstream of Mrf However, we demonstrate that regulatory relationships between Tbx1/10, Ebf and Mrf differ between the OSM and ASM lineages. We propose that Tbx1, Ebf and Mrf homologs form an ancient conserved regulatory state for pharyngeal muscle specification, whereas their regulatory relationships might be more evolutionarily variable.
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Affiliation(s)
- Theadora Tolkin
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
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18
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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.
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Affiliation(s)
- A Di Gregorio
- New York University College of Dentistry, New York, NY, United States.
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Regulation and evolution of cardiopharyngeal cell identity and behavior: insights from simple chordates. Curr Opin Genet Dev 2015; 32:119-28. [PMID: 25819888 DOI: 10.1016/j.gde.2015.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/16/2015] [Accepted: 02/23/2015] [Indexed: 01/08/2023]
Abstract
The vertebrate heart arises from distinct first and second heart fields. The latter also share a common origin with branchiomeric muscles in the pharyngeal mesoderm and transcription regulators, such as Nkx2-5, Tbx1 and Islet1. Despite significant progress, the complexity of vertebrate embryos has hindered the identification of multipotent cardiopharyngeal progenitors. Here, we summarize recent insights in cardiopharyngeal development gained from ascidian models, among the closest relatives to vertebrates. In a simplified cellular context, progressive fate specification of the ascidian cardiopharyngeal precursors presents striking similarities with their vertebrate counterparts. Multipotent cardiopharyngeal progenitors are primed to activate both the early cardiac and pharyngeal muscles programs, which segregate following asymmetric cells divisions as a result of regulatory cross-antagonisms involving Tbx1 and Nkx2-5 homologs. Activation of Ebf in pharyngeal muscle founder cells triggers both Myogenic Regulatory Factor-associated differentiation and Notch-mediated maintenance of an undifferentiated state in distinct precursors. Cross-species comparisons revealed the deep conservation of the cardiopharyngeal developmental sequence in spite of extreme genome sequence divergence, gene network rewiring and specific morphogenetic differences. Finally, analyses are beginning to uncover the influence of surrounding tissues in determining cardiopharyngeal cell identity and behavior. Thus, ascidian embryos offer a unique opportunity to study gene regulation and cell behaviors at the cellular level throughout cardiopharyngeal morphogenesis and evolution.
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Satou Y, Imai KS. Gene regulatory systems that control gene expression in the Ciona embryo. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:33-51. [PMID: 25748582 PMCID: PMC4406867 DOI: 10.2183/pjab.91.33] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/05/2014] [Indexed: 06/04/2023]
Abstract
Transcriptional control of gene expression is one of the most important regulatory systems in animal development. Specific gene expression is basically determined by combinatorial regulation mediated by multiple sequence-specific transcription factors. The decoding of animal genomes has provided an opportunity for us to systematically examine gene regulatory networks consisting of successive layers of control of gene expression. It remains to be determined to what extent combinatorial regulation encoded in gene regulatory networks can explain spatial and temporal gene-expression patterns. The ascidian Ciona intestinalis is one of the animals in which the gene regulatory network has been most extensively studied. In this species, most specific gene expression patterns in the embryo can be explained by combinations of upstream regulatory genes encoding transcription factors and signaling molecules. Systematic scrutiny of gene expression patterns and regulatory interactions at the cellular resolution have revealed incomplete parts of the network elucidated so far, and have identified novel regulatory genes and novel regulatory mechanisms.
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Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University; CREST, JST, Saitama, Japan.
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22
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Razy-Krajka F, Lam K, Wang W, Stolfi A, Joly M, Bonneau R, Christiaen L. Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors. Dev Cell 2014; 29:263-76. [PMID: 24794633 DOI: 10.1016/j.devcel.2014.04.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 01/26/2014] [Accepted: 04/01/2014] [Indexed: 01/09/2023]
Abstract
In vertebrates, pluripotent pharyngeal mesoderm progenitors produce the cardiac precursors of the second heart field as well as the branchiomeric head muscles and associated stem cells. However, the mechanisms underlying the transition from multipotent progenitors to distinct muscle precursors remain obscured by the complexity of vertebrate embryos. Using Ciona intestinalis as a simple chordate model, we show that bipotent cardiopharyngeal progenitors are primed to activate both heart and pharyngeal muscle transcriptional programs, which progressively become restricted to corresponding precursors. The transcription factor COE (Collier/OLF/EBF) orchestrates the transition to pharyngeal muscle fate both by promoting an MRF-associated myogenic program in myoblasts and by maintaining an undifferentiated state in their sister cells through Notch-mediated lateral inhibition. The latter are stem cell-like muscle precursors that form most of the juvenile pharyngeal muscles. We discuss the implications of our findings for the development and evolution of the chordate cardiopharyngeal mesoderm.
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Affiliation(s)
- Florian Razy-Krajka
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Karen Lam
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Wei Wang
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Alberto Stolfi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Marine Joly
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Richard Bonneau
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA.
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Patterns of positive selection of the myogenic regulatory factor gene family in vertebrates. PLoS One 2014; 9:e92873. [PMID: 24651579 PMCID: PMC3961423 DOI: 10.1371/journal.pone.0092873] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/26/2014] [Indexed: 11/19/2022] Open
Abstract
The functional divergence of transcriptional factors is critical in the evolution of transcriptional regulation. However, the mechanism of functional divergence among these factors remains unclear. Here, we performed an evolutionary analysis for positive selection in members of the myogenic regulatory factor (MRF) gene family of vertebrates. We selected 153 complete vertebrate MRF nucleotide sequences from our analyses, which revealed substantial evidence of positive selection. Here, we show that sites under positive selection were more frequently detected and identified from the genes encoding the myogenic differentiation factors (MyoG and Myf6) than the genes encoding myogenic determination factors (Myf5 and MyoD). Additionally, the functional divergence within the myogenic determination factors or differentiation factors was also under positive selection pressure. The positive selection sites were more frequently detected from MyoG and MyoD than Myf6 and Myf5, respectively. Amino acid residues under positive selection were identified mainly in their transcription activation domains and on the surface of protein three-dimensional structures. These data suggest that the functional gain and divergence of myogenic regulatory factors were driven by distinct positive selection of their transcription activation domains, whereas the function of the DNA binding domains was conserved in evolution. Our study evaluated the mechanism of functional divergence of the transcriptional regulation factors within a family, whereby the functions of their transcription activation domains diverged under positive selection during evolution.
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Andrikou C, Iovene E, Rizzo F, Oliveri P, Arnone MI. Myogenesis in the sea urchin embryo: the molecular fingerprint of the myoblast precursors. EvoDevo 2013; 4:33. [PMID: 24295205 PMCID: PMC4175510 DOI: 10.1186/2041-9139-4-33] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 10/02/2013] [Indexed: 01/01/2023] Open
Abstract
Background In sea urchin larvae the circumesophageal fibers form a prominent muscle system of mesodermal origin. Although the morphology and later development of this muscle system has been well-described, little is known about the molecular signature of these cells or their precise origin in the early embryo. As an invertebrate deuterostome that is more closely related to the vertebrates than other commonly used model systems in myogenesis, the sea urchin fills an important phylogenetic gap and provides a unique perspective on the evolution of muscle cell development. Results Here, we present a comprehensive description of the development of the sea urchin larval circumesophageal muscle lineage beginning with its mesodermal origin using high-resolution localization of the expression of several myogenic transcriptional regulators and differentiation genes. A few myoblasts are bilaterally distributed at the oral vegetal side of the tip of the archenteron and first appear at the late gastrula stage. The expression of the differentiation genes Myosin Heavy Chain, Tropomyosin I and II, as well as the regulatory genes MyoD2, FoxF, FoxC, FoxL1, Myocardin, Twist, and Tbx6 uniquely identify these cells. Interestingly, evolutionarily conserved myogenic factors such as Mef2, MyoR and Six1/2 are not expressed in sea urchin myoblasts but are found in other mesodermal domains of the tip of the archenteron. The regulatory states of these domains were characterized in detail. Moreover, using a combinatorial analysis of gene expression we followed the development of the FoxF/FoxC positive cells from the onset of expression to the end of gastrulation. Our data allowed us to build a complete map of the Non-Skeletogenic Mesoderm at the very early gastrula stage, in which specific molecular signatures identify the precursors of different cell types. Among them, a small group of cells within the FoxY domain, which also express FoxC and SoxE, have been identified as plausible myoblast precursors. Together, these data support a very early gastrula stage segregation of the myogenic lineage. Conclusions From this analysis, we are able to precisely define the regulatory and differentiation signatures of the circumesophageal muscle in the sea urchin embryo. Our findings have important implications in understanding the evolution of development of the muscle cell lineage at the molecular level. The data presented here suggest a high level of conservation of the myogenic specification mechanisms across wide phylogenetic distances, but also reveal clear cases of gene cooption.
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Affiliation(s)
| | | | | | | | - Maria Ina Arnone
- Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy.
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25
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Izzi SA, Colantuono BJ, Sullivan K, Khare P, Meedel TH. Functional studies of the Ciona intestinalis myogenic regulatory factor reveal conserved features of chordate myogenesis. Dev Biol 2013; 376:213-23. [PMID: 23391688 DOI: 10.1016/j.ydbio.2013.01.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/08/2013] [Accepted: 01/24/2013] [Indexed: 10/27/2022]
Abstract
Ci-MRF is the sole myogenic regulatory factor (MRF) of the ascidian Ciona intestinalis, an invertebrate chordate. In order to investigate its properties we developed a simple in vivo assay based on misexpressing Ci-MRF in the notochord of Ciona embryos. We used this assay to examine the roles of three structural motifs that are conserved among MRFs: an alanine-threonine (Ala-Thr) dipeptide of the basic domain that is known in vertebrates as the myogenic code, a cysteine/histidine-rich (C/H) domain found just N-terminal to the basic domain, and a carboxy-terminal amphipathic α-helix referred to as Helix III. We show that the Ala-Thr dipeptide is necessary for normal Ci-MRF function, and that while eliminating the C/H domain or Helix III individually has no demonstrable effect on Ci-MRF, simultaneous loss of both motifs significantly reduces its activity. Our studies also indicate that direct interaction between CiMRF and an essential E-box of Ciona Troponin I is required for the expression of this muscle-specific gene and that multiple classes of MRF-regulated genes exist in Ciona. These findings are consistent with substantial conservation of MRF-directed myogenesis in chordates and demonstrate for the first time that the Ala/Thr dipeptide of the basic domain of an invertebrate MRF behaves as a myogenic code.
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Affiliation(s)
- Stephanie A Izzi
- Department of Biology, Rhode Island College, Providence, RI 02908, USA
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26
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Chenevert J, Pruliere G, Ishii H, Sardet C, Nishikata T. Purification of mitochondrial proteins HSP60 and ATP synthase from ascidian eggs: implications for antibody specificity. PLoS One 2013; 8:e52996. [PMID: 23326373 PMCID: PMC3542361 DOI: 10.1371/journal.pone.0052996] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 11/20/2012] [Indexed: 01/25/2023] Open
Abstract
Use of antibodies is a cornerstone of biological studies and it is important to identify the recognized protein with certainty. Generally an antibody is considered specific if it labels a single band of the expected size in the tissue of interest, or has a strong affinity for the antigen produced in a heterologous system. The identity of the antibody target protein is rarely confirmed by purification and sequencing, however in many cases this may be necessary. In this study we sought to characterize the myoplasm, a mitochondria-rich domain present in eggs and segregated into tadpole muscle cells of ascidians (urochordates). The targeted proteins of two antibodies that label the myoplasm were purified using both classic immunoaffinity methods and a novel protein purification scheme based on sequential ion exchange chromatography followed by two-dimensional gel electrophoresis. Surprisingly, mass spectrometry sequencing revealed that in both cases the proteins recognized are unrelated to the original antigens. NN18, a monoclonal antibody which was raised against porcine spinal cord and recognizes the NF-M neurofilament subunit in vertebrates, in fact labels mitochondrial ATP synthase in the ascidian embryo. PMF-C13, an antibody we raised to and purified against PmMRF, which is the MyoD homolog of the ascidian Phallusia mammillata, in fact recognizes mitochondrial HSP60. High resolution immunolabeling on whole embryos and isolated cortices demonstrates localization to the inner mitochondrial membrane for both ATP synthase and HSP60. We discuss the general implications of our results for antibody specificity and the verification methods which can be used to determine unequivocally an antibody's target.
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Affiliation(s)
- Janet Chenevert
- Université Pierre et Marie Curie and CNRS, Developmental Biology Unit UMR7009, Villefranche-sur-mer, France.
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Characterization of the compact bicistronic microRNA precursor, miR-1/miR-133, expressed specifically in Ciona muscle tissues. Gene Expr Patterns 2013; 13:43-50. [DOI: 10.1016/j.gep.2012.11.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/20/2012] [Accepted: 11/05/2012] [Indexed: 12/31/2022]
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28
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Similarity and diversity in mechanisms of muscle fate induction between ascidian species. Biol Cell 2012; 100:265-77. [DOI: 10.1042/bc20070144] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
The study of cis-regulatory DNAs that control developmental gene expression is integral to the modeling of comprehensive genomic regulatory networks for embryogenesis. Ascidian embryos provide a unique opportunity for the analysis of cis-regulatory DNAs with cellular resolution in the context of a simple but typical chordate body plan. Here, we review landmark studies that have laid the foundations for the study of transcriptional enhancers, among other cis-regulatory DNAs, and their roles in ascidian development. The studies using ascidians of the Ciona genus have capitalized on a unique electroporation technique that permits the simultaneous transfection of hundreds of fertilized eggs, which develop rapidly and express transgenes with little mosaicism. Current studies using the ascidian embryo benefit from extensively annotated genomic resources to characterize transcript models in silico. The search for functional noncoding sequences can be guided by bioinformatic analyses combining evolutionary conservation, gene coexpression, and combinations of overrepresented short-sequence motifs. The power of the transient transfection assays has allowed thorough dissection of numerous cis-regulatory modules, which provided insights into the functional constraints that shape enhancer architecture and diversification. Future studies will benefit from pioneering stable transgenic lines and the analysis of chromatin states. Whole genome expression, functional and DNA binding data are being integrated into comprehensive genomic regulatory network models of early ascidian cell specification with a single-cell resolution that is unique among chordate model systems.
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30
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Nishida H. The maternal muscle determinant in the ascidian egg. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:425-33. [DOI: 10.1002/wdev.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hudson C, Ba M, Rouvière C, Yasuo H. Divergent mechanisms specify chordate motoneurons: evidence from ascidians. Development 2011; 138:1643-52. [DOI: 10.1242/dev.055426] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ascidians are members of the vertebrate sister group Urochordata. Their larvae exhibit a chordate body plan, which forms by a highly accelerated embryonic strategy involving a fixed cell lineage and small cell numbers. We report a detailed analysis of the specification of three of the five pairs of motoneurons in the ascidian Ciona intestinalis and show that despite well-conserved gene expression patterns and embryological outcomes compared with vertebrates, key signalling molecules have adopted different roles. We employed a combination of cell ablation and gene manipulation to analyse the function of two signalling molecules with key roles in vertebrate motoneuron specification that are known to be expressed equivalently in ascidians: the inducer Sonic hedgehog, produced ventrally by the notochord and floorplate; and the inhibitory BMP2/4, produced on the lateral/dorsal side of the neural plate. Our surprising conclusion is that neither BMP2/4 signalling nor the ventral cell lineages expressing hedgehog play crucial roles in motoneuron formation in Ciona. Furthermore, BMP2/4 overexpression induced ectopic motoneurons, the opposite of its vertebrate role. We suggest that the specification of motoneurons has been modified during ascidian evolution, such that BMP2/4 has adopted a redundant inductive role rather than a repressive role and Nodal, expressed upstream of BMP2/4 in the dorsal neural tube precursors, acts as a motoneuron inducer during normal development. Thus, our results uncover significant differences in the mechanisms used for motoneuron specification within chordates and also highlight the dangers of interpreting equivalent expression patterns as indicative of conserved function in evo-devo studies.
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Affiliation(s)
- Clare Hudson
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
| | - Moly Ba
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
| | - Christian Rouvière
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
| | - Hitoyoshi Yasuo
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
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Kugler JE, Gazdoiu S, Oda-Ishii I, Passamaneck YJ, Erives AJ, Di Gregorio A. Temporal regulation of the muscle gene cascade by Macho1 and Tbx6 transcription factors in Ciona intestinalis. J Cell Sci 2010; 123:2453-63. [PMID: 20592183 DOI: 10.1242/jcs.066910] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For over a century, muscle formation in the ascidian embryo has been representative of 'mosaic' development. The molecular basis of muscle-fate predetermination has been partly elucidated with the discovery of Macho1, a maternal zinc-finger transcription factor necessary and sufficient for primary muscle development, and of its transcriptional intermediaries Tbx6b and Tbx6c. However, the molecular mechanisms by which the maternal information is decoded by cis-regulatory modules (CRMs) associated with muscle transcription factor and structural genes, and the ways by which a seamless transition from maternal to zygotic transcription is ensured, are still mostly unclear. By combining misexpression assays with CRM analyses, we have identified the mechanisms through which Ciona Macho1 (Ci-Macho1) initiates expression of Ci-Tbx6b and Ci-Tbx6c, and we have unveiled the cross-regulatory interactions between the latter transcription factors. Knowledge acquired from the analysis of the Ci-Tbx6b CRM facilitated both the identification of a related CRM in the Ci-Tbx6c locus and the characterization of two CRMs associated with the structural muscle gene fibrillar collagen 1 (CiFCol1). We use these representative examples to reconstruct how compact CRMs orchestrate the muscle developmental program from pre-localized ooplasmic determinants to differentiated larval muscle in ascidian embryos.
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Affiliation(s)
- Jamie E Kugler
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, Box 60, New York, NY 10065, USA
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Kubo A, Suzuki N, Yuan X, Nakai K, Satoh N, Imai KS, Satou Y. Genomic cis-regulatory networks in the early Ciona intestinalis embryo. Development 2010; 137:1613-23. [PMID: 20392745 DOI: 10.1242/dev.046789] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Precise spatiotemporal gene expression during animal development is achieved through gene regulatory networks, in which sequence-specific transcription factors (TFs) bind to cis-regulatory elements of target genes. Although numerous cis-regulatory elements have been identified in a variety of systems, their global architecture in the gene networks that regulate animal development is not well understood. Here, we determined the structure of the core networks at the cis-regulatory level in early embryos of the chordate Ciona intestinalis by chromatin immunoprecipitation (ChIP) of 11 TFs. The regulatory systems of the 11 TF genes examined were tightly interconnected with one another. By combining analysis of the ChIP data with the results of previous comprehensive analyses of expression profiles and knockdown of regulatory genes, we found that most of the previously determined interactions are direct. We focused on cis-regulatory networks responsible for the Ciona mesodermal tissues by examining how the networks specify these tissues at the level of their cis-regulatory architecture. We also found many interactions that had not been predicted by simple gene knockdown experiments, and we showed that a significant fraction of TF-DNA interactions make major contributions to the regulatory control of target gene expression.
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Affiliation(s)
- Atsushi Kubo
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
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Kataoka Y, Mishina R, Fujiwara S. Mechanism of DNA replication-dependent transcriptional activation of the acetylcholinesterase gene in the Ciona intestinalis embryo. Dev Growth Differ 2009; 51:841-50. [PMID: 19951326 DOI: 10.1111/j.1440-169x.2009.01147.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The acetylcholinesterase-encoding gene in the ascidian Ciona intestinalis (Ci-AChE) is expressed in tail muscle cells from the gastrula stage. When the embryo was continuously treated with aphidicolin from the 32-cell stage, Ci-AChE was not expressed even when control embryos reached the tailbud stage. This result suggests that Ci-AChE acquires the competence to be transcribed after passing through a certain number of DNA replication cycles. A lacZ reporter gene containing the 5' flanking region of Ci-AChE was expressed in the tail muscle cells. Aphidicolin treatment from the 32-cell stage affected, but did not completely suppress, the expression of lacZ. A bisulfite sequencing analysis was carried out to examine the methylation status of four regions within the 5' flanking sequence and the first exon. However, all of these regions remained unmethylated from the 16-cell to 110-cell stages. The results suggested that the DNA of the Ci-AChE locus is not responsible for counting the rounds of replication. We examined the expression of the C. intestinalis MyoD (Ci-MyoD), a transcription factor that activates Ci-AChE. Aphidicolin treatment from the 32-cell stage suppressed the expression of Ci-MyoD, even when control embryos reached the gastrula stage. These results suggest that a lack of Ci-MyoD is critical to the suppression of Ci-AChE in aphidicolin-treated embryos.
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Affiliation(s)
- Yumiko Kataoka
- Department of Applied Science, Kochi University, 2-5-1 Akebono-cho, Kochi-shi, Kochi, Japan
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Noda T, Hamada M, Hamaguchi M, Fujie M, Satoh N. Early zygotic expression of transcription factors and signal molecules in fully dissociated embryonic cells of Ciona intestinalis: A microarray analysis. Dev Growth Differ 2009; 51:639-55. [PMID: 19712267 DOI: 10.1111/j.1440-169x.2009.01124.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Specification of early embryonic cells of animals is established by maternally provided factors and interactions of neighboring cells. The present study addressed a question of autonomous versus non-autonomous specification of embryonic cells by using the Ciona intestinalis embryo, in particular the genetic cascade of zygotic expression of transcription factor genes responsible for notochord specification. To examine this issue, we combined the classic experiment of continuous dissociation of embryonic cells with the modern technique of oligonucleotide-based microarrays. We measured early zygotic expression of 389 core transcription factors genes and 118 major signal molecule genes in embryonic cells that were fully dissociated from the first cleavage. Our results indicated that even if cells are free from contact with neighbors, the major transcription factor genes that have primary roles in embryonic cell specification commence their zygotic expression at the same time as in normal embryos. Dissociation of embryonic cells did not affect extracellular signal-regulated kinases (ERK) activity. Although normal embryos treated with U0126 failed to express Bra and Twist-like-1, dissociated embryonic cells treated with U0126 expressed the genes. These results are discussed in relation to the grade of autonomous versus non-autonomous genetic cascades that are responsible for the specification of early Ciona embryonic cells.
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Affiliation(s)
- Takeshi Noda
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Degasperi V, Gasparini F, Shimeld SM, Sinigaglia C, Burighel P, Manni L. Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations. BMC DEVELOPMENTAL BIOLOGY 2009; 9:48. [PMID: 19737381 PMCID: PMC2753633 DOI: 10.1186/1471-213x-9-48] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 09/08/2009] [Indexed: 11/24/2022]
Abstract
BACKGROUND Ascidians are tunicates, the taxon recently proposed as sister group to the vertebrates. They possess a chordate-like swimming larva, which metamorphoses into a sessile adult. Several ascidian species form colonies of clonal individuals by asexual reproduction. During their life cycle, ascidians present three muscle types: striated in larval tail, striated in the heart, and unstriated in the adult body-wall. RESULTS In the colonial ascidian Botryllus schlosseri, we investigated organisation, differentiation and gene expression of muscle beginning from early buds to adults and during zooid regression. We characterised transcripts for troponin T (BsTnT-c), adult muscle-type (BsMA2) and cytoplasmic-type (BsCA1) actins, followed by in situ hybridisation (ISH) on sections to establish the spatio-temporal expression of BsTnT-c and BsMA2 during asexual reproduction and in the larva. Moreover, we characterised actin genomic sequences, which by comparison with other metazoans revealed conserved intron patterns. CONCLUSION Integration of data from ISH, phalloidin staining and TEM allowed us to follow the phases of differentiation of the three muscle kinds, which differ in expression pattern of the two transcripts. Moreover, phylogenetic analyses provided evidence for the close relationship between tunicate and vertebrate muscle genes. The characteristics and plasticity of muscles in tunicates are discussed.
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Affiliation(s)
- Valentina Degasperi
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Fabio Gasparini
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Sebastian M Shimeld
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Chiara Sinigaglia
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Paolo Burighel
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
| | - Lucia Manni
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy
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Unfolding a chordate developmental program, one cell at a time: Invariant cell lineages, short-range inductions and evolutionary plasticity in ascidians. Dev Biol 2009; 332:48-60. [DOI: 10.1016/j.ydbio.2009.05.540] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 04/27/2009] [Accepted: 05/03/2009] [Indexed: 12/25/2022]
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Andersen Ø, Dahle SW, van Nes S, Bardal T, Tooming-Klunderud A, Kjørsvik E, Galloway TF. Differential spatio-temporal expression and functional diversification of the myogenic regulatory factors MyoD1 and MyoD2 in Atlantic halibut (Hippoglossus hippoglossus). Comp Biochem Physiol B Biochem Mol Biol 2009; 154:93-101. [PMID: 19454321 DOI: 10.1016/j.cbpb.2009.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 04/30/2009] [Accepted: 05/11/2009] [Indexed: 10/20/2022]
Abstract
Development of the vertebrate skeletal muscle is orchestrated by the myogenic regulatory factors MyoD, Myf5, myogenin and MRF4, which likely arose from the duplications of a single ancestral gene early in vertebrate evolution. We have isolated two myod genes from Atlantic halibut and examined their differential expression during embryogenesis using quantitative PCR and in situ hybridization to address their functional roles in this asymmetrically organized flatfish. myod1 was initially maternally expressed, while myod2 mRNA was first detectable during gastrulation. The myod1 mRNA levels predominated throughout somitogenesis, and both slow and fast muscle precursor cells displayed the bilateral symmetric myod1 signal during the formation of the symmetric somite pairs. In contrast, myod2 was left-right asymmetrically expressed in the fast muscle precursors. The random expression of myod2 was not associated with the right-sided eye migration and the development of thicker fast skeletal muscle on the eyed side than on the blind side. The nucleotide substitution analysis indicated that the teleost MyoDs essentially have evolved under purifying selection, but a subset of amino acid sites under strong positive selection were identified in the MyoD2 branch. Altogether, halibut MyoD1 seems to have retained the central role of MyoD in driving skeletal myogenesis, whereas the function of MyoD2 is uncertain in this flatfish species.
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Hinits Y, Osborn DPS, Hughes SM. Differential requirements for myogenic regulatory factors distinguish medial and lateral somitic, cranial and fin muscle fibre populations. Development 2009; 136:403-14. [PMID: 19141670 DOI: 10.1242/dev.028019] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Myogenic regulatory factors of the Myod family (MRFs) are transcription factors essential for mammalian skeletal myogenesis. However, the roles of each gene in myogenesis remain unclear, owing partly to genetic linkage at the Myf5/Mrf4 locus and to rapid morphogenetic movements in the amniote somite. In mice, Myf5 is essential for the earliest epaxial myogenesis, whereas Myod is required for timely differentiation of hypaxially derived muscle. A second major subdivision of the somite is between primaxial muscle of the somite proper and abaxial somite-derived migratory muscle precursors. Here, we use a combination of mutant and morphant analysis to ablate the function of each of the four conserved MRF genes in zebrafish, an organism that has retained a more ancestral bodyplan. We show that a fundamental distinction in somite myogenesis is into medial versus lateral compartments, which correspond to neither epaxial/hypaxial nor primaxial/abaxial subdivisions. In the medial compartment, Myf5 and/or Myod drive adaxial slow fibre and medial fast fibre differentiation. Myod-driven Myogenin activity alone is sufficient for lateral fast somitic and pectoral fin fibre formation from the lateral compartment, as well as for cranial myogenesis. Myogenin activity is a significant contributor to fast fibre differentiation. Mrf4 does not contribute to early myogenesis in zebrafish. We suggest that the differential use of duplicated MRF paralogues in this novel two-component myogenic system facilitated the diversification of vertebrates.
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Affiliation(s)
- Yaniv Hinits
- Randall Division for Cell and Molecular Biophysics and MRC Centre for Developmental Neurobiology, New Hunt's House, Guy's Campus, King's College London, SE1 1UL, UK
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The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord. Dev Biol 2009; 328:561-74. [PMID: 19217895 DOI: 10.1016/j.ydbio.2009.02.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 01/21/2009] [Accepted: 02/03/2009] [Indexed: 11/22/2022]
Abstract
In Ciona intestinalis, leprecan was identified as a target of the notochord-specific transcription factor Ciona Brachyury (Ci-Bra) (Takahashi, H., Hotta, K., Erives, A., Di Gregorio, A., Zeller, R.W., Levine, M., Satoh, N., 1999. Brachyury downstream notochord differentiation in the ascidian embryo. Genes Dev. 13, 1519-1523). By screening approximately 14 kb of the Ci-leprecan locus for cis-regulatory activity, we have identified a 581-bp minimal notochord-specific cis-regulatory module (CRM) whose activity depends upon T-box binding sites located at the 3'-end of its sequence. These sites are specifically bound in vitro by a GST-Ci-Bra fusion protein, and mutations that abolish binding in vitro result in loss or decrease of regulatory activity in vivo. Serial deletions of the 581-bp notochord CRM revealed that this sequence is also able to direct expression in muscle cells through the same T-box sites that are utilized by Ci-Bra in the notochord, which are also bound in vitro by the muscle-specific T-box activators Ci-Tbx6b and Ci-Tbx6c. Additionally, we created plasmids aimed to interfere with the function of Ci-leprecan and categorized the resulting phenotypes, which consist of variable dislocations of notochord cells along the anterior-posterior axis. Together, these observations provide mechanistic insights generally applicable to T-box transcription factors and their target sequences, as well as a first set of clues on the function of Leprecan in early chordate development.
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Vandenbon A, Miyamoto Y, Takimoto N, Kusakabe T, Nakai K. Markov chain-based promoter structure modeling for tissue-specific expression pattern prediction. DNA Res 2008; 15:3-11. [PMID: 18258700 PMCID: PMC2650632 DOI: 10.1093/dnares/dsm034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional regulation is the first level of regulation of gene expression and is therefore a major topic in computational biology. Genes with similar expression patterns can be assumed to be co-regulated at the transcriptional level by promoter sequences with a similar structure. Current approaches for modeling shared regulatory features tend to focus mainly on clustering of cis-regulatory sites. Here we introduce a Markov chain-based promoter structure model that uses both shared motifs and shared features from an input set of promoter sequences to predict candidate genes with similar expression. The model uses positional preference, order, and orientation of motifs. The trained model is used to score a genomic set of promoter sequences: high-scoring promoters are assumed to have a structure similar to the input sequences and are thus expected to drive similar expression patterns. We applied our model on two datasets in Caenorhabditis elegans and in Ciona intestinalis. Both computational and experimental verifications indicate that this model is capable of predicting candidate promoters driving similar expression patterns as the input-regulatory sequences. This model can be useful for finding promising candidate genes for wet-lab experiments and for increasing our understanding of transcriptional regulation.
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Affiliation(s)
- Alexis Vandenbon
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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Brown CD, Johnson DS, Sidow A. Functional architecture and evolution of transcriptional elements that drive gene coexpression. Science 2007; 317:1557-60. [PMID: 17872446 DOI: 10.1126/science.1145893] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Transcriptional coexpression of interacting gene products is required for complex molecular processes; however, the function and evolution of cis-regulatory elements that orchestrate coexpression remain largely unexplored. We mutagenized 19 regulatory elements that drive coexpression of Ciona muscle genes and obtained quantitative estimates of the cis-regulatory activity of the 77 motifs that comprise these elements. We found that individual motif activity ranges broadly within and among elements, and among different instantiations of the same motif type. The activity of orthologous motifs is strongly constrained, although motif arrangement, type, and activity vary greatly among the elements of different co-regulated genes. Thus, the syntactical rules governing this regulatory function are flexible but become highly constrained evolutionarily once they are established in a particular element.
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Affiliation(s)
- Christopher D Brown
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Hudson C, Lotito S, Yasuo H. Sequential and combinatorial inputs from Nodal, Delta2/Notch and FGF/MEK/ERK signalling pathways establish a grid-like organisation of distinct cell identities in the ascidian neural plate. Development 2007; 134:3527-37. [PMID: 17728350 DOI: 10.1242/dev.002352] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ascidian neural plate has a grid-like organisation, with six rows and eight columns of aligned cells, generated by a series of stereotypical cell divisions. We have defined unique molecular signatures for each of the eight cells in the posterior-most two rows of the neural plate - rows I and II. Using a combination of morpholino gene knockdown, dominant-negative forms and pharmacological inhibitors, we tested the role of three signalling pathways in defining these distinct cell identities. Nodal signalling at the 64-cell stage was found to be required to define two different neural plate domains - medial and lateral - with Nodal inducing lateral and repressing medial identities. Delta2, an early Nodal target, was found to then subdivide each of the lateral and medial domains to generate four columns. Finally, a separate signalling system along the anteroposterior axis, involving restricted ERK1/2 activation, was found to promote row I fates and repress row II fates. Our results reveal how the sequential integration of three signalling pathways - Nodal, Delta2/Notch and FGF/MEK/ERK - defines eight different sub-domains that characterise the ascidian caudal neural plate. Most remarkably, the distinct fates of the eight neural precursors are each determined by a unique combination of inputs from these three signalling pathways.
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Affiliation(s)
- Clare Hudson
- Developmental Biology Unit, Université Pierre et Marie Curie (Paris 6 Villefranche-sur-Mer, France.
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Passamaneck YJ, Hadjantonakis AK, Di Gregorio A. Dynamic and polarized muscle cell behaviors accompany tail morphogenesis in the ascidian Ciona intestinalis. PLoS One 2007; 2:e714. [PMID: 17684560 PMCID: PMC1934933 DOI: 10.1371/journal.pone.0000714] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 07/04/2007] [Indexed: 11/19/2022] Open
Abstract
Background Axial elongation is a key morphogenetic process that serves to shape developing organisms. Tail extension in the ascidian larva represents a striking example of this process, wherein paraxially positioned muscle cells undergo elongation and differentiation independent of the segmentation process that characterizes the formation of paraxial mesoderm in vertebrates. Investigating the cell behaviors underlying the morphogenesis of muscle in ascidians may therefore reveal the evolutionarily conserved mechanisms operating during this process. Methodology/Principle Findings A live cell imaging approach utilizing subcellularly-localized fluorescent proteins was employed to investigate muscle cell behaviors during tail extension in the ascidian Ciona intestinalis. Changes in the position and morphology of individual muscle cells were analyzed in vivo in wild type embryos undergoing tail extension and in embryos in which muscle development was perturbed. Muscle cells were observed to undergo elongation in the absence of positional reorganization. Furthermore, high-speed high-resolution live imaging revealed that the onset and progression of tail extension were characterized by the presence of dynamic and polarized actin-based protrusive activity at the plasma membrane of individual muscle cells. Conclusions/Significance Our results demonstrate that in the Ciona muscle, tissue elongation resulted from gradual and coordinated changes in cell geometry and not from changes in cell topology. Proper formation of muscle cells was found to be necessary not only for muscle tissue elongation, but also more generally for completion of tail extension. Based upon the characterized dynamic changes in cell morphology and plasma membrane protrusive activity, a three-phase model is proposed to describe the cell behavior operating during muscle morphogenesis in the ascidian embryo.
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Affiliation(s)
- Yale J. Passamaneck
- 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
- * To whom correspondence should be addressed. E-mail: (A-KH), and (ADG)
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45
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Gyoja F, Satou Y, Shin-i T, Kohara Y, Swalla BJ, Satoh N. Analysis of large scale expression sequenced tags (ESTs) from the anural ascidian, Molgula tectiformis. Dev Biol 2007; 307:460-82. [PMID: 17540363 DOI: 10.1016/j.ydbio.2007.03.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Revised: 03/19/2007] [Accepted: 03/23/2007] [Indexed: 11/27/2022]
Abstract
Anural ascidians show embryogenesis during which tail formation does not take place. This mode of development is a derived character acquired several times independently in ascidian evolution. We identified approximately 20,000 each ESTs (i. e. 10,000 clones each were sequenced from both 5' and 3' ends) of adult gonads, cleaving-embryos, gastrulae/neurulae, embryos before hatching, and hatched larvae of the anural ascidian Molgula tectiformis, in order to comprehensively investigate the molecular mechanism of tailless evolution. Analyses of these ESTs showed that in this species, (1) the expression of embryonic/larval muscle structural genes which are expressed abundantly during embryogenesis of the urodele ascidian Ciona intestinalis, is suppressed; (2) genes that encode proteins with no similarity to known proteins of other organisms are abundantly expressed; (3) genes that show similarity with those up-regulated at metamorphosis in urodele ascidians are up-regulated within several hours after hatching; and (4) 15 of 35 putative orthologues of the downstream components of Brachyury, a key transcription factor for ascidian notochord formation, were found in the ESTs, even though differentiation of notochord is suppressed in this species. We discuss these remarkable results that allow insight into the molecular mechanism(s) responsible for the anural mode of ascidian development.
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Affiliation(s)
- Fuki Gyoja
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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