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Buono L, Annona G, Magri MS, Negueruela S, Sepe RM, Caccavale F, Maeso I, Arnone MI, D’Aniello S. Conservation of cis-Regulatory Syntax Underlying Deuterostome Gastrulation. Cells 2024; 13:1121. [PMID: 38994973 PMCID: PMC11240583 DOI: 10.3390/cells13131121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/22/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Throughout embryonic development, the shaping of the functional and morphological characteristics of embryos is orchestrated by an intricate interaction between transcription factors and cis-regulatory elements. In this study, we conducted a comprehensive analysis of deuterostome cis-regulatory landscapes during gastrulation, focusing on four paradigmatic species: the echinoderm Strongylocentrotus purpuratus, the cephalochordate Branchiostoma lanceolatum, the urochordate Ciona intestinalis, and the vertebrate Danio rerio. Our approach involved comparative computational analysis of ATAC-seq datasets to explore the genome-wide blueprint of conserved transcription factor binding motifs underlying gastrulation. We identified a core set of conserved DNA binding motifs associated with 62 known transcription factors, indicating the remarkable conservation of the gastrulation regulatory landscape across deuterostomes. Our findings offer valuable insights into the evolutionary molecular dynamics of embryonic development, shedding light on conserved regulatory subprograms and providing a comprehensive perspective on the conservation and divergence of gene regulation underlying the gastrulation process.
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Affiliation(s)
- Lorena Buono
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Research Infrastructure for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarollo (CABD), Universidad Pablo de Olavide, 41013 Sevilla, Spain;
| | | | - Rosa Maria Sepe
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio Ferdinando Acton, 80133 Naples, Italy
| | - Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), 08028 Barcelona, Spain;
- Institut de Recerca de la Biodiversitat (IRBio), University of Barcelona (UB), 08028 Barcelona, Spain
| | - Maria Ina Arnone
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; (G.A.); (R.M.S.); (F.C.); (M.I.A.)
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2
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Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B. Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nat Commun 2024; 15:2395. [PMID: 38493164 PMCID: PMC10944513 DOI: 10.1038/s41467-024-46780-0] [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: 01/27/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidian species to symmetrically document the dynamics of ZGA. We identify two coordinated ZGA waves represent early developmental and housekeeping gene reactivation, respectively. Single-cell RNA sequencing reveals that the major expression wave exhibits spatial heterogeneity and significantly correlates with cell fate. Moreover, allele-specific expression occurs in a species- rather than parent-related manner, demonstrating the divergence of cis-regulatory elements between the two species. These findings provide insights into ZGA in chordates.
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Affiliation(s)
- Jiankai Wei
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wei Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - An Jiang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongzhe Peng
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yuting Li
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jianqing Bi
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Linting Wang
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Penghui Liu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jing Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yonghang Ge
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liya Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Haiyan Yu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Lei Li
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shi Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119 Haibin Rd, Nansha Dist., Guangzhou, 511458, China.
| | - Bo Dong
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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3
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Kawamura K, Fujiwara S. The transcription factor AP2 and downstream genes shared by asexual reproduction and zooidal regeneration in the tunicate, Polyandrocarpa misakiensis. Cells Dev 2024; 177:203885. [PMID: 38007002 DOI: 10.1016/j.cdev.2023.203885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/05/2023] [Accepted: 11/12/2023] [Indexed: 11/27/2023]
Abstract
Epithelial outpocketing, tunic softening, mesenchymal cell death, dedifferentiation/transdifferentiation, and resistance to environmental stress are major events that occur during asexual reproduction by budding in the tunicate, Polyandrocarpa misakiensis. To identify the molecules underlying these events and compare them with those operating in regeneration, differential gene expression profiles were developed in buds and zooids. Among approximately 40,000 contigs, 21 genes were identified as potentially being involved in asexual reproduction. Genes related to tunic softening, phagocytosis-stimulating opsonin, and stress resistance were activated in the very early stage of budding. At the later stage of budding when buds separated from the parent and entered the developmental stage, genes for cell adhesion, cell death, and differentiation were activated. The transcription factor AP2 was spatio-temporally expressed in a similar pattern to the tunic-softening gene endoglucanase (EndoG). AP2 mRNA activated EndoG when introduced into zooids by electroporation. Eight out of 21 budding-related genes were significantly activated by AP2 mRNA. Polyandrocarpa zooids possess regenerative potential other than budding. Zooidal regeneration accompanied cell death/phagocytosis, cell-cell adhesion/communication, and dedifferentiation/redifferentiation. Consistent with morphological features, eight related genes including SP8 transcription factor were activated during zooidal regeneration. Most of these genes were identical to those induced by AP2 mRNA, indicating that asexual reproduction in P. misakiensis shares AP2-regulated downstream genes with zooidal regeneration. The present results suggest that SP8 may be indispensable for both budding and regeneration and that the potential dedifferentiation-related gene SOXB1 plays a minor role in zooidal regeneration.
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Affiliation(s)
- Kaz Kawamura
- Laboratory of Cellular and Molecular Biotechnology, Faculty of Science, Kochi University, Kochi 780, Japan.
| | - Shigeki Fujiwara
- Laboratory of Cellular and Molecular Biotechnology, Faculty of Science, Kochi University, Kochi 780, Japan; Department of Chemistry and Biotechnology, Faculty of Science and Technology, Kochi University, Kochi 780, Japan.
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4
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Treen N, Konishi S, Nishida H, Onuma TA, Sasakura Y. Zic-r.b controls cell numbers in Ciona embryos by activating CDKN1B. Dev Biol 2023; 498:26-34. [PMID: 36965841 DOI: 10.1016/j.ydbio.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 01/25/2023] [Accepted: 03/20/2023] [Indexed: 03/27/2023]
Abstract
The control of cell numbers and the establishment of cell types are two processes that are essential in early embryonic development. We have a reasonable understanding of how these processes occur individually, but we have considerably less sophisticated understanding of how these processes are linked. Tunicates have fixed cell lineages with predictable cell cycles, making them well suited to investigate these processes. In the ascidian Ciona, we show that the transcription factor Zic-r.b, known to be involved in establishing several cell types in early development also activates the expression of the cell cycle inhibitor CDKN1B. Zic-r.b is a major missing component of the cell division clock establishing specific cell numbers. We also show that a larvacean homolog of Zic-r.b is expressed one cell cycle earlier than its Ciona counterpart. The early expression in larvaceans may explain why they have half as many notochord cells as ascidians and may illustrate a general mechanism to evolve changes in morphology.
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Affiliation(s)
- Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan.
| | - Shohei Konishi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Takeshi A Onuma
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
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5
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Treen N, Chavarria E, Weaver CJ, Brangwynne CP, Levine M. An FGF timer for zygotic genome activation. Genes Dev 2023; 37:80-85. [PMID: 36801820 PMCID: PMC10069452 DOI: 10.1101/gad.350164.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/19/2023] [Indexed: 02/19/2023]
Abstract
Zygotic genome activation has been extensively studied in a variety of systems including flies, frogs, and mammals. However, there is comparatively little known about the precise timing of gene induction during the earliest phases of embryogenesis. Here we used high-resolution in situ detection methods, along with genetic and experimental manipulations, to study the timing of zygotic activation in the simple model chordate Ciona with minute-scale temporal precision. We found that two Prdm1 homologs in Ciona are the earliest genes that respond to FGF signaling. We present evidence for a FGF timing mechanism that is driven by ERK-mediated derepression of the ERF repressor. Depletion of ERF results in ectopic activation of FGF target genes throughout the embryo. A highlight of this timer is the sharp transition in FGF responsiveness between the eight- and 16-cell stages of development. We propose that this timer is an innovation of chordates that is also used by vertebrates.
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Affiliation(s)
- Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA;
| | - Emily Chavarria
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Claire J Weaver
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Clifford P Brangwynne
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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6
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Roca M, Besnardeau L, Christians E, McDougall A, Chenevert J, Castagnetti S. Acquisition of the spindle assembly checkpoint and its modulation by cell fate and cell size in a chordate embryo. Development 2023; 150:285941. [PMID: 36515557 DOI: 10.1242/dev.201145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022]
Abstract
The spindle assembly checkpoint (SAC) is a surveillance system that preserves genome integrity by delaying anaphase onset until all chromosomes are correctly attached to spindle microtubules. Recruitment of SAC proteins to unattached kinetochores generates an inhibitory signal that prolongs mitotic duration. Chordate embryos are atypical in that spindle defects do not delay mitotic progression during early development, implying that either the SAC is inactive or the cell-cycle target machinery is unresponsive. Here, we show that in embryos of the chordate Phallusia mammillata, the SAC delays mitotic progression from the 8th cleavage divisions. Unattached kinetochores are not recognized by the SAC machinery until the 7th cell cycle, when the SAC is acquired. After acquisition, SAC strength, which manifests as the degree of mitotic lengthening induced by spindle perturbations, is specific to different cell types and is modulated by cell size, showing similarity to SAC control in early Caenorhabditis elegans embryos. We conclude that SAC acquisition is a process that is likely specific to chordate embryos, while modulation of SAC efficiency in SAC proficient stages depends on cell fate and cell size, which is similar to non-chordate embryos.
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Affiliation(s)
- Marianne Roca
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Lydia Besnardeau
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Elisabeth Christians
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Alex McDougall
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Janet Chenevert
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
| | - Stefania Castagnetti
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), 06230 Villefranche-sur-Mer, France
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7
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Zhang T, Xu Y, Imai K, Fei T, Wang G, Dong B, Yu T, Satou Y, Shi W, Bao Z. A single-cell analysis of the molecular lineage of chordate embryogenesis. SCIENCE ADVANCES 2020; 6:eabc4773. [PMID: 33148647 PMCID: PMC7673699 DOI: 10.1126/sciadv.abc4773] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/16/2020] [Indexed: 05/05/2023]
Abstract
Progressive unfolding of gene expression cascades underlies diverse embryonic lineage development. Here, we report a single-cell RNA sequencing analysis of the complete and invariant embryonic cell lineage of the tunicate Ciona savignyi from fertilization to the onset of gastrulation. We reconstructed a developmental landscape of 47 cell types over eight cell cycles in the wild-type embryo and identified eight fate transformations upon fibroblast growth factor (FGF) inhibition. For most FGF-dependent asymmetric cell divisions, the bipotent mother cell displays the gene signature of the default daughter fate. In convergent differentiation of the two notochord lineages, we identified additional gene pathways parallel to the master regulator T/Brachyury Last, we showed that the defined Ciona cell types can be matched to E6.5-E8.5 stage mouse cell types and display conserved expression of limited number of transcription factors. This study provides a high-resolution single-cell dataset to understand chordate early embryogenesis and cell lineage differentiation.
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Affiliation(s)
- Tengjiao Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200123, China
| | - Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Kaoru Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Teng Fei
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Guilin Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bo Dong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Tianwei Yu
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen, Guangdong 518172, China
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Weiyang Shi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA.
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8
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Ilsley GR, Suyama R, Noda T, Satoh N, Luscombe NM. Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq. Sci Rep 2020; 10:4961. [PMID: 32188910 PMCID: PMC7080732 DOI: 10.1038/s41598-020-61591-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/24/2020] [Indexed: 11/09/2022] Open
Abstract
Single-cell RNA-seq has been established as a reliable and accessible technique enabling new types of analyses, such as identifying cell types and studying spatial and temporal gene expression variation and change at single-cell resolution. Recently, single-cell RNA-seq has been applied to developing embryos, which offers great potential for finding and characterising genes controlling the course of development along with their expression patterns. In this study, we applied single-cell RNA-seq to the 16-cell stage of the Ciona embryo, a marine chordate and performed a computational search for cell-specific gene expression patterns. We recovered many known expression patterns from our single-cell RNA-seq data and despite extensive previous screens, we succeeded in finding new cell-specific patterns, which we validated by in situ and single-cell qPCR.
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Affiliation(s)
- Garth R Ilsley
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ritsuko Suyama
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeshi Noda
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Shinshu University, Matsumoto, Nagano, 390-8621, Japan
| | - Nori Satoh
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Nicholas M Luscombe
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan. .,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. .,UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
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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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Imai KS, Kobayashi K, Kari W, Rothbächer U, Ookubo N, Oda-Ishii I, Satou Y. Gata is ubiquitously required for the earliest zygotic gene transcription in the ascidian embryo. Dev Biol 2019; 458:215-227. [PMID: 31751550 DOI: 10.1016/j.ydbio.2019.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 10/25/2022]
Abstract
In ascidian embryos, the earliest transcription from the zygotic genome begins between the 8-cell and 16-cell stages. Gata.a, a maternally expressed Gata transcription factor, activates target genes specifically in the animal hemisphere, whereas the complex of β-catenin and Tcf7 antagonizes the activity of Gata.a and activates target genes specifically in the vegetal hemisphere. Here, we show that genes zygotically expressed at the 16-cell stage have significantly more Gata motifs in their upstream regions. These genes included not only genes with animal hemisphere-specific expression but also genes with vegetal hemisphere-specific expression. On the basis of this finding, we performed knockdown experiments for Gata.a and reporter assays, and found that Gata.a is required for the expression of not only genes with animal hemisphere-specific expression, but also genes with vegetal hemisphere-specific expression. Our data indicated that weak Gata.a activity that cannot induce animal hemisphere-specific expression can allow β-catenin/Tcf7 targets to be expressed in the vegetal cells. Because genes zygotically expressed at the 32-cell stage also had significantly more Gata motifs in their upstream regions, Gata.a function may not be limited to the genes expressed specifically in the animal or vegetal hemispheres at the 16-cell stage, and Gata.a may play an important role in the earliest transcription of the zygotic genome.
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Affiliation(s)
- Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan.
| | - Kenji Kobayashi
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Willi Kari
- Department of Evolution and Developmental Biology, Zoological Institute, University, Innsbruck, Innsbruck, Austria
| | - Ute Rothbächer
- Department of Evolution and Developmental Biology, Zoological Institute, University, Innsbruck, Innsbruck, Austria
| | - Naoki Ookubo
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, 560-0043, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
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11
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Antero-posterior ectoderm patterning by canonical Wnt signaling during ascidian development. PLoS Genet 2019; 15:e1008054. [PMID: 30925162 PMCID: PMC6457572 DOI: 10.1371/journal.pgen.1008054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/10/2019] [Accepted: 02/28/2019] [Indexed: 01/21/2023] Open
Abstract
Wnt/β-catenin signaling is an ancient pathway in metazoans and controls various developmental processes, in particular the establishment and patterning of the embryonic primary axis. In vertebrates, a graded Wnt activity from posterior to anterior endows cells with positional information in the central nervous system. Recent studies in hemichordates support a conserved role for Wnt/β-catenin in ectoderm antero-posterior patterning at the base of the deuterostomes. Ascidians are marine invertebrates and the closest relatives of vertebrates. By combining gain- and loss-of-function approaches, we have determined the role of Wnt/β-catenin in patterning the three ectoderm derivatives of the ascidian Ciona intestinalis, central nervous system, peripheral nervous system and epidermis. Activating Wnt/β-catenin signaling from gastrulation led to a dramatic transformation of the ectoderm with a loss of anterior identities and a reciprocal anterior extension of posterior identities, consistent with studies in other metazoans. Surprisingly, inhibiting Wnt signaling did not produce a reciprocal anteriorization of the embryo with a loss of more posterior identities like in vertebrates and hemichordate. Epidermis patterning was overall unchanged. Only the identity of two discrete regions of the central nervous system, the anteriormost and the posteriormost regions, were under the control of Wnt. Finally, the caudal peripheral nervous system, while being initially Wnt dependent, formed normally. Our results show that the Ciona embryonic ectoderm responds to Wnt activation in a manner that is compatible with the proposed function for this pathway at the base of the deuterostomes. However, possibly because of its fast and divergent mode of development that includes extensive use of maternal determinants, the overall antero-posterior patterning of the Ciona ectoderm is Wnt independent, and Wnt/β-catenin signaling controls the formation of some sub-domains. Our results thus indicate that there has likely been a drift in the developmental systems controlling ectoderm patterning in the lineage leading to ascidians. The Wnt/β-catenin pathway is a system of cell-cell communication. It has an ancient origin in animals and plays multiple roles during embryogenesis and adult life. In particular, it is involved in determining, in the vertebrate embryo, the identity of the different parts of the body and their relative positions along the antero-posterior axis. We have investigated in an ascidian (or sea squirt) species, a marine invertebrate that is closely related to vertebrates, whether this pathway had a similar role. Like in vertebrates, activating Wnt/β-catenin led to a posteriorization of the embryo with a loss of anterior structures. By contrast, unlike vertebrates, ascidian embryos formed rather normally following Wnt/β-catenin inactivation. Since hemichordates (or acorn worms), earlier divergent invertebrates, use Wnt/β-catenin in a manner comparable to vertebrates, it is in the ascidian lineage that changes have occurred. Consequently, ascidians build an antero-posterior axis, very similarly organized to that of vertebrates, but in a different way.
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Madgwick A, Magri MS, Dantec C, Gailly D, Fiuza UM, Guignard L, Hettinger S, Gomez-Skarmeta JL, Lemaire P. Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians. Dev Biol 2019; 448:71-87. [PMID: 30661644 DOI: 10.1016/j.ydbio.2019.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/31/2018] [Accepted: 01/01/2019] [Indexed: 01/21/2023]
Abstract
Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.
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Affiliation(s)
- Alicia Madgwick
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain
| | - Christelle Dantec
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Damien Gailly
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Ulla-Maj Fiuza
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Léo Guignard
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix drive, Ashburn, VA, USA
| | - Sabrina Hettinger
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain
| | - Patrick Lemaire
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France.
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Treen N, Heist T, Wang W, Levine M. Depletion of Maternal Cyclin B3 Contributes to Zygotic Genome Activation in the Ciona Embryo. Curr Biol 2018; 28:1150-1156.e4. [PMID: 29576477 PMCID: PMC5996753 DOI: 10.1016/j.cub.2018.02.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/18/2017] [Accepted: 02/16/2018] [Indexed: 10/17/2022]
Abstract
Most animal embryos display a delay in the activation of zygotic transcription during early embryogenesis [1]. This process is thought to help coordinate rapid increases in cell number during early development [2]. The timing of zygotic genome activation (ZGA) during the maternal-to-zygotic transition (MZT) remains uncertain despite extensive efforts. We explore ZGA in the simple protovertebrate, Ciona intestinalis. Single-cell RNA sequencing (RNA-seq) assays identified Cyclin B3 (Ccnb3) as a putative mediator of ZGA. Maternal Ccnb3 transcripts rapidly diminish in abundance during the onset of zygotic transcription at the 8-cell and 16-cell stages. Disruption of Ccnb3 activity results in precocious activation of zygotic transcription, while overexpression abolishes normal activation. These observations suggest that the depletion of maternal Cyclin B3 products is a critical component of the MZT and ZGA. We discuss evidence that this mechanism might play a conserved role in the MZT of other metazoans, including mice and humans.
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Affiliation(s)
- Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Tyler Heist
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Wei Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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Darras S, Fritzenwanker JH, Uhlinger KR, Farrelly E, Pani AM, Hurley IA, Norris RP, Osovitz M, Terasaki M, Wu M, Aronowicz J, Kirschner M, Gerhart JC, Lowe CJ. Anteroposterior axis patterning by early canonical Wnt signaling during hemichordate development. PLoS Biol 2018; 16:e2003698. [PMID: 29337984 PMCID: PMC5786327 DOI: 10.1371/journal.pbio.2003698] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/26/2018] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
The Wnt family of secreted proteins has been proposed to play a conserved role in early specification of the bilaterian anteroposterior (A/P) axis. This hypothesis is based predominantly on data from vertebrate embryogenesis as well as planarian regeneration and homeostasis, indicating that canonical Wnt (cWnt) signaling endows cells with positional information along the A/P axis. Outside of these phyla, there is strong support for a conserved role of cWnt signaling in the repression of anterior fates, but little comparative support for a conserved role in promotion of posterior fates. We further test the hypothesis by investigating the role of cWnt signaling during early patterning along the A/P axis of the hemichordate Saccoglossus kowalevskii. We have cloned and investigated the expression of the complete Wnt ligand and Frizzled receptor complement of S. kowalevskii during early development along with many secreted Wnt modifiers. Eleven of the 13 Wnt ligands are ectodermally expressed in overlapping domains, predominantly in the posterior, and Wnt antagonists are localized predominantly to the anterior ectoderm in a pattern reminiscent of their distribution in vertebrate embryos. Overexpression and knockdown experiments, in combination with embryological manipulations, establish the importance of cWnt signaling for repression of anterior fates and activation of mid-axial ectodermal fates during the early development of S. kowalevskii. However, surprisingly, terminal posterior fates, defined by posterior Hox genes, are unresponsive to manipulation of cWnt levels during the early establishment of the A/P axis at late blastula and early gastrula. We establish experimental support for a conserved role of Wnt signaling in the early specification of the A/P axis during deuterostome body plan diversification, and further build support for an ancestral role of this pathway in early evolution of the bilaterian A/P axis. We find strong support for a role of cWnt in suppression of anterior fates and promotion of mid-axial fates, but we find no evidence that cWnt signaling plays a role in the early specification of the most posterior axial fates in S. kowalevskii. This posterior autonomy may be a conserved feature of early deuterostome axis specification.
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Affiliation(s)
- Sébastien Darras
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, CNRS UMR 7288, Marseille, France
| | - Jens H. Fritzenwanker
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California
| | - Kevin R. Uhlinger
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California
| | - Ellyn Farrelly
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois
| | - Ariel M. Pani
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois
| | - Imogen A. Hurley
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois
| | - Rachael P. Norris
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut
| | - Michelle Osovitz
- Department of Natural Sciences, St. Petersburg College, Clearwater, Florida
| | - Mark Terasaki
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut
| | - Mike Wu
- Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California
| | - Jochanan Aronowicz
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois
| | - Marc Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - John C. Gerhart
- Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California
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Tokuhiro SI, Tokuoka M, Kobayashi K, Kubo A, Oda-Ishii I, Satou Y. Differential gene expression along the animal-vegetal axis in the ascidian embryo is maintained by a dual functional protein Foxd. PLoS Genet 2017; 13:e1006741. [PMID: 28520732 PMCID: PMC5453608 DOI: 10.1371/journal.pgen.1006741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 06/01/2017] [Accepted: 04/05/2017] [Indexed: 11/19/2022] Open
Abstract
In many animal embryos, a specific gene expression pattern is established along the animal-vegetal axis soon after zygotic transcription begins. In the embryo of the ascidian Ciona intestinalis, soon after the division that separates animal and vegetal hemispheres into distinct blastomeres, maternal Gata.a and β-catenin activate specific genes in the animal and vegetal blastomeres, respectively. On the basis of these initial distinct gene expression patterns, gene regulatory networks promote animal cells to become ectodermal tissues and vegetal cells to become endomesodermal tissues and a part of the nerve cord. In the vegetal hemisphere, β-catenin directly activates Foxd, an essential transcription factor gene for specifying endomesodermal fates. In the present study, we found that Foxd also represses the expression of genes that are activated specifically in the animal hemisphere, including Dmrt1, Prdm1-r.a (Bz1), Prdm1-r.b (Bz2), and Otx. A reporter assay showed that Dmrt1 expression was directly repressed by Foxd, and a chromatin immunoprecipitation assay showed that Foxd was bound to the upstream regions of Dmrt1, Prdm1-r.a, Prdm1-r.b, and Otx. Thus, Foxd has a dual function of activating specific gene expression in the vegetal hemisphere and of repressing the expression of genes that are normally expressed in the animal hemisphere. This dual function stabilizes the initial patterning along the animal-vegetal axis by β-catenin and Gata.a. In embryogenesis of most animals, a specific gene expression pattern is established along the animal-vegetal axis first. In the embryo of the ascidian Ciona intestinalis, the activity of the maternal factor Gata.a is suppressed by β-catenin, which is active only in the vegetal hemisphere, and thereby these two factors activate specific genes in the animal and vegetal blastomeres, respectively. We found that a gene encoding a transcription factor, Foxd, which is a direct target of β-catenin, works as a promoter for endomesodermal fate and an inhibitor for ectodermal fate. In the ascidian embryo, the animal-vegetal axis initially established by the maternal factors is not stable enough for subsequent developmental processes, and needs to be maintained by Foxd. Thus, the animal hemisphere fate is suppressed first by the maternal factor β-catenin, and then by Foxd, which is activated by β-catenin. The primary embryonic axis is not stable initially, and stabilized by a transcription factor, which is expressed differentially along the axis.
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Affiliation(s)
- Shin-ichi Tokuhiro
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Miki Tokuoka
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Kenji Kobayashi
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Atsushi Kubo
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
- * E-mail:
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Ikeda T, Satou Y. Differential temporal control of Foxa.a and Zic-r.b specifies brain versus notochord fate in the ascidian embryo. Development 2016; 144:38-43. [PMID: 27888196 DOI: 10.1242/dev.142174] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/14/2016] [Indexed: 01/25/2023]
Abstract
In embryos of an invertebrate chordate, Ciona intestinalis, two transcription factors, Foxa.a and Zic-r.b, are required for specification of the brain and the notochord, which are derived from distinct cell lineages. In the brain lineage, Foxa.a and Zic-r.b are expressed with no temporal overlap. In the notochord lineage, Foxa.a and Zic-r.b are expressed simultaneously. In the present study, we found that the temporally non-overlapping expression of Foxa.a and Zic-r.b in the brain lineage was regulated by three repressors: Prdm1-r.a (formerly called BZ1), Prdm1-r.b (BZ2) and Hes.a. In morphant embryos of these three repressor genes, Foxa.a expression was not terminated at the normal time, and Zic-r.b was precociously expressed. Consequently, Foxa.a and Zic-r.b were expressed simultaneously, which led to ectopic activation of Brachyury and its downstream pathways for notochord differentiation. Thus, temporal controls by transcriptional repressors are essential for specification of the two distinct fates of brain and notochord by Foxa.a and Zic-r.b Such a mechanism might enable the repeated use of a limited repertoire of transcription factors in developmental gene regulatory networks.
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Affiliation(s)
- Tatsuro Ikeda
- 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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Hudson C, Sirour C, Yasuo H. Co-expression of Foxa.a, Foxd and Fgf9/16/20 defines a transient mesendoderm regulatory state in ascidian embryos. eLife 2016; 5. [PMID: 27351101 PMCID: PMC4945153 DOI: 10.7554/elife.14692] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/24/2016] [Indexed: 12/12/2022] Open
Abstract
In many bilaterian embryos, nuclear β-catenin (nβ-catenin) promotes mesendoderm over ectoderm lineages. Although this is likely to represent an evolutionary ancient developmental process, the regulatory architecture of nβ-catenin-induced mesendoderm remains elusive in the majority of animals. Here, we show that, in ascidian embryos, three nβ-catenin transcriptional targets, Foxa.a, Foxd and Fgf9/16/20, are each required for the correct initiation of both the mesoderm and endoderm gene regulatory networks. Conversely, these three factors are sufficient, in combination, to produce a mesendoderm ground state that can be further programmed into mesoderm or endoderm lineages. Importantly, we show that the combinatorial activity of these three factors is sufficient to reprogramme developing ectoderm cells to mesendoderm. We conclude that in ascidian embryos, the transient mesendoderm regulatory state is defined by co-expression of Foxa.a, Foxd and Fgf9/16/20. DOI:http://dx.doi.org/10.7554/eLife.14692.001
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Affiliation(s)
- Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, Villefranche-sur-Mer, France
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, Villefranche-sur-Mer, France
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The central nervous system of ascidian larvae. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:538-61. [DOI: 10.1002/wdev.239] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/05/2016] [Accepted: 04/09/2016] [Indexed: 11/07/2022]
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Ricci L, Cabrera F, Lotito S, Tiozzo S. Redeployment of germ layers related TFs shows regionalized expression during two non-embryonic developments. Dev Biol 2016; 416:235-248. [PMID: 27208394 DOI: 10.1016/j.ydbio.2016.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 11/26/2022]
Abstract
In all non-vertebrate metazoan phyla, species that evolved non-embryonic developmental pathways as means of propagation or regeneration can be found. In this context, new bodies arise through asexual reproduction processes (such as budding) or whole body regeneration, that lack the familiar temporal and spatial cues classically associated with embryogenesis, like maternal determinants, or gastrulation. The molecular mechanisms underlying those non-embryonic developments (i.e., regeneration and asexual reproduction), and their relationship to those deployed during embryogenesis are poorly understood. We have addressed this question in the colonial ascidian Botryllus schlosseri, which undergoes an asexual reproductive process via palleal budding (PB), as well as a whole body regeneration by vascular budding (VB). We identified early regenerative structures during VB and then followed the fate of differentiating tissues during both non-embryonic developments (PB and VB) by monitoring the expression of genes known to play key functions in germ layer specification with well conserved expression patterns in solitary ascidian embryogenesis. The expression patterns of FoxA1, GATAa, GATAb, Otx, Bra, Gsc and Tbx2/3 were analysed during both PB and VB. We found that the majority of these transcription factors were expressed during both non-embryonic developmental processes, revealing a regionalization of the palleal and vascular buds. Knockdown of GATAa by siRNA in palleal buds confirmed that preventing the correct development of one of these regions blocks further tissue specification. Our results indicate that during both normal and injury-induced budding, a similar alternative developmental program operates via early commitment of epithelial regions.
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Affiliation(s)
- Lorenzo Ricci
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche sur-mer, France
| | - Fabien Cabrera
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche sur-mer, France
| | - Sonia Lotito
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche sur-mer, France
| | - Stefano Tiozzo
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Villefranche sur-mer, France.
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Ogura Y, Sasakura Y. Developmental Control of Cell-Cycle Compensation Provides a Switch for Patterned Mitosis at the Onset of Chordate Neurulation. Dev Cell 2016; 37:148-61. [DOI: 10.1016/j.devcel.2016.03.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 01/28/2016] [Accepted: 03/16/2016] [Indexed: 10/21/2022]
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Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A, Fujiwara S, Gineste M, Lowe EK, Piette J, Racioppi C, Ristoratore F, Sasakura Y, Takatori N, Brown TC, Delsuc F, Douzery E, Gissi C, McDougall A, Nishida H, Sawada H, Swalla BJ, Yasuo H, Lemaire P. ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Res 2016; 44:D808-18. [PMID: 26420834 PMCID: PMC4702943 DOI: 10.1093/nar/gkv966] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/14/2015] [Indexed: 11/24/2022] Open
Abstract
Ascidians belong to the tunicates, the sister group of vertebrates and are recognized model organisms in the field of embryonic development, regeneration and stem cells. ANISEED is the main information system in the field of ascidian developmental biology. This article reports the development of the system since its initial publication in 2010. Over the past five years, we refactored the system from an initial custom schema to an extended version of the Chado schema and redesigned all user and back end interfaces. This new architecture was used to improve and enrich the description of Ciona intestinalis embryonic development, based on an improved genome assembly and gene model set, refined functional gene annotation, and anatomical ontologies, and a new collection of full ORF cDNAs. The genomes of nine ascidian species have been sequenced since the release of the C. intestinalis genome. In ANISEED 2015, all nine new ascidian species can be explored via dedicated genome browsers, and searched by Blast. In addition, ANISEED provides full functional gene annotation, anatomical ontologies and some gene expression data for the six species with highest quality genomes. ANISEED is publicly available at: http://www.aniseed.cnrs.fr.
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Affiliation(s)
- Matija Brozovic
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Cyril Martin
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Christelle Dantec
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Delphine Dauga
- Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France Bioself Communication, 28 rue de la Bibliothèque, F-13001 Marseille, France
| | - Mickaël Mendez
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Paul Simion
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Madeline Percher
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Baptiste Laporte
- Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France
| | - Céline Scornavacca
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Shigeki Fujiwara
- Department of Applied Science, Kochi University, Kochi-shi, Kochi 780-8520, Japan
| | - Mathieu Gineste
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Jacques Piette
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France
| | - Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Filomena Ristoratore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Naohito Takatori
- Developmental Biology Laboratory, Department of Biological Sciences, School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamioosawa, Hachiooji, Tokyo 192-0397, Japan Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Titus C Brown
- Population Health and Reproduction, UC Davis, Davis, CA 95616, USA
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Emmanuel Douzery
- Institut des Sciences de l'Evolution de Montpellier (ISE-M), UMR 5554 CNRS-IRD-Université de Montpellier, F-34090 Montpellier, France
| | - Carmela Gissi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Alex McDougall
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Hitoshi Sawada
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, 429-63 Sugashima, Toba 517-0004, Japan
| | - Billie J Swalla
- Friday Harbor Laboratories, 620 University Road, Friday Harbor, WA 98250-9299, USA
| | - Hitoyoshi Yasuo
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Patrick Lemaire
- Centre de Recherches de Biochimie Macromoléculaire (CRBM), UMR5237, CNRS-Université de Montpellier, 1919 route de Mende, F-34090 Montpellier, France Institut de Biologie du Développement de Marseille (IBDM), UMR7288 CNRS-Aix Marseille Université, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France
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A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis. Dev Biol 2015; 404:149-63. [PMID: 26025923 PMCID: PMC4528069 DOI: 10.1016/j.ydbio.2015.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/17/2022]
Abstract
Genome-wide resources, such as collections of cDNA clones encoding for complete proteins (full-ORF clones), are crucial tools for studying the evolution of gene function and genetic interactions. Non-model organisms, in particular marine organisms, provide a rich source of functional diversity. Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes. The construction of full-ORF clone collections from non-model organisms is hindered by the difficulty of predicting accurately the N-terminal ends of proteins, and distinguishing recent paralogs from highly polymorphic alleles. We report a computational strategy that overcomes these difficulties, and allows for accurate gene level clustering of transcript data followed by the automated identification of full-ORFs with correct 5'- and 3'-ends. It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms. We developed this pipeline for the ascidian Ciona intestinalis, a highly polymorphic member of the divergent sister group of the vertebrates, emerging as a powerful model organism to study chordate gene function, Gene Regulatory Networks and molecular mechanisms underlying human pathologies. Using this pipeline we have generated the first full-ORF collection for a highly polymorphic marine invertebrate. It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.
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Oonuma K, Hirose D, Takatori N, Saiga H. Analysis of the Transcription Regulatory Mechanism of Otx During the Development of the Sensory Vesicle in Ciona intestinalis. Zoolog Sci 2014; 31:565-72. [DOI: 10.2108/zs140060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kouhei Oonuma
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
| | - Dan Hirose
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
| | - Naohito Takatori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
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An otx/nodal regulatory signature for posterior neural development in ascidians. PLoS Genet 2014; 10:e1004548. [PMID: 25121599 PMCID: PMC4133040 DOI: 10.1371/journal.pgen.1004548] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/18/2014] [Indexed: 12/25/2022] Open
Abstract
In chordates, neural induction is the first step of a complex developmental process through which ectodermal cells acquire a neural identity. In ascidians, FGF-mediated neural induction occurs at the 32-cell stage in two blastomere pairs, precursors respectively of anterior and posterior neural tissue. We combined molecular embryology and cis-regulatory analysis to unveil in the ascidian Ciona intestinalis the remarkably simple proximal genetic network that controls posterior neural fate acquisition downstream of FGF. We report that the combined action of two direct FGF targets, the TGFβ factor Nodal, acting via Smad- and Fox-binding sites, and the transcription factor Otx suffices to trigger ascidian posterior neural tissue formation. Moreover, we found that this strategy is conserved in the distantly related ascidian Phallusia mammillata, in spite of extreme sequence divergence in the cis-regulatory sequences involved. Our results thus highlight that the modes of gene regulatory network evolution differ with the evolutionary scale considered. Within ascidians, developmental regulatory networks are remarkably robust to genome sequence divergence. Between ascidians and vertebrates, major fate determinants, such as Otx and Nodal, can be co-opted into different networks. Comparative developmental studies in ascidians with divergent genomes will thus uncover shared ascidian strategies, and contribute to a better understanding of the diversity of developmental strategies within chordates.
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25
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Ikeda T, Matsuoka T, Satou Y. A time delay gene circuit is required for palp formation in the ascidian embryo. Development 2014; 140:4703-8. [PMID: 24255097 DOI: 10.1242/dev.100339] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The ascidian larval brain and palps (a putative rudimentary placode) are specified by two transcription factor genes, ZicL and FoxC, respectively. FGF9/16/20 induces ZicL expression soon after the bi-potential ancestral cells divide into the brain and palp precursors at the early gastrula stage. FGF9/16/20 begins to be expressed at the 16-cell stage, and induces several target genes, including Otx, before the gastrula stage. Here, we show that ZicL expression in the brain lineage is transcriptionally repressed by Hes-a and two Blimp-1-like zinc finger proteins, BZ1 and BZ2, in the bi-potential ancestral cells. ZicL is precociously expressed in the bi-potential cells in embryos in which these repressors are knocked down. This precocious ZicL expression produces extra brain cells at the expense of palp cells. The expression of BZ1 and BZ2 is turned off by a negative auto-feedback loop. This auto-repression acts as a delay circuit that prevents ZicL from being expressed precociously before the brain and palp fates split, thereby making room within the neural plate for the palps to be specified. Addition of the BZ1/2 delay timer circuit to the gene regulatory network responsible for brain formation might represent a key event in the acquisition of the primitive palps/placodes in an ancestral animal.
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Affiliation(s)
- Tatsuro Ikeda
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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26
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Ohta N, Satou Y. Multiple signaling pathways coordinate to induce a threshold response in a chordate embryo. PLoS Genet 2013; 9:e1003818. [PMID: 24098142 PMCID: PMC3789818 DOI: 10.1371/journal.pgen.1003818] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/07/2013] [Indexed: 12/11/2022] Open
Abstract
In animal development, secreted signaling molecules evoke all-or-none threshold responses of target gene transcription to specify cell fates. In the chordate Ciona intestinalis, the neural markers Otx and Nodal are induced at early embryonic stages by Fgf9/16/20 signaling. Here we show that three additional signaling molecules act negatively to generate a sharp expression boundary for neural genes. EphrinA signaling antagonizes FGF signaling by inhibiting ERK phosphorylation more strongly in epidermal cells than in neural cells, which accentuates differences in the strength of ERK activation. However, even weakly activated ERK activates Otx and Nodal transcription occasionally, probably because of the inherently stochastic nature of signal transduction processes and binding of transcription factors to target sequences. This occasional and undesirable activation of neural genes by weak residual ERK activity is directly repressed by Smad transcription factors activated by Admp and Gdf1/3-like signaling, further sharpening the differential responses of cells to FGF signaling. Thus, these signaling pathways coordinate to evoke a threshold response that delineates a sharp expression boundary.
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Affiliation(s)
- Naoyuki Ohta
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
- * E-mail:
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27
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Irvine SQ. Study of Cis-regulatory Elements in the Ascidian Ciona intestinalis. Curr Genomics 2013; 14:56-67. [PMID: 23997651 PMCID: PMC3580780 DOI: 10.2174/138920213804999192] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 12/30/2012] [Accepted: 01/01/2013] [Indexed: 01/31/2023] Open
Abstract
The ascidian (sea squirt) C. intestinalis has become an important model organism for the study of cis-regulation. This is largely due to the technology that has been developed for assessing cis-regulatory activity through the use of transient reporter transgenes introduced into fertilized eggs. This technique allows the rapid and inexpensive testing of endogenous or altered DNA for regulatory activity in vivo. This review examines evidence that C. intestinaliscis-regulatory elements are located more closely to coding regions than in other model organisms. I go on to compare the organization of cis-regulatory elements and conserved non-coding sequences in Ciona, mammals, and other deuterostomes for three representative C.intestinalis genes, Pax6, FoxAa, and the DlxA-B cluster, along with homologs in the other species. These comparisons point out some of the similarities and differences between cis-regulatory elements and their study in the various model organisms. Finally, I provide illustrations of how C. intestinalis lends itself to detailed study of the structure of cis-regulatory elements, which have led, and promise to continue to lead, to important insights into the fundamentals of transcriptional regulation.
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Affiliation(s)
- Steven Q Irvine
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
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28
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Robertshaw E, Kiecker C. Phylogenetic origins of brain organisers. SCIENTIFICA 2012; 2012:475017. [PMID: 24278699 PMCID: PMC3820451 DOI: 10.6064/2012/475017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/21/2012] [Indexed: 06/02/2023]
Abstract
The regionalisation of the nervous system begins early in embryogenesis, concomitant with the establishment of the anteroposterior (AP) and dorsoventral (DV) body axes. The molecular mechanisms that drive axis induction appear to be conserved throughout the animal kingdom and may be phylogenetically older than the emergence of bilateral symmetry. As a result of this process, groups of patterning genes that are equally well conserved are expressed at specific AP and DV coordinates of the embryo. In the emerging nervous system of vertebrate embryos, this initial pattern is refined by local signalling centres, secondary organisers, that regulate patterning, proliferation, and axonal pathfinding in adjacent neuroepithelium. The main secondary organisers for the AP neuraxis are the midbrain-hindbrain boundary, zona limitans intrathalamica, and anterior neural ridge and for the DV neuraxis the notochord, floor plate, and roof plate. A search for homologous secondary organisers in nonvertebrate lineages has led to controversy over their phylogenetic origins. Based on a recent study in hemichordates, it has been suggested that the AP secondary organisers evolved at the base of the deuterostome superphylum, earlier than previously thought. According to this view, the lack of signalling centres in some deuterostome lineages is likely to reflect a secondary loss due to adaptive processes. We propose that the relative evolutionary flexibility of secondary organisers has contributed to a broader morphological complexity of nervous systems in different clades.
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Affiliation(s)
- Ellen Robertshaw
- MRC Centre for Developmental Neurobiology, King's College London, 4th Floor, New Hunt's House, Guy's Hospital Campus, London SE1 1UL, UK
| | - Clemens Kiecker
- MRC Centre for Developmental Neurobiology, King's College London, 4th Floor, New Hunt's House, Guy's Hospital Campus, London SE1 1UL, UK
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29
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Wagner E, Levine M. FGF signaling establishes the anterior border of the Ciona neural tube. Development 2012; 139:2351-9. [PMID: 22627287 DOI: 10.1242/dev.078485] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Ciona tadpole is constructed from simple, well-defined cell lineages governed by provisional gene networks that have been defined via extensive gene disruption assays. Here, we examine the patterning of the anterior neural plate, which produces placodal derivatives such as the adhesive palps and stomodeum, as well as the sensory vesicle (simple brain) of the Ciona tadpole. Evidence is presented that the doublesex-related gene DMRT is expressed throughout the anterior neural plate of neurulating embryos. It leads to the activation of FoxC and ZicL in the palp placode and anterior neural tube, respectively. This differential expression depends on FGF signaling, which inhibits FoxC expression in the anterior neural tube. Inhibition of FGF signaling leads to expanded expression of FoxC, the loss of ZicL, and truncation of the anterior neural tube.
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Affiliation(s)
- Eileen Wagner
- Center for Integrative Genomics, Division of Genetics, Genomics, and Development, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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30
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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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31
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Mii Y, Taira M. Secreted Wnt "inhibitors" are not just inhibitors: regulation of extracellular Wnt by secreted Frizzled-related proteins. Dev Growth Differ 2011; 53:911-23. [PMID: 21995331 DOI: 10.1111/j.1440-169x.2011.01299.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Gradient formation and signaling ranges of secreted proteins are crucial problems to understand how morphogens work for positional information and patterning in animal development. Yet, extracellular behaviors of secreted signaling molecules remain unexplored compared to their downstream pathways inside the cell. Recent advances in bioimaging make it possible to directly visualize morphogen molecules, and this simple strategy has, at least partly, succeeded in uncovering molecular behaviors of morphogens, such as Wnt (wingless-type MMTV integration site family member) and BMP (bone morphogenetic protein) as well as secreted Wnt binding proteins, sFRPs (secreted Frizzled-related proteins), in embryonic tissues. Here, we review the regulation of Wnt signaling by sFRPs, focusing on extracellular regulation of Wnt ligands in comparison with other morphogens. We also discuss evolutionary aspects with comprehensive syntenic and phylogenetic information about vertebrate sfrp genes. We newly annotated several sfrp genes including sfrp2-like 1 (sfrp2l1) in frogs and fishes and crescent in mammals.
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Affiliation(s)
- Yusuke Mii
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Shirae-Kurabayashi M, Matsuda K, Nakamura A. Ci-Pem-1 localizes to the nucleus and represses somatic gene transcription in the germline of Ciona intestinalis embryos. Development 2011; 138:2871-81. [PMID: 21693510 DOI: 10.1242/dev.058131] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In many animal embryos, germ-cell formation depends on maternal factors located in the germ plasm. To ensure the development of germ cells, germline progenitors must be prevented from differentiating inappropriately into somatic cells. A common mechanism for this appears to be the active repression of somatic gene transcription. Species-specific germ-plasm components, such as Pgc in Drosophila and PIE-1 in C. elegans, establish germline transcriptional quiescence by inhibiting general transcriptional machineries. In the ascidian Ciona intestinalis, although transcriptional repression in the germline has been proposed, the factors and mechanisms involved have been unknown. We found that the protein products of Ci-pem-1 RNA, which is an ascidian-specific component of the postplasm (the germ plasm equivalent in ascidians), localized to the nucleus of germline blastomeres, as well as to the postplasm. Morpholino oligonucleotide-mediated Ci-pem-1 knockdown resulted in the ectopic expression of several somatic genes that are usually silent in the germline. In the Ci-pem-1 knockdown embryos, the expression of both β-catenin- and GATAa-dependent genes was derepressed in the germline blastomeres, suggesting that Ci-Pem-1 broadly represses germline mRNA transcription. Immunoprecipitation assays showed that Ci-Pem-1 could interact with two C. intestinalis homologs of Groucho, which is a general co-repressor of mRNA transcription. These results suggest that Ci-pem-1 is the C. intestinalis version of a germ-plasm RNA whose protein product represses the transcription of somatic genes during specification of the germ-cell fate, and that this repression may be operated through interactions between Ci-Pem-1 and Groucho co-repressors.
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Affiliation(s)
- Maki Shirae-Kurabayashi
- Laboratory for Germline Development, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan.
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33
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Kumano G, Takatori N, Negishi T, Takada T, Nishida H. A maternal factor unique to ascidians silences the germline via binding to P-TEFb and RNAP II regulation. Curr Biol 2011; 21:1308-13. [PMID: 21782435 DOI: 10.1016/j.cub.2011.06.050] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/19/2011] [Accepted: 06/21/2011] [Indexed: 12/11/2022]
Abstract
Suppression of zygotic transcription in early embryonic germline cells is tightly linked to their separation from the somatic lineage. Many invertebrate embryos utilize localized maternal factors that are successively inherited by the germline cells for silencing the germline. Germline quiescence has also been associated with the underphosphorylation of Ser2 of the C-terminal domain (CTD-Ser2) of RNA polymerase II [1-3]. Here, using the ascidian Halocynthia roretzi, we identified a first deuterostome example of a maternally localized factor, posterior end mark (PEM), which globally represses germline transcription. PEM knockdown resulted in ectopic transcription and ectopic phosphorylation of CTD-Ser2 in the germline. Overexpression of PEM abolished all transcription and led to the underphosphorylation of CTD-Ser2 in the somatic cells. PEM protein was reiteratively detected in the nucleus of the germline cells and coimmunoprecipitated with CDK9, a component of posterior transcription elongation factor b (P-TEFb). These results suggest that nonhomologous proteins, PEM and Pgc of Drosophila [3-5] and PIE-1 of C. elegans [1, 6, 7], repress germline gene expression through analogous functions: by keeping CTD-Ser2 underphosphorylated through binding to the P-TEFb complex. The present study is an interesting example of evolutionary constraint on how a mechanism of germline silencing can evolve in diverse animals.
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Affiliation(s)
- Gaku Kumano
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
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Khoueiry P, Rothbächer U, Ohtsuka Y, Daian F, Frangulian E, Roure A, Dubchak I, Lemaire P. A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr Biol 2010; 20:792-802. [PMID: 20434338 DOI: 10.1016/j.cub.2010.03.063] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 03/12/2010] [Accepted: 03/23/2010] [Indexed: 12/22/2022]
Abstract
BACKGROUND Transcription initiation is controlled by cis-regulatory modules. Although these modules are usually made of clusters of short transcription factor binding sites, a small minority of such clusters in the genome have cis-regulatory activity. This paradox is currently unsolved. RESULTS To identify what discriminates active from inactive clusters, we focused our attention on short topologically unconstrained clusters of two ETS and two GATA binding sites, similar to the early neural enhancer of Ciona intestinalis Otx. We first computationally identified 55 such clusters, conserved between the two Ciona genomes. In vivo assay of the activity of 19 hits identified three novel early neural enhancers, all located next to genes coexpressed with Otx. Optimization of ETS and GATA binding sites was not always sufficient to confer activity to inactive clusters. Rather, a dinucleotide sequence code associated to nucleosome depletion showed a robust correlation with enhancer potential. Identification of a large collection of Ciona regulatory regions revealed that predicted nucleosome depletion constitutes a general signature of Ciona enhancers, which is conserved between orthologous loci in the two Ciona genomes and which partitions conserved noncoding sequences into a major nucleosome-bound fraction and a minor nucleosome-free fraction with higher cis-regulatory potential. We also found this signature in a large fraction of short Drosophila cis-regulatory modules. CONCLUSION This study indicates that a sequence-based dinucleotide signature, previously associated with nucleosome depletion and independent of transcription factor binding sites, contributes to the definition of a local cis-regulatory potential in two metazoa, Ciona intestinalis and Drosophila melanogaster.
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Affiliation(s)
- Pierre Khoueiry
- Institut du Biologie de Développement de Marseille Luminy (IBDML, UMR 6216), CNRS, Université de la Méditerranée, Parc Scientifique de Luminy Case 907, F-13288, Marseille Cedex 9, France.
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35
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Shimai K, Kitaura Y, Tamari Y, Nishikata T. Upstream Regulatory Sequences Required for Specific Gene Expression in the Ascidian Neural Tube. Zoolog Sci 2010; 27:76-83. [DOI: 10.2108/zsj.27.76] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kotaro Shimai
- Graduate School of Natural Science, Konan University, Kobe 658-8501, Japan
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36
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Retinoic acid signaling targets Hox genes during the amphioxus gastrula stage: Insights into early anterior–posterior patterning of the chordate body plan. Dev Biol 2010; 338:98-106. [DOI: 10.1016/j.ydbio.2009.11.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Revised: 11/06/2009] [Accepted: 11/06/2009] [Indexed: 01/08/2023]
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37
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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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38
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Patterning of an ascidian embryo along the anterior–posterior axis through spatial regulation of competence and induction ability by maternally localized PEM. Dev Biol 2009; 331:78-88. [DOI: 10.1016/j.ydbio.2009.04.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 04/02/2009] [Accepted: 04/22/2009] [Indexed: 11/21/2022]
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39
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Satou Y, Satoh N, Imai KS. Gene regulatory networks in the early ascidian embryo. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:268-73. [DOI: 10.1016/j.bbagrm.2008.03.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 03/06/2008] [Accepted: 03/18/2008] [Indexed: 12/19/2022]
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Auger H, Lamy C, Haeussler M, Khoueiry P, Lemaire P, Joly JS. Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5. Dev Biol 2009; 329:364-73. [PMID: 19248777 DOI: 10.1016/j.ydbio.2009.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 01/22/2009] [Accepted: 02/03/2009] [Indexed: 10/21/2022]
Abstract
Anteroposterior patterning of the ectoderm in the invertebrate chordate Ciona intestinalis first relies on key zygotic activators, such as FoxA, and later on the coordinated responses to inducing signals from the underlying mesendoderm. Here, we focus on a mechanism of coordination of these responses by looking at the cis-regulatory logics of Ci-Rora and Ci-Rorb, which are coding for putative non-canonical transmembrane Wnt receptors, and are present in tandem along the C. intestinalis chromosome 08q. We showed that during cleavage stages, both Ci-Rora and Ci-Rorb genes are initially expressed in all blastomeres of the anterior ectoderm (a-line), as sFRP1/5 (Lamy, C., Rothbächer, U., Caillol, D., Lemaire, P., 2006. Ci-FoxA-a is the earliest zygotic determinant of the ascidian anterior ectoderm and directly activates Ci-sFRP1/5. Development 133, 2835-2844.). We then carried out a functional analysis of cis-regulatory regions and showed that both genes have elements enriched in Ci-FoxA-a binding sites. We dissected one of these early enhancers, and showed that it is directly activated by Ci-FoxA-a, as one sFRP1/5 cis-regulatory element. We also showed that although FoxA binding sites are abundant in genomes, dense clusters of these sites are found upstream from very few genes, and have a high predictive value of a-line expression. These data indicate an important role for FoxA in anterior specification, via the transcriptional regulation of target genes belonging to various signalling pathways.
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Affiliation(s)
- Hélène Auger
- INRA "Morphogenèse du Système Nerveux des Chordés" Group, DEPSN, UPR2197, Institut Fessard, CNRS, 1 Avenue de la Terrasse, 91198 GIF SUR YVETTE, France
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Bovolenta P, Esteve P, Ruiz JM, Cisneros E, Lopez-Rios J. Beyond Wnt inhibition: new functions of secreted Frizzled-related proteins in development and disease. J Cell Sci 2008; 121:737-46. [PMID: 18322270 DOI: 10.1242/jcs.026096] [Citation(s) in RCA: 460] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The secreted Frizzled-related proteins (SFRPs) are a family of soluble proteins that are structurally related to Frizzled (Fz) proteins, the serpentine receptors that mediate the extensively used cell-cell communication pathway involving Wnt signalling. Because of their homology with the Wnt-binding domain on the Fz receptors, SFRPs were immediately characterised as antagonists that bind to Wnt proteins to prevent signal activation. Since these initial studies, interest in the family of SFRPs has grown progressively, offering new perspectives on their function and mechanism of action in both development and disease. These studies indicate that SFRPs are not merely Wnt-binding proteins, but can also antagonise one another's activity, bind to Fz receptors and influence axon guidance, interfere with BMP signalling by acting as proteinase inhibitors, and interact with other receptors or matrix molecules. Furthermore, their expression is altered in different types of cancers, bone pathologies, retinal degeneration and hypophosphatemic diseases, indicating that their activity is fundamental for tissue homeostasis. Here we review some of the debated aspects of SFRP-Wnt interactions and discuss the new and emerging roles of SFRPs.
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Affiliation(s)
- Paola Bovolenta
- Departamento de Neurobiología Molecular, Celular y del Desarrollo, Instituto Cajal, CSIC, Dr Arce 37, Madrid 28002, Spain.
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Rothbächer U, Bertrand V, Lamy C, Lemaire P. A combinatorial code of maternal GATA, Ets and beta-catenin-TCF transcription factors specifies and patterns the early ascidian ectoderm. Development 2008; 134:4023-32. [PMID: 17965050 DOI: 10.1242/dev.010850] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Our understanding of the maternal factors that initiate early chordate development, and of their direct zygotic targets, is still fragmentary. A molecular cascade is emerging for the mesendoderm, but less is known about the ectoderm, giving rise to epidermis and nervous tissue. Our cis-regulatory analysis surprisingly places the maternal transcription factor Ci-GATAa (GATA4/5/6) at the top of the ectodermal regulatory network in ascidians. Initially distributed throughout the embryo, Ci-GATAa activity is progressively repressed in vegetal territories by accumulating maternal beta-catenin. Once restricted to the animal hemisphere, Ci-GATAa directly activates two types of zygotic ectodermal genes. First, Ci-fog is activated from the 8-cell stage throughout the ectoderm, then Ci-otx is turned on from the 32-cell stage in neural precursors only. Whereas the enhancers of both genes contain critical and interchangeable GATA sites, their distinct patterns of activation stem from the additional presence of two Ets sites in the Ci-otx enhancer. Initially characterized as activating elements in the neural lineages, these Ets sites additionally act as repressors in non-neural lineages, and restrict GATA-mediated activation of Ci-otx. We thus identify a precise combinatorial code of maternal factors responsible for zygotic onset of a chordate ectodermal genetic program.
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Affiliation(s)
- Ute Rothbächer
- Institut de Biologie du Développement de Marseille Luminy (IBDML), CNRS-UMR6216/Université de la Méditerranée Aix-Marseille, F-13288 Marseille Cedex 9, France.
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Roure A, Rothbächer U, Robin F, Kalmar E, Ferone G, Lamy C, Missero C, Mueller F, Lemaire P. A multicassette Gateway vector set for high throughput and comparative analyses in ciona and vertebrate embryos. PLoS One 2007; 2:e916. [PMID: 17878951 PMCID: PMC1976267 DOI: 10.1371/journal.pone.0000916] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 08/01/2007] [Indexed: 01/26/2023] Open
Abstract
Background The past few years have seen a vast increase in the amount of genomic data available for a growing number of taxa, including sets of full length cDNA clones and cis-regulatory sequences. Large scale cross-species comparisons of protein function and cis-regulatory sequences may help to understand the emergence of specific traits during evolution. Principal Findings To facilitate such comparisons, we developed a Gateway compatible vector set, which can be used to systematically dissect cis-regulatory sequences, and overexpress wild type or tagged proteins in a variety of chordate systems. It was developed and first characterised in the embryos of the ascidian Ciona intestinalis, in which large scale analyses are easier to perform than in vertebrates, owing to the very efficient embryo electroporation protocol available in this organism. Its use was then extended to fish embryos and cultured mammalian cells. Conclusion This versatile vector set opens the way to the mid- to large-scale comparative analyses of protein function and cis-regulatory sequences across chordate evolution. A complete user manual is provided as supplemental material.
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Affiliation(s)
- Agnès Roure
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
- * To whom correspondence should be addressed. E-mail: (AR); (PL)
| | - Ute Rothbächer
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
| | - François Robin
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
| | - Eva Kalmar
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany
| | - Giustina Ferone
- CEINGE Biotecnologie Avanzate SCarl (Center for Genetic Engineering), Napoli, Italy
| | - Clément Lamy
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate SCarl (Center for Genetic Engineering), Napoli, Italy
| | - Ferenc Mueller
- Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe, Germany
| | - Patrick Lemaire
- Institut de Biologie du Développement de Marseille Luminy, UMR 6216 CNRS/Université de la Méditerranée, Marseille, France
- * To whom correspondence should be addressed. E-mail: (AR); (PL)
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Takatori N, Wada S, Saiga H. Regionalization of the Tail-tip Epidermis Requires Inductive Influence from Vegetal Cells and FGF Signaling in the Development of an Ascidian, Halocynthia roretzi. Zoolog Sci 2007; 24:441-8. [PMID: 17867843 DOI: 10.2108/zsj.24.441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 12/13/2006] [Indexed: 11/17/2022]
Abstract
The epidermis of an ascidian larva derived from animal-hemisphere cells is regionalized along the anterior-posterior (AP) axis through inductive signals emanating from vegetal-hemisphere cells in early stages of the development. Previously, we showed by blastomere isolation and ablation experiments that the contact between the animal and vegetal hemispheres until the 32-cell stage is necessary for the proper AP patterning of the epidermis in the tailbud-stage embryo. We here addressed the patterning mechanism of the posteriormost epidermis using a tail-tip epidermis marker, HrTT-1. Employing blastomere isolation and ablation experiments along with knockdown of a master regulator gene for posterior mesoderm, we have demonstrated that presence of the posterior vegetal cells after the 32-cell stage is necessary for the expression of HrTT-1. To explore the timing and nature of the influence of the posterior vegetal cells, we treated the embryos with FGF signaling inhibitors at various developmental stages and found that HrTT-1 expression was lost from embryos treated with the inhibitors from stages earlier than the late neurula stage, just prior to the onset of HrTT-1 expression but not after the initial tailbud stage, at which the expression of HrTT-1 had started. In embryos lacking HrTT-1 expression, the expression domain of Hrcad, which would otherwise be localized anterior to that of HrTT-1, expanded to the tail-tip. These results suggest that FGF signaling from the neurula to initial tailbud stages is necessary for the initiation but not maintenance of HrTT-1 expression in the tail-tip epidermis. The contact with posterior vegetal cells until and after the 32-cell stage may be required for FGF signaling to occur in the posterior tail, which in turn regionalizes the tail-tip epidermal territory.
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Affiliation(s)
- Naohito Takatori
- Department of Biological Science, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
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Kimura-Yoshida C, Tian E, Nakano H, Amazaki S, Shimokawa K, Rossant J, Aizawa S, Matsuo I. Crucial roles of Foxa2 in mouse anterior-posterior axis polarization via regulation of anterior visceral endoderm-specific genes. Proc Natl Acad Sci U S A 2007; 104:5919-24. [PMID: 17389379 PMCID: PMC1851592 DOI: 10.1073/pnas.0607779104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anterior visceral endoderm (AVE) plays essential roles with respect to anterior-posterior axis development in the early mouse embryo. To assess the genetic cascade involved in AVE formation, the cis-regulatory elements directing expression of vertebrate Otx2 genes in the AVE were analyzed via generation of transgenic mice. Otx2 expression in AVE is regulated directly by the forkhead transcription factor, Foxa2. Moreover, Foxa2 is essential for expression of the Wnt antagonists, Dkk1 and Cerl, in visceral endoderm during the pre- to early streak stages; however, Foxa2 appears to be dispensable for subsequent Dkk1 expression associated with forebrain induction. Thus, we propose that Foxa2 is crucial in early anterior-posterior axis polarization in terms of regulation of expression of AVE-specific genes. These findings provide profound insights into conserved roles of Foxa2 transcription factors in anterior specification throughout the evolution of the chordate body plan.
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Affiliation(s)
- Chiharu Kimura-Yoshida
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
| | - E. Tian
- Department of Morphogenesis, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hiroshi Nakano
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
| | - Saori Amazaki
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Kayo Shimokawa
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Janet Rossant
- Program in Developmental Biology, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8; and
| | - Shinichi Aizawa
- Vertebrate Body Plan Group, RIKEN CDB, Kobe, Hyogo 650-0047, Japan
| | - Isao Matsuo
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
- To whom correspondence should be addressed. E-mail:
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Kumano G, Nishida H. Ascidian embryonic development: An emerging model system for the study of cell fate specification in chordates. Dev Dyn 2007; 236:1732-47. [PMID: 17366575 DOI: 10.1002/dvdy.21108] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The ascidian tadpole larva represents the basic body plan of all chordates in a relatively small number of cells and tissue types. Although it had been considered that ascidians develop largely in a determinative way, whereas vertebrates develop in an inductive way, recent studies at the molecular and cellular levels have uncovered several similarities in the way developmental fates are specified. In this review, we describe ascidian embryogenesis and its cell lineages, introduce several characteristics of ascidian embryos, describe recent advances in understanding of the mechanisms of cell fate specification, and discuss them in the context of what is known in vertebrates and other organisms.
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Affiliation(s)
- Gaku Kumano
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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