1
|
Copley RR, Buttin J, Arguel MJ, Williaume G, Lebrigand K, Barbry P, Hudson C, Yasuo H. Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis. Dev Biol 2024; 514:1-11. [PMID: 38878991 DOI: 10.1016/j.ydbio.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024]
Abstract
In chordates, the central nervous system arises from precursors that have distinct developmental and transcriptional trajectories. Anterior nervous systems are ontogenically associated with ectodermal lineages while posterior nervous systems are associated with mesoderm. Taking advantage of the well-documented cell lineage of ascidian embryos, we asked to what extent the transcriptional states of the different neural lineages become similar during the course of progressive lineage restriction. We performed single-cell RNA sequencing (scRNA-seq) analyses on hand-dissected neural precursor cells of the two distinct lineages, together with those of their sister cell lineages, with a high temporal resolution covering five successive cell cycles from the 16-cell to neural plate stages. A transcription factor binding site enrichment analysis of neural specific genes at the neural plate stage revealed limited evidence for shared transcriptional control between the two neural lineages, consistent with their different ontogenies. Nevertheless, PCA analysis and hierarchical clustering showed that, by neural plate stages, the two neural lineages cluster together. Consistent with this, we identified a set of genes enriched in both neural lineages at the neural plate stage, including miR-124, Celf3.a, Zic.r-b, and Ets1/2. Altogether, the current study has revealed genome-wide transcriptional dynamics of neural progenitor cells of two distinct developmental origins. Our scRNA-seq dataset is unique and provides a valuable resource for future analyses, enabling a precise temporal resolution of cell types not previously described from dissociated embryos.
Collapse
Affiliation(s)
- Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France.
| | - Julia Buttin
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS UMR 7275, 06560, Sophia Antipolis, France
| | - Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS UMR 7275, 06560, Sophia Antipolis, France
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, CNRS UMR 7275, 06560, Sophia Antipolis, France
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-mer, Institut de la Mer de Villefranche-sur-mer, Sorbonne Université, CNRS UMR7009, 06230, Villefranche-sur-mer, France.
| |
Collapse
|
2
|
Pickett CJ, Gruner HN, Davidson B. Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling. PLoS Biol 2024; 22:e3002169. [PMID: 38271304 PMCID: PMC10810493 DOI: 10.1371/journal.pbio.3002169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Individual signaling pathways, such as fibroblast growth factors (FGFs), can regulate a plethora of inductive events. According to current paradigms, signal-dependent transcription factors (TFs), such as FGF/MapK-activated Ets family factors, partner with lineage-determining factors to achieve regulatory specificity. However, many aspects of this model have not been rigorously investigated. One key question relates to whether lineage-determining factors dictate lineage-specific responses to inductive signals or facilitate these responses in collaboration with other inputs. We utilize the chordate model Ciona robusta to investigate mechanisms generating lineage-specific induction. Previous studies in C. robusta have shown that cardiopharyngeal progenitor cells are specified through the combined activity of FGF-activated Ets1/2.b and an inferred ATTA-binding transcriptional cofactor. Here, we show that the homeobox TF Lhx3/4 serves as the lineage-determining TF that dictates cardiopharyngeal-specific transcription in response to pleiotropic FGF signaling. Targeted knockdown of Lhx3/4 leads to loss of cardiopharyngeal gene expression. Strikingly, ectopic expression of Lhx3/4 in a neuroectodermal lineage subject to FGF-dependent specification leads to ectopic cardiopharyngeal gene expression in this lineage. Furthermore, ectopic Lhx3/4 expression disrupts neural plate morphogenesis, generating aberrant cell behaviors associated with execution of incompatible morphogenetic programs. Based on these findings, we propose that combinatorial regulation by signal-dependent and lineage-determinant factors represents a generalizable, previously uncategorized regulatory subcircuit we term "cofactor-dependent induction." Integration of this subcircuit into theoretical models will facilitate accurate predictions regarding the impact of gene regulatory network rewiring on evolutionary diversification and disease ontogeny.
Collapse
Affiliation(s)
- C. J. Pickett
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Hannah N. Gruner
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| |
Collapse
|
3
|
Hudson C. Signals, grids, and geometry: In pursuit of understanding cell fate switches. Genesis 2023; 61:e23546. [PMID: 37715353 DOI: 10.1002/dvg.23546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/10/2023] [Accepted: 08/28/2023] [Indexed: 09/17/2023]
Affiliation(s)
- Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Institut de la Mer de Villefranche (IMEV), Sorbonne Université, CNRS, Villefranche-sur-mer, France
| |
Collapse
|
4
|
Kostyuchenko RP, Amosov AV. Spatial Colinear but Broken Temporal Expression of Duplicated ParaHox Genes in Asexually Reproducing Annelids, Nais communis and Pristina longiseta. Genes (Basel) 2023; 14:1501. [PMID: 37510405 PMCID: PMC10379933 DOI: 10.3390/genes14071501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
ParaHox genes are key developmental regulators involved in the patterning of the digestive tract along the anteroposterior axis and the development of the nervous system. Most studies have focused on the function of these genes in embryogenesis, while their expression patterns in postembryonic development often remain unknown. In this study, we identified for the first time all ParaHox orthologs in two naidid oligochaetes, N. communis and P. longiseta, and described their expression patterns during normal growth and fission in these animals. We showed that Gsx and Cdx are presented by two paralogs, while Xlox is a single copy gene in both species. Using whole-mount in situ hybridization, we also found that orthologs, except for the Xlox gene, have similar activity patterns with minor differences in details, while the expression patterns of paralogs can differ significantly. However, all these genes are involved in axial patterning and/or in tissue remodeling during growth and asexual reproduction in naidids. Moreover, during paratomic fission, these genes are expressed with spatial colinearity but temporal colinearity is broken. The results of this study may be evidence of the functional diversification of duplicated genes and suggest involvement of the ParaHox genes in whole-body patterning during growth and asexual reproduction in annelids.
Collapse
Affiliation(s)
- Roman P Kostyuchenko
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| | - Artem V Amosov
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| |
Collapse
|
5
|
Bettoni R, Hudson C, Williaume G, Sirour C, Yasuo H, de Buyl S, Dupont G. Model of neural induction in the ascidian embryo. PLoS Comput Biol 2023; 19:e1010335. [PMID: 36735746 PMCID: PMC9931142 DOI: 10.1371/journal.pcbi.1010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/15/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
How cell specification can be controlled in a reproducible manner is a fundamental question in developmental biology. In ascidians, a group of invertebrate chordates, geometry plays a key role in achieving this control. Here, we use mathematical modeling to demonstrate that geometry dictates the neural-epidermal cell fate choice in the 32-cell stage ascidian embryo by a two-step process involving first the modulation of ERK signaling and second, the expression of the neural marker gene, Otx. The model describes signal transduction by the ERK pathway that is stimulated by FGF and attenuated by ephrin, and ERK-mediated control of Otx gene expression, which involves both an activator and a repressor of ETS-family transcription factors. Considering the measured area of cell surface contacts with FGF- or ephrin-expressing cells as inputs, the solutions of the model reproduce the experimental observations about ERK activation and Otx expression in the different cells under normal and perturbed conditions. Sensitivity analyses and computations of Hill coefficients allow us to quantify the robustness of the specification mechanism controlled by cell surface area and to identify the respective role played by each signaling input. Simulations also predict in which conditions the dual control of gene expression by an activator and a repressor that are both under the control of ERK can induce a robust ON/OFF control of neural fate induction.
Collapse
Affiliation(s)
- Rossana Bettoni
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| |
Collapse
|
6
|
Ducos B, Bensimon D, Scerbo P. Vertebrate Cell Differentiation, Evolution, and Diseases: The Vertebrate-Specific Developmental Potential Guardians VENTX/ NANOG and POU5/ OCT4 Enter the Stage. Cells 2022; 11:cells11152299. [PMID: 35892595 PMCID: PMC9331430 DOI: 10.3390/cells11152299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/09/2022] [Accepted: 07/13/2022] [Indexed: 01/02/2023] Open
Abstract
During vertebrate development, embryonic cells pass through a continuum of transitory pluripotent states that precede multi-lineage commitment and morphogenesis. Such states are referred to as “refractory/naïve” and “competent/formative” pluripotency. The molecular mechanisms maintaining refractory pluripotency or driving the transition to competent pluripotency, as well as the cues regulating multi-lineage commitment, are evolutionarily conserved. Vertebrate-specific “Developmental Potential Guardians” (vsDPGs; i.e., VENTX/NANOG, POU5/OCT4), together with MEK1 (MAP2K1), coordinate the pluripotency continuum, competence for multi-lineage commitment and morphogenesis in vivo. During neurulation, vsDPGs empower ectodermal cells of the neuro-epithelial border (NEB) with multipotency and ectomesenchyme potential through an “endogenous reprogramming” process, giving rise to the neural crest cells (NCCs). Furthermore, vsDPGs are expressed in undifferentiated-bipotent neuro-mesodermal progenitor cells (NMPs), which participate in posterior axis elongation and growth. Finally, vsDPGs are involved in carcinogenesis, whereby they confer selective advantage to cancer stem cells (CSCs) and therapeutic resistance. Intriguingly, the heterogenous distribution of vsDPGs in these cell types impact on cellular potential and features. Here, we summarize the findings about the role of vsDPGs during vertebrate development and their selective advantage in evolution. Our aim to present a holistic view regarding vsDPGs as facilitators of both cell plasticity/adaptability and morphological innovation/variation. Moreover, vsDPGs may also be at the heart of carcinogenesis by allowing malignant cells to escape from physiological constraints and surveillance mechanisms.
Collapse
Affiliation(s)
- Bertrand Ducos
- LPENS, PSL, CNRS, 24 rue Lhomond, 75005 Paris, France
- IBENS, PSL, CNRS, 46 rue d’Ulm, 75005 Paris, France
- High Throughput qPCR Core Facility, ENS, PSL, 46 rue d’Ulm, 75005 Paris, France
- Correspondence: (B.D.); (D.B.); (P.S.)
| | - David Bensimon
- LPENS, PSL, CNRS, 24 rue Lhomond, 75005 Paris, France
- IBENS, PSL, CNRS, 46 rue d’Ulm, 75005 Paris, France
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90094, USA
- Correspondence: (B.D.); (D.B.); (P.S.)
| | - Pierluigi Scerbo
- LPENS, PSL, CNRS, 24 rue Lhomond, 75005 Paris, France
- IBENS, PSL, CNRS, 46 rue d’Ulm, 75005 Paris, France
- Correspondence: (B.D.); (D.B.); (P.S.)
| |
Collapse
|
7
|
Williaume G, de Buyl S, Sirour C, Haupaix N, Bettoni R, Imai KS, Satou Y, Dupont G, Hudson C, Yasuo H. Cell geometry, signal dampening, and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction. Dev Cell 2021; 56:2966-2979.e10. [PMID: 34672970 DOI: 10.1016/j.devcel.2021.09.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/16/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Precise control of lineage segregation is critical for the development of multicellular organisms, but our quantitative understanding of how variable signaling inputs are integrated to activate lineage-specific gene programs remains limited. Here, we show how precisely two out of eight ectoderm cells adopt neural fates in response to ephrin and FGF signals during ascidian neural induction. In each ectoderm cell, FGF signals activate ERK to a level that mirrors its cell contact surface with FGF-expressing mesendoderm cells. This gradual interpretation of FGF inputs is followed by a bimodal transcriptional response of the immediate early gene, Otx, resulting in its activation specifically in the neural precursors. At low levels of ERK, Otx is repressed by an ETS family transcriptional repressor, ERF2. Ephrin signals are critical for dampening ERK activation levels across ectoderm cells so that only neural precursors exhibit above-threshold levels, evade ERF repression, and "switch on" Otx transcription.
Collapse
Affiliation(s)
- Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Nicolas Haupaix
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Rossana Bettoni
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium; Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
| |
Collapse
|
8
|
Winkley KM, Reeves WM, Veeman MT. Single-cell analysis of cell fate bifurcation in the chordate Ciona. BMC Biol 2021; 19:180. [PMID: 34465302 PMCID: PMC8408944 DOI: 10.1186/s12915-021-01122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. RESULTS AND CONCLUSIONS We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a "broad-hourglass" model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.
Collapse
Affiliation(s)
- Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
| |
Collapse
|
9
|
Smith HM, Khairallah SM, Nguyen AH, Newman-Smith E, Smith WC. Misregulation of cell adhesion molecules in the Ciona neural tube closure mutant bugeye. Dev Biol 2021; 480:14-24. [PMID: 34407458 DOI: 10.1016/j.ydbio.2021.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/16/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
Neural tube closure (NTC) is a complex multi-step morphogenetic process that transforms the flat neural plate found on the surface of the post-gastrulation embryo into the hollow and subsurface central nervous system (CNS). Errors in this process underlie some of the most prevalent human birth defects, and occur in about 1 out of every 1000 births. Previously, we discovered a mutant in the basal chordate Ciona savignyi (named bugeye) that revealed a novel role for a T-Type Calcium Channel (Cav3) in this process. Moreover, the requirement for CAV3s in Xenopus NTC suggests a conserved function among the chordates. Loss of CAV3 leads to defects restricted to anterior NTC, with the brain apparently fully developed, but protruding from the head. Here we report first on a new Cav3 mutant in the related species C. robusta. RNAseq analysis of both C. robusta and C. savignyi bugeye mutants reveals misregulation of a number of transcripts including ones that are involved in cell-cell recognition and adhesion. Two in particular, Selectin and Fibronectin leucine-rich repeat transmembrane, which are aberrantly upregulated in the mutant, are expressed in the closing neural tube, and when disrupted by CRISPR gene editing lead to the open brain phenotype displayed in bugeye mutants. We speculate that these molecules play a transient role in tissue separation and adhesion during NTC and failure to downregulate them leads to an open neural tube.
Collapse
Affiliation(s)
- Haley M Smith
- Department of Molecular, Cellular and Developmental Biology, USA
| | | | - Ann Hong Nguyen
- Department of Molecular, Cellular and Developmental Biology, USA
| | | | - William C Smith
- Department of Molecular, Cellular and Developmental Biology, USA; Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.
| |
Collapse
|
10
|
Oonuma K, Kusakabe TG. The complete cell lineage and MAPK- and Otx-dependent specification of the dopaminergic cells in the Ciona brain. Development 2021; 148:269114. [PMID: 34121117 DOI: 10.1242/dev.198754] [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: 11/17/2020] [Accepted: 05/17/2021] [Indexed: 11/20/2022]
Abstract
The Ciona larva has served as a unique model for understanding the development of dopaminergic cells at single-cell resolution owing to the exceptionally small number of neurons in its brain and its fixed cell lineage during embryogenesis. A recent study suggested that the transcription factors Fer2 and Meis directly regulate the dopamine synthesis genes in Ciona, but the dopaminergic cell lineage and the gene regulatory networks that control the development of dopaminergic cells have not been fully elucidated. Here, we reveal that the dopaminergic cells in Ciona are derived from a bilateral pair of cells called a9.37 cells at the center of the neural plate. The a9.37 cells divide along the anterior-posterior axis, and all of the descendants of the posterior daughter cells differentiate into the dopaminergic cells. We show that the MAPK pathway and the transcription factor Otx are required for the expression of Fer2 in the dopaminergic cell lineage. Our findings establish the cellular and molecular framework for fully understanding the commitment to dopaminergic cells in the simple chordate brain.
Collapse
Affiliation(s)
- Kouhei Oonuma
- Institute for Integrative Neurobiology and Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Takehiro G Kusakabe
- Institute for Integrative Neurobiology and Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| |
Collapse
|
11
|
Hudson C, Yasuo H. Neuromesodermal Lineage Contribution to CNS Development in Invertebrate and Vertebrate Chordates. Genes (Basel) 2021; 12:genes12040592. [PMID: 33920662 PMCID: PMC8073528 DOI: 10.3390/genes12040592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Ascidians are invertebrate chordates and the closest living relative to vertebrates. In ascidian embryos a large part of the central nervous system arises from cells associated with mesoderm rather than ectoderm lineages. This seems at odds with the traditional view of vertebrate nervous system development which was thought to be induced from ectoderm cells, initially with anterior character and later transformed by posteriorizing signals, to generate the entire anterior-posterior axis of the central nervous system. Recent advances in vertebrate developmental biology, however, show that much of the posterior central nervous system, or spinal cord, in fact arises from cells that share a common origin with mesoderm. This indicates a conserved role for bi-potential neuromesoderm precursors in chordate CNS formation. However, the boundary between neural tissue arising from these distinct neural lineages does not appear to be fixed, which leads to the notion that anterior-posterior patterning and neural fate formation can evolve independently.
Collapse
|
12
|
Guignard L, Fiúza UM, Leggio B, Laussu J, Faure E, Michelin G, Biasuz K, Hufnagel L, Malandain G, Godin C, Lemaire P. Contact area-dependent cell communication and the morphological invariance of ascidian embryogenesis. Science 2020; 369:369/6500/eaar5663. [PMID: 32646972 DOI: 10.1126/science.aar5663] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/29/2020] [Indexed: 12/18/2022]
Abstract
Marine invertebrate ascidians display embryonic reproducibility: Their early embryonic cell lineages are considered invariant and are conserved between distantly related species, despite rapid genomic divergence. Here, we address the drivers of this reproducibility. We used light-sheet imaging and automated cell segmentation and tracking procedures to systematically quantify the behavior of individual cells every 2 minutes during Phallusia mammillata embryogenesis. Interindividual reproducibility was observed down to the area of individual cell contacts. We found tight links between the reproducibility of embryonic geometries and asymmetric cell divisions, controlled by differential sister cell inductions. We combined modeling and experimental manipulations to show that the area of contact between signaling and responding cells is a key determinant of cell communication. Our work establishes the geometric control of embryonic inductions as an alternative to classical morphogen gradients and suggests that the range of cell signaling sets the scale at which embryonic reproducibility is observed.
Collapse
Affiliation(s)
- Léo Guignard
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ulla-Maj Fiúza
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bruno Leggio
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France.,Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Inria, 69342 Lyon, France
| | - Julien Laussu
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Emmanuel Faure
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.,Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France.,Institut de Recherche en Informatique de Toulouse (IRIT), Universités Toulouse I et III, CNRS, INPT, ENSEEIHT, 31071 Toulouse, France
| | - Gaël Michelin
- Morpheme, Université Côte d'Azur, Inria, CNRS, I3S, France
| | - Kilian Biasuz
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | | | - Christophe Godin
- Virtual Plants, Université de Montpellier, CIRAD, INRA, Inria, 34095 Montpellier, France. .,Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Inria, 69342 Lyon, France
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France.
| |
Collapse
|
13
|
Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
| |
Collapse
|
14
|
Liu B, Satou Y. The genetic program to specify ectodermal cells in ascidian embryos. Dev Growth Differ 2020; 62:301-310. [PMID: 32130723 DOI: 10.1111/dgd.12660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 12/18/2022]
Abstract
The ascidian belongs to the sister group of vertebrates and shares many features with them. The gene regulatory network (GRN) controlling gene expression in ascidian embryonic development leading to the tadpole larva has revealed evolutionarily conserved gene circuits between ascidians and vertebrates. These conserved mechanisms are indeed useful to infer the original developmental programs of the ancestral chordates. Simultaneously, these studies have revealed which gene circuits are missing in the ascidian GRN; these gene circuits may have been acquired in the vertebrate lineage. In particular, the GRN responsible for gene expression in ectodermal cells of ascidian embryos has revealed the genetic programs that regulate the regionalization of the brain, formation of palps derived from placode-like cells, and differentiation of sensory neurons derived from neural crest-like cells. We here discuss how these studies have given insights into the evolution of these traits.
Collapse
Affiliation(s)
- Boqi Liu
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
15
|
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]
|
16
|
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.
Collapse
|
17
|
Kugler JE, Wu Y, Katikala L, Passamaneck YJ, Addy J, Caballero N, Oda-Ishii I, Maguire JE, Li R, Di Gregorio A. Positioning a multifunctional basic helix-loop-helix transcription factor within the Ciona notochord gene regulatory network. Dev Biol 2019; 448:119-135. [PMID: 30661645 DOI: 10.1016/j.ydbio.2019.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/27/2018] [Accepted: 01/01/2019] [Indexed: 11/26/2022]
Abstract
In a multitude of organisms, transcription factors of the basic helix-loop-helix (bHLH) family control the expression of genes required for organ development and tissue differentiation. The functions of different bHLH transcription factors in the specification of nervous system and paraxial mesoderm have been widely investigated in various model systems. Conversely, the knowledge of the role of these regulators in the development of the axial mesoderm, the embryonic territory that gives rise to the notochord, and the identities of their target genes, remain still fragmentary. Here we investigated the transcriptional regulation and target genes of Bhlh-tun1, a bHLH transcription factor expressed in the developing Ciona notochord as well as in additional embryonic territories that contribute to the formation of both larval and adult structures. We describe its possible role in notochord formation, its relationship with the key notochord transcription factor Brachyury, and suggest molecular mechanisms through which Bhlh-tun1 controls the spatial and temporal expression of its effectors.
Collapse
Affiliation(s)
- Jamie E Kugler
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Yushi Wu
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Lavanya Katikala
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Yale J Passamaneck
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Jermyn Addy
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Natalia Caballero
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Izumi Oda-Ishii
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Julie E Maguire
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Raymond Li
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA
| | - Anna Di Gregorio
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E 24th Street, New York, NY 10010, USA.
| |
Collapse
|
18
|
Transcriptional regulation of the Ciona Gsx gene in the neural plate. Dev Biol 2018; 448:88-100. [PMID: 30583796 DOI: 10.1016/j.ydbio.2018.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 12/29/2022]
Abstract
The ascidian neural plate consists of a defined number of identifiable cells organized in a grid of rows and columns, representing a useful model to investigate the molecular mechanisms controlling neural patterning in chordates. Distinct anterior brain lineages are specified via unique combinatorial inputs of signalling pathways with Nodal and Delta-Notch signals patterning along the medial-lateral axis and FGF/MEK/ERK signals patterning along the anterior-posterior axis of the neural plate. The Ciona Gsx gene is specifically expressed in the a9.33 cells in the row III/column 2 position of anterior brain lineages, characterised by a combinatorial input of Nodal-OFF, Notch-ON and FGF-ON. Here, we identify the minimal cis-regulatory element (CRE) of 376 bp, which can recapitulate the early activation of Gsx. We show that this minimal CRE responds in the same way as the endogenous Gsx gene to manipulation of FGF- and Notch-signalling pathways and to overexpression of Snail, a mediator of Nodal signals, and Six3/6, which is required to demarcate the anterior boundary of Gsx expression at the late neurula stage. We reveal that sequences proximal to the transcription start site include a temporal regulatory element required for the precise transcriptional onset of gene expression. We conclude that sufficient spatial and temporal information for Gsx expression is integrated in 376 bp of non-coding cis-regulatory sequences.
Collapse
|
19
|
Prünster MM, Ricci L, Brown FD, Tiozzo S. De novo neurogenesis in a budding chordate: Co-option of larval anteroposterior patterning genes in a transitory neurogenic organ. Dev Biol 2018; 448:342-352. [PMID: 30563648 DOI: 10.1016/j.ydbio.2018.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/29/2018] [Accepted: 10/16/2018] [Indexed: 01/29/2023]
Abstract
During metamorphosis of solitary ascidians, part of the larval tubular nervous system is recruited to form the adult central nervous system (CNS) through neural stem-like cells called ependymal cells. The anteroposterior (AP) gene expression patterning of the larval CNS regionalize the distribution of the ependymal cells, which contains the positional information of the neurons of the adult nervous system. In colonial ascidians, the CNS of asexually developed zooids has the same morphology of the one of the post-metamorphic zooids. However, its development follows a completely different organogenesis that lacks embryogenesis, a larval phase and metamorphosis. In order to describe neurogenesis during asexual development (blastogenesis), we followed the expression of six CNS AP patterning genes conserved in chordates and five neural-related genes to determine neural cell identity in Botryllus schlosseri. We observed that a neurogenesis occurs de novo on each blastogenic cycle starting from a neurogenic transitory structure, the dorsal tube. The dorsal tube partially co-opts the AP patterning of the larval CNS markers, and potentially combine the neurogenesis role and provider of positional clues for neuron patterning. This study shows how a larval developmental module is reused in a direct asexual development in order to generate the same structures.
Collapse
Affiliation(s)
- Maria Mandela Prünster
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France
| | - Lorenzo Ricci
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France; Harvard University, Department of Organismic&Evolutionary Biology, 52 Oxford Street, Cambridge, MA 02138, United States
| | - Federico D Brown
- Departamento de Zoologia - Instituto Biociências, Universidade de São Paulo, São Paulo, SP CEP 05508-090, Brazil; Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, São Sebastião, SP CEP 11612-109, Brazil
| | - Stefano Tiozzo
- Sorbonne Universités, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), 06230 Paris, France.
| |
Collapse
|
20
|
Abstract
The extracellular signal-regulated kinase (ERK) pathway leads to activation of the effector molecule ERK, which controls downstream responses by phosphorylating a variety of substrates, including transcription factors. Crucial insights into the regulation and function of this pathway came from studying embryos in which specific phenotypes arise from aberrant ERK activation. Despite decades of research, several important questions remain to be addressed for deeper understanding of this highly conserved signaling system and its function. Answering these questions will require quantifying the first steps of pathway activation, elucidating the mechanisms of transcriptional interpretation and measuring the quantitative limits of ERK signaling within which the system must operate to avoid developmental defects.
Collapse
Affiliation(s)
- Aleena L Patel
- Lewis Sigler Institute for Integrative Genomics, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Stanislav Y Shvartsman
- Lewis Sigler Institute for Integrative Genomics, Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
| |
Collapse
|
21
|
Abstract
Ascidians are tunicates, which constitute the sister group of vertebrates. The ascidian genome contains two Zic genes, called Zic-r.a (also called Macho-1) and Zic-r.b (ZicL). The latter is a multi-copy gene, and the precise copy number has not yet been determined. Zic-r.a is maternally expressed, and soon after fertilization Zic-r.a mRNA is localized in the posterior pole of the zygote. Zic-r.a protein is translated there and is involved in specification of posterior fate; in particular it is important for specification of muscle fate. Zic-r.a is also expressed zygotically in neural cells of the tailbud stage. On the other hand, Zic-r.b is first expressed in marginal cells of the vegetal hemisphere of 32-cell embryos and then in neural cells that contribute to the central nervous system during gastrulation. Zic-r.b is required first for specification of mesodermal tissues and then for specification of the central nervous system. Their upstream and downstream genetic pathways have been studied extensively by functional assays, which include gene knockdown and chromatin immunoprecipitation assays. Thus, ascidian Zic genes play central roles in specification of mesodermal and neural fates.
Collapse
Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan.
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| |
Collapse
|
22
|
Farley EK, Olson KM, Levine MS. Regulatory Principles Governing Tissue Specificity of Developmental Enhancers. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:27-32. [PMID: 27325706 DOI: 10.1101/sqb.2015.80.027227] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transcriptional enhancers are short segments of genomic DNA (50 bp to 1 kb in length) that can work over long distances (≥1 Mb) to regulate gene expression in specific cells and tissues. Genomic assays have identified on the order of 400,000 to one million putative enhancers in the human genome (e.g., ENCODE Consortium). This suggests that a typical gene is regulated by tens of enhancers, ensuring stringent regulation of gene expression in response to a variety of intrinsic and external signals. Despite the discovery of the first transcriptional enhancer more than 30 years ago, we know surprisingly little about how enhancers regulate gene expression. In particular, the relationship between primary DNA sequence and enhancer specificity remains obscure. Here we summarize recent high-throughput studies in whole embryos aimed at the systematic identification of the sequence and organizational constraints underlying enhancer function and specificity.
Collapse
Affiliation(s)
- Emma K Farley
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
| | - Katrina M Olson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
| |
Collapse
|
23
|
Boutet A. The evolution of asymmetric photosensitive structures in metazoans and the Nodal connection. Mech Dev 2017; 147:49-60. [PMID: 28986126 DOI: 10.1016/j.mod.2017.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 07/26/2017] [Accepted: 09/25/2017] [Indexed: 01/12/2023]
Abstract
Asymmetries are observed in a great number of taxa in metazoans. More particularly, functional lateralization and neuroanatomical asymmetries within the central nervous system have been a matter of intense research for at least two hundred years. While asymmetries of some paired structures/organs (e.g. eyes, ears, kidneys, legs, arms) constitute random deviations from a pure bilateral symmetry, brain asymmetries such as those observed in the cortex and epithalamus are directional. This means that molecular and anatomical features located on one side of a given structure are observed in most individuals. For instance, in humans, the neuronal tract connecting the language areas is enlarged in the left hemisphere. When asymmetries are fixed, their molecular mechanisms can be studied using mutants displaying different phenotypes: left or right isomerism of the structure, reversed asymmetry or random asymmetry. Our understanding of asymmetry in the nervous system has been widely enriched thanks to the characterization of mutants affecting epithalamus asymmetry. Furthermore, two decades ago, pioneering studies revealed that a specific morphogen, Nodal, active only on one side of the embryo during development is an important molecule in asymmetry patterning. In this review, I have gathered important data bringing insight into the origin and evolution of epithalamus asymmetry and the role of Nodal in metazoans. After a short introduction on brain asymmetries (chapter I), I secondly focus on the molecular and anatomical characteristics of the epithalamus in vertebrates and explore some functional aspects such as its photosensitive ability related to the pineal complex (chapter II). Third, I discuss homology relationship of the parapineal organ among vertebrates (chapter III). Fourth, I discuss the possible origin of the epithalamus, presenting cells displaying photosensitive properties and/or asymmetry in the anterior part of the body in non-vertebrates (chapter IV). Finally, I report Nodal signaling expression data and functional experiments performed in different metazoan groups (chapter V).
Collapse
Affiliation(s)
- Agnès Boutet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS UMR 8227, Laboratoire de Biologie Intégrative des Modèles Marins, Station Biologique, F-29688 Roscoff, France.
| |
Collapse
|
24
|
Kaul-Strehlow S, Urata M, Praher D, Wanninger A. Neuronal patterning of the tubular collar cord is highly conserved among enteropneusts but dissimilar to the chordate neural tube. Sci Rep 2017; 7:7003. [PMID: 28765531 PMCID: PMC5539250 DOI: 10.1038/s41598-017-07052-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/23/2017] [Indexed: 11/09/2022] Open
Abstract
A tubular nervous system is present in the deuterostome groups Chordata (cephalochordates, tunicates, vertebrates) and in the non-chordate Enteropneusta. However, the worm-shaped enteropneusts possess a less complex nervous system featuring only a short hollow neural tube, whereby homology to its chordate counterpart remains elusive. Since the majority of data on enteropneusts stem from the harrimaniid Saccoglossus kowalevskii, putative interspecific variations remain undetected resulting in an unreliable ground pattern that impedes homology assessments. In order to complement the missing data from another enteropneust family, we investigated expression of key neuronal patterning genes in the ptychoderid Balanoglossus misakiensis. The collar cord of B. misakiensis shows anterior Six3/6 and posterior Otx + Engrailed expression, in a region corresponding to the chordate brain. Neuronal Nk2.1/Nk2.2 expression is absent. Interestingly, we found median Dlx and lateral Pax6 expression domains, i.e., a condition that is reversed compared to chordates. Comparative analyses reveal that adult nervous system patterning is highly conserved among the enteropneust families Harrimaniidae, Spengelidae and Ptychoderidae. BmiDlx and BmiPax6 have no corresponding expression domains in the chordate brain, which may be indicative of independent acquisition of a tubular nervous system in Enteropneusta and Chordata.
Collapse
Affiliation(s)
- Sabrina Kaul-Strehlow
- Department for Integrative Zoology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria. .,Research Center for Marine Biology, Tohoku University, Asamushi, Aomori, Aomori, 039-3501, Japan. .,Department for Molecular Evolution and Development, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| | - Makoto Urata
- Noto Marine Laboratory, Division of Marine Environmental Studies, Institute of Nature and Environmental Technology, Kanazawa University, Ogi, Noto-cho, Ishikawa, 927-0553, Japan
| | - Daniela Praher
- Department for Molecular Evolution and Development, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | - Andreas Wanninger
- Department for Integrative Zoology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| |
Collapse
|
25
|
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.
Collapse
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:
| |
Collapse
|
26
|
Yoshida K, Nakahata A, Treen N, Sakuma T, Yamamoto T, Sasakura Y. Hox-mediated endodermal identity patterns the pharyngeal muscle formation in the chordate pharynx. Development 2017; 144:1629-1634. [DOI: 10.1242/dev.144436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 03/07/2017] [Indexed: 01/10/2023]
Abstract
The pharynx, possessing gill slits and the endostyle, is a characteristic of chordates that is a complex of multiple tissues well organized along the anterior-posterior (AP) axis. Although Hox genes show AP coordinated expression in the pharyngeal endoderm, tissue specific roles of these factors for establishing the regional identities within this tissue is largely unknown. Here, we show that Hox1 is essential for the establishment of AP axial identity of the endostyle, a major structure of the pharyngeal endoderm, in the ascidian Ciona intestinalis. We found that Hox1 knockout causes posterior to anterior transformation of the endostyle identity, and Hox1 represses Otx expression and anterior identity, and vice versa. Furthermore, alteration of the regional identity of the endostyle disrupts the formation of body wall muscles, suggesting that the endodermal axial identity is essential for the coordinated pharyngeal development. Our results reveal an essential role of Hox genes for establishment of the AP regional identity in the pharyngeal endoderm and crosstalk between endoderm and mesoderm for the development of chordate pharynx.
Collapse
Affiliation(s)
- Keita Yoshida
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Azusa Nakahata
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Nicholas Treen
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1 Shimoda, Shizuoka, 415-0025, Japan
| |
Collapse
|
27
|
Esposito R, Yasuo H, Sirour C, Palladino A, Spagnuolo A, Hudson C. Patterning of brain precursors in ascidian embryos. Development 2016; 144:258-264. [PMID: 27993985 DOI: 10.1242/dev.142307] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/02/2016] [Indexed: 11/20/2022]
Abstract
In terms of their embryonic origins, the anterior and posterior parts of the ascidian central nervous system (CNS) are associated with distinct germ layers. The anterior part of the sensory vesicle, or brain, originates from ectoderm lineages following a neuro-epidermal binary fate decision. In contrast, a large part of the remaining posterior CNS is generated following neuro-mesodermal binary fate decisions. Here, we address the mechanisms that pattern the anterior brain precursors along the medial-lateral axis (future ventral-dorsal) at neural plate stages. Our functional studies show that Nodal signals are required for induction of lateral genes, including Delta-like, Snail, Msxb and Trp Delta-like/Notch signalling induces intermediate (Gsx) over medial (Meis) gene expression in intermediate cells, whereas the combinatorial action of Snail and Msxb prevents the expression of Gsx in lateral cells. We conclude that despite the distinct embryonic lineage origins within the larval CNS, the mechanisms that pattern neural precursors are remarkably similar.
Collapse
Affiliation(s)
- Rosaria Esposito
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Hitoyoshi Yasuo
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Villefranche-sur-mer 06230, France
| | - Cathy Sirour
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Villefranche-sur-mer 06230, France
| | - Antonio Palladino
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Antonietta Spagnuolo
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Clare Hudson
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanologique, Villefranche-sur-mer 06230, France
| |
Collapse
|
28
|
Imai KS, Hikawa H, Kobayashi K, Satou Y. Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos. Development 2016; 144:33-37. [PMID: 27888190 DOI: 10.1242/dev.142109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/14/2016] [Indexed: 12/17/2022]
Abstract
Epidermis and neural tissues differentiate from the ectoderm in animal embryos. Although epidermal fate is thought to be induced in vertebrate embryos, embryological evidence has indicated that no intercellular interactions during early stages are required for epidermal fate in ascidian embryos. To test this hypothesis, we determined the gene regulatory circuits for epidermal and neural specification in the ascidian embryo. These circuits started with Tfap2-r.b and Sox1/2/3, which are expressed in the ectodermal lineage immediately after zygotic genome activation. Tfap2-r.b expression was diminished in the neural lineages upon activation of fibroblast growth factor signaling, which is known to induce neural fate, and sustained only in the epidermal lineage. Tfap2-r.b specified the epidermal fate cooperatively with Dlx.b, which was activated by Sox1/2/3 This Sox1/2/3-Dlx.b circuit was also required for specification of the anterior neural fate. In the posterior neural lineage, Sox1/2/3 activated Nodal, which is required for specification of the posterior neural fate. Our findings support the hypothesis that the epidermal fate is specified autonomously in ascidian embryos.
Collapse
Affiliation(s)
- Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Hiroki Hikawa
- 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
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Negishi T, Miyazaki N, Murata K, Yasuo H, Ueno N. Physical association between a novel plasma-membrane structure and centrosome orients cell division. eLife 2016; 5:e16550. [PMID: 27502556 PMCID: PMC4978527 DOI: 10.7554/elife.16550] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/20/2016] [Indexed: 01/16/2023] Open
Abstract
In the last mitotic division of the epidermal lineage in the ascidian embryo, the cells divide stereotypically along the anterior-posterior axis. During interphase, we found that a unique membrane structure invaginates from the posterior to the centre of the cell, in a microtubule-dependent manner. The invagination projects toward centrioles on the apical side of the nucleus and associates with one of them. Further, a cilium forms on the posterior side of the cell and its basal body remains associated with the invagination. A laser ablation experiment suggests that the invagination is under tensile force and promotes the posterior positioning of the centrosome. Finally, we showed that the orientation of the invaginations is coupled with the polarized dynamics of centrosome movements and the orientation of cell division. Based on these findings, we propose a model whereby this novel membrane structure orchestrates centrosome positioning and thus the orientation of cell division axis.
Collapse
Affiliation(s)
- Takefumi Negishi
- Division of Morphogenesis, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Laboratoire de Biologie du Développement de Villefranche-sur-mer UMR7009, Observatoire Océanologique, Sorbonne Universités, UPMC Université Paris 06, CNRS, Villefranche-sur-Mer, France
| | - Naoyuki Miyazaki
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-mer UMR7009, Observatoire Océanologique, Sorbonne Universités, UPMC Université Paris 06, CNRS, Villefranche-sur-Mer, France
| | - Naoto Ueno
- Division of Morphogenesis, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, Okazaki, Japan
| |
Collapse
|
31
|
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.
Collapse
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.
| |
Collapse
|
32
|
Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. Proc Natl Acad Sci U S A 2016; 113:6508-13. [PMID: 27155014 DOI: 10.1073/pnas.1605085113] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Transcriptional enhancers are short segments of DNA that switch genes on and off in response to a variety of intrinsic and extrinsic signals. Despite the discovery of the first enhancer more than 30 y ago, the relationship between primary DNA sequence and enhancer activity remains obscure. In particular, the importance of "syntax" (the order, orientation, and spacing of binding sites) is unclear. A high-throughput screen identified synthetic notochord enhancers that are activated by the combination of ZicL and ETS transcription factors in Ciona embryos. Manipulation of these enhancers elucidated a "regulatory code" of sequence and syntax features for notochord-specific expression. This code enabled in silico discovery of bona fide notochord enhancers, including those containing low-affinity binding sites that would be excluded by standard motif identification methods. One of the newly identified enhancers maps upstream of the known enhancer that regulates Brachyury (Ci-Bra), a key determinant of notochord specification. This newly identified Ci-Bra shadow enhancer contains binding sites with very low affinity, but optimal syntax, and therefore mediates surprisingly strong expression in the notochord. Weak binding sites are compensated by optimal syntax, whereas enhancers containing high-affinity binding affinities possess suboptimal syntax. We suggest this balance has obscured the importance of regulatory syntax, as noncanonical binding motifs are typically disregarded by enhancer detection methods. As a result, enhancers with low binding affinities but optimal syntax may be a vastly underappreciated feature of the regulatory genome.
Collapse
|
33
|
Imai KS, Satoh N, Satou Y. Region specific gene expressions in the central nervous system of the ascidian embryo. Mech Dev 2016; 119 Suppl 1:S275-7. [PMID: 14516697 DOI: 10.1016/s0925-4773(03)00128-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The vertebrate brain is regionalized during development into forebrain, midbrain and hindbrain. Fibroblast growth factor 8 (FGF8) is expressed in the midbrain/hindbrain boundary (MHB) and functions as an organizer molecule. Previous studies demonstrated that the brain of basal chordates or ascidians is also regionalized at least into fore/midbrain and hindbrain. To better understand the ascidian brain regionalization, the expression of the Ciona Fgf8/17/18 gene was compared with the expression of Otx, En and Pax2/5/8 genes. The expression pattern of these genes resembled that of the genes in the vertebrate forebrain, midbrain, MHB and hindbrain, each of those domains being characterized by sole or combined expression of Otx, Pax2/5/8, En and Fgf8/17/18. In addition, the putative forebrain and midbrain expressed Ci-FgfL and Ci-Fgf9/16/20, respectively. Therefore, the regionalization of the ascidian larval central nervous system was also marked by the expression of Fgf genes.
Collapse
Affiliation(s)
- Kaoru S Imai
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | | | | |
Collapse
|
34
|
Garstang MG, Osborne PW, Ferrier DEK. TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. BMC Evol Biol 2016; 16:57. [PMID: 26940763 PMCID: PMC4776371 DOI: 10.1186/s12862-016-0614-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/11/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ParaHox genes play an integral role in the anterior-posterior (A-P) patterning of the nervous system and gut of most animals. The ParaHox cluster is an ideal system in which to study the evolution and regulation of developmental genes and gene clusters, as it displays similar regulatory phenomena to its sister cluster, the Hox cluster, but offers a much simpler system with only three genes. RESULTS Using Ciona intestinalis transgenics, we isolated a regulatory element upstream of Branchiostoma floridae Gsx that drives expression within the central nervous system of Ciona embryos. The minimal amphioxus enhancer region required to drive CNS expression has been identified, along with surrounding sequence that increases the efficiency of reporter expression throughout the Ciona CNS. TCF/Lef binding sites were identified and mutagenized and found to be required to drive the CNS expression. Also, individual contributions of TCF/Lef sites varied across the regulatory region, revealing a partial division of function across the Bf-Gsx-Up regulatory element. Finally, when all TCF/Lef binding sites are mutated CNS expression is not only abolished, but a latent repressive function is also unmasked. CONCLUSIONS We have identified a B. floridae Gsx upstream regulatory element that drives CNS expression within transgenic Ciona intestinalis, and have shown that this CNS expression is dependent upon TCF/Lef binding sites. We examine the evolutionary and developmental implications of these results, and discuss the possibility of TCF/Lef not only as a regulator of chordate Gsx, but as a deeply conserved regulatory factor controlling all three ParaHox genes across the Metazoa.
Collapse
Affiliation(s)
- Myles G Garstang
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| | - Peter W Osborne
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| |
Collapse
|
35
|
Ordered expression pattern of Hox and ParaHox genes along the alimentary canal in the ascidian juvenile. Cell Tissue Res 2016; 365:65-75. [DOI: 10.1007/s00441-016-2360-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/07/2016] [Indexed: 01/03/2023]
|
36
|
Morales Diaz H, Mejares E, Newman-Smith E, Smith WC. ACAM, a novel member of the neural IgCAM family, mediates anterior neural tube closure in a primitive chordate. Dev Biol 2016; 409:288-296. [PMID: 26542009 DOI: 10.1016/j.ydbio.2015.10.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 01/18/2023]
Abstract
The neural IgCAM family of cell adhesion molecules, which includes NCAM and related molecules, has evolved via gene duplication and alternative splicing to allow for a wide range of isoforms with distinct functions and homophilic binding properties. A search for neural IgCAMs in ascidians (Ciona intestinalis, Ciona savignyi, and Phallusia mammillata) has identified a novel set of truncated family members that, unlike the known members, lack fibronectin III domains and consist of only repeated Ig domains. Within the tunicates this form appears to be unique to the ascidians, and it was designated ACAM, for Ascidian Cell Adhesion Molecule. In C. intestinalis ACAM is expressed in the developing neural plate and neural tube, with strongest expression in the anterior sensory vesicle precursor. Unlike the two other conventional neural IgCAMs in C. intestinalis, which are expressed maternally and throughout the morula and blastula stages, ACAM expression initiates at the gastrula stage. Moreover, C. intestinalis ACAM is a target of the homeodomain transcription factor OTX, which plays an essential role in the development of the anterior central nervous system. Morpholino (MO) knockdown shows that ACAM is required for neural tube closure. In MO-injected embryos neural tube closure was normal caudally, but the anterior neuropore remained open. A similar phenotype was seen with overexpression of a secreted version of ACAM. The presence of ACAM in ascidians highlights the diversity of this gene family in morphogenesis and neurodevelopment.
Collapse
Affiliation(s)
- Heidi Morales Diaz
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - Emil Mejares
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - Erin Newman-Smith
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - William C Smith
- Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, United States.
| |
Collapse
|
37
|
Ohta N, Waki K, Mochizuki A, Satou Y. A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo. PLoS Comput Biol 2015; 11:e1004687. [PMID: 26714026 PMCID: PMC4695095 DOI: 10.1371/journal.pcbi.1004687] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 12/01/2015] [Indexed: 01/12/2023] Open
Abstract
A complex system of multiple signaling molecules often produce differential gene expression patterns in animal embryos. In the ascidian embryo, four signaling ligands, Ephrin-A.d (Efna.d), Fgf9/16/20, Admp, and Gdf1/3-r, coordinately induce Otx expression in the neural lineage at the 32-cell stage. However, it has not been determined whether differential inputs of all of these signaling pathways are really necessary. It is possible that differential activation of one of these signaling pathways is sufficient and the remaining signaling pathways are activated in all cells at similar levels. To address this question, we developed a parameter-free method for determining a Boolean function for Otx expression in the present study. We treated activities of signaling pathways as Boolean values, and we also took all possible patterns of signaling gradients into consideration. We successfully determined a Boolean function that explains Otx expression in the animal hemisphere of wild-type and morphant embryos at the 32-cell stage. This Boolean function was not inconsistent with three sensing patterns, which represented whether or not individual cells received sufficient amounts of the signaling molecules. These sensing patterns all indicated that differential expression of Otx in the neural lineage is primarily determined by Efna.d, but not by differential inputs of Fgf9/16/20, Admp, and Gdf1/3-r signaling. To confirm this hypothesis experimentally, we simultaneously knocked-down Admp, Gdf1/3-r, and Fgf9/16/20, and treated this triple morphant with recombinant bFGF and BMP4 proteins, which mimic Fgf9/16/20 and Admp/Gdf1/3-r activity, respectively. Although no differential inputs of Admp, Gdf1/3-r and Fgf9/16/20 signaling were expected under this experimental condition, Otx was expressed specifically in the neural lineage. Thus, direct cell–cell interactions through Efna.d play a critical role in patterning the ectoderm of the early ascidian embryo. It is often difficult to understand a complex system of multiple signaling molecules in animal embryos only with experimental procedures. Although theoretical analysis might solve this problem, it is often difficult to precisely determine parameters for signaling gradients and kinetics of signaling molecules. In the present study, we developed a parameter-free method for determining a Boolean function for understanding a complex signaling system using gene expression patterns of signaling molecules and geometrical configurations of individual cells within the embryo. In the ascidian embryo, four signaling ligands, Ephrin-A.d (Efna.d), Fgf9/16/20, Admp, and Gdf1/3-r, coordinately induce Otx expression in the neural lineage at the 32-cell stage. In addition to determining a Boolean function, our method determined sensing patterns, which represented whether or not individual cells received sufficient amounts of the signaling molecules. The sensing patterns predicted that differential expression of Otx in the neural lineage is primarily determined by Efna.d, but not by differential inputs of Fgf9/16/20, Admp, and Gdf1/3-r. We confirmed this prediction by an experiment. As a result, we found that only Efna.d signaling pathway is differentially activated between ectodermal cells and the remaining signaling pathways are activated in all ectodermal cells at similar levels.
Collapse
Affiliation(s)
- Naoyuki Ohta
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Kana Waki
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
| | - Atsushi Mochizuki
- RIKEN Advanced Science Institute, Wako, Saitama, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- * E-mail:
| |
Collapse
|
38
|
Wollesen T, Rodríguez Monje SV, McDougall C, Degnan BM, Wanninger A. The ParaHox gene Gsx patterns the apical organ and central nervous system but not the foregut in scaphopod and cephalopod mollusks. EvoDevo 2015; 6:41. [PMID: 26715985 PMCID: PMC4693441 DOI: 10.1186/s13227-015-0037-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/17/2015] [Indexed: 11/21/2022] Open
Abstract
Background It has been hypothesized that the ParaHox gene Gsx patterned the foregut of the last common bilaterian ancestor. This notion was corroborated by Gsx expression in three out of four lophotrochozoan species, several ecdysozoans, and some deuterostomes. Remarkably, Gsx is also expressed in the bilaterian anterior-most central nervous system (CNS) and the gastropod and annelid apical organ. To infer whether these findings are consistent with other mollusks or even lophotrochozoans, we investigated Gsx expression in developmental stages of representatives of two other molluscan classes, the scaphopod Antalis entalis and the cephalopod Idiosepius notoides. Results Gsx is not expressed in the developing digestive tract of Antalis entalis and Idiosepius notoides. Instead, it is expressed in cells of the apical organ in the scaphopod trochophore and in two cells adjacent to this organ. Late-stage trochophores express Aen-Gsx in cells of the developing cerebral and pedal ganglia and in cells close to the pavilion, mantle, and foot. In postmetamorphic specimens, Aen-Gsx is expressed in the cerebral and pedal ganglia, the foot, and the nascent captacula. In early squid embryos, Ino-Gsx is expressed in the cerebral, palliovisceral, and optic ganglia. In late-stage embryos, Ino-Gsx is additionally expressed close to the eyes and in the supraesophageal and posterior subesophageal masses and optic lobes. Developmental stages close to hatching express Ino-Gsx only close to the eyes. Conclusions Our results suggest that Gsx expression in the foregut might not be a plesiomorphic trait of the Lophotrochozoa as insinuated previously. Since neither ecdysozoans nor deuterostomes express Gsx in their gut, a role in gut formation in the last common bilaterian ancestor appears unlikely. Gsx is consistently expressed in the bilaterian anterior-most CNS and the apical organ of lophotrochozoan larvae, suggesting a recruitment of Gsx into the formation of this organ in the Lophotrochozoa. The cephalopod posterior subesophageal mass and optic ganglia and the scaphopod pedal ganglia also express Gsx. In summary, Gsx expression only appears to be conserved in the anterior-most brain region during evolution. Accordingly, Gsx appears to have been recruited into the formation of other expression domains, e.g., the apical organ or the foregut, in some lophotrochozoans.
Collapse
Affiliation(s)
- Tim Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | | | - Carmel McDougall
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Andreas Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| |
Collapse
|
39
|
Waki K, Imai KS, Satou Y. Genetic pathways for differentiation of the peripheral nervous system in ascidians. Nat Commun 2015; 6:8719. [PMID: 26515371 PMCID: PMC4640076 DOI: 10.1038/ncomms9719] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/24/2015] [Indexed: 11/17/2022] Open
Abstract
Ascidians belong to tunicates, the sister group of vertebrates. Peripheral nervous systems (PNSs) including epidermal sensory neurons (ESNs) in the trunk and dorsal tail regions of ascidian larvae are derived from cells adjacent to the neural plate, as in vertebrates. On the other hand, peripheral ESNs in the ventral tail region are derived from the ventral ectoderm under the control of BMP signalling, reminiscent of sensory neurons of amphioxus and protostomes. In this study, we show that two distinct mechanisms activate a common gene circuit consisting of Msx, Ascl.b, Tox, Delta.b and Pou4 in the dorsal and ventral regions to differentiate ESNs. Our results suggest that ventral ESNs of the ascidian larva are not directly homologous to vertebrate PNSs. The dorsal ESNs might have arisen via co-option of the original PNS gene circuit to the neural plate border in an ancestral chordate. The evolutionary origin of the peripheral nervous systems (PNSs) is poorly understood. Here, the authors show that two mechanisms activate gene circuits in ascidians to differentiate epidermal sensory neurons, which suggests that vertebrate PNSs arose via cooption of the ancient PNS gene circuit.
Collapse
Affiliation(s)
- Kana Waki
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kaoru S Imai
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,CREST, JST, Sakyo, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
40
|
Abstract
Transcriptional enhancers direct precise on-off patterns of gene expression during development. To explore the basis for this precision, we conducted a high-throughput analysis of the Otx-a enhancer, which mediates expression in the neural plate of Ciona embryos in response to fibroblast growth factor (FGF) signaling and a localized GATA determinant. We provide evidence that enhancer specificity depends on submaximal recognition motifs having reduced binding affinities ("suboptimization"). Native GATA and ETS (FGF) binding sites contain imperfect matches to consensus motifs. Perfect matches mediate robust but ectopic patterns of gene expression. The native sites are not arranged at optimal intervals, and subtle changes in their spacing alter enhancer activity. Multiple tiers of enhancer suboptimization produce specific, but weak, patterns of expression, and we suggest that clusters of weak enhancers, including certain "superenhancers," circumvent this trade-off in specificity and activity.
Collapse
Affiliation(s)
- Emma K Farley
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Katrina M Olson
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Wei Zhang
- Department of Medicine, University of California, San Diego, CA 92093-0688, USA
| | - Alexander J Brandt
- Department of Chemistry, University of California, Berkeley, CA 94720-3200, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA
| | - Michael S Levine
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
41
|
Organizer regions in marine colonial hydrozoans. ZOOLOGY 2015; 118:89-101. [DOI: 10.1016/j.zool.2014.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/20/2014] [Accepted: 12/21/2014] [Indexed: 01/08/2023]
|
42
|
Schlosser G. Vertebrate cranial placodes as evolutionary innovations--the ancestor's tale. Curr Top Dev Biol 2015; 111:235-300. [PMID: 25662263 DOI: 10.1016/bs.ctdb.2014.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Evolutionary innovations often arise by tinkering with preexisting components building new regulatory networks by the rewiring of old parts. The cranial placodes of vertebrates, ectodermal thickenings that give rise to many of the cranial sense organs (ear, nose, lateral line) and ganglia, originated as such novel structures, when vertebrate ancestors elaborated their head in support of a more active and exploratory life style. This review addresses the question of how cranial placodes evolved by tinkering with ectodermal patterning mechanisms and sensory and neurosecretory cell types that have their own evolutionary history. With phylogenetic relationships among the major branches of metazoans now relatively well established, a comparative approach is used to infer, which structures evolved in which lineages and allows us to trace the origin of placodes and their components back from ancestor to ancestor. Some of the core networks of ectodermal patterning and sensory and neurosecretory differentiation were already established in the common ancestor of cnidarians and bilaterians and were greatly elaborated in the bilaterian ancestor (with BMP- and Wnt-dependent patterning of dorsoventral and anteroposterior ectoderm and multiple neurosecretory and sensory cell types). Rostral and caudal protoplacodal domains, giving rise to some neurosecretory and sensory cells, were then established in the ectoderm of the chordate and tunicate-vertebrate ancestor, respectively. However, proper cranial placodes as clusters of proliferating progenitors producing high-density arrays of neurosecretory and sensory cells only evolved and diversified in the ancestors of vertebrates.
Collapse
Affiliation(s)
- Gerhard Schlosser
- School of Natural Sciences & Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Ireland.
| |
Collapse
|
43
|
Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate. Dev Biol 2015; 399:218-25. [PMID: 25576927 DOI: 10.1016/j.ydbio.2014.12.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 11/24/2022]
Abstract
The ascidian Ciona intestinalis is a marine invertebrate belonging to the sister group of the vertebrates, the tunicates. Its compact genome and simple, experimentally tractable embryos make Ciona well-suited for the study of cell-fate specification in chordates. Tunicate larvae possess a characteristic chordate body plan, and many developmental pathways are conserved between tunicates and vertebrates. Previous studies have shown that FGF signals are essential for neural induction and patterning at sequential steps of Ciona embryogenesis. Here we show that two different ETS family transcription factors, Ets1/2 and Elk1/3/4, have partially redundant activities in the anterior neural plate of gastrulating embryos. Whereas Ets1/2 promotes pigment cell formation in lateral lineages, both Ets1/2 and Elk1/3/4 are involved in the activation of Myt1L in medial lineages and the restriction of Six3/6 expression to the anterior-most regions of the neural tube. We also provide evidence that photoreceptor cells arise from posterior regions of the presumptive sensory vesicle, and do not depend on FGF signaling. Cells previously identified as photoreceptor progenitors instead form ependymal cells and neurons of the larval brain. Our results extend recent findings on FGF-dependent patterning of anterior-posterior compartments in the Ciona central nervous system.
Collapse
|
44
|
Satou Y, Imai KS. Gene regulatory systems that control gene expression in the Ciona embryo. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2015; 91:33-51. [PMID: 25748582 PMCID: PMC4406867 DOI: 10.2183/pjab.91.33] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/05/2014] [Indexed: 06/04/2023]
Abstract
Transcriptional control of gene expression is one of the most important regulatory systems in animal development. Specific gene expression is basically determined by combinatorial regulation mediated by multiple sequence-specific transcription factors. The decoding of animal genomes has provided an opportunity for us to systematically examine gene regulatory networks consisting of successive layers of control of gene expression. It remains to be determined to what extent combinatorial regulation encoded in gene regulatory networks can explain spatial and temporal gene-expression patterns. The ascidian Ciona intestinalis is one of the animals in which the gene regulatory network has been most extensively studied. In this species, most specific gene expression patterns in the embryo can be explained by combinations of upstream regulatory genes encoding transcription factors and signaling molecules. Systematic scrutiny of gene expression patterns and regulatory interactions at the cellular resolution have revealed incomplete parts of the network elucidated so far, and have identified novel regulatory genes and novel regulatory mechanisms.
Collapse
Affiliation(s)
- Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University; CREST, JST, Saitama, Japan.
| | | |
Collapse
|
45
|
Veeman M, Reeves W. Quantitative and in toto imaging in ascidians: working toward an image-centric systems biology of chordate morphogenesis. Genesis 2015; 53:143-59. [PMID: 25262824 PMCID: PMC4378666 DOI: 10.1002/dvg.22828] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/20/2014] [Accepted: 09/25/2014] [Indexed: 12/16/2022]
Abstract
Developmental biology relies heavily on microscopy to image the finely controlled cell behaviors that drive embryonic development. Most embryos are large enough that a field of view with the resolution and magnification needed to resolve single cells will not span more than a small region of the embryo. Ascidian embryos, however, are sufficiently small that they can be imaged in toto with fine subcellular detail using conventional microscopes and objectives. Unlike other model organisms with particularly small embryos, ascidians have a chordate embryonic body plan that includes a notochord, hollow dorsal neural tube, heart primordium and numerous other anatomical details conserved with the vertebrates. Here we compare the size and anatomy of ascidian embryos with those of more traditional model organisms, and relate these features to the capabilities of both conventional and exotic imaging methods. We review the emergence of Ciona and related ascidian species as model organisms for a new era of image-based developmental systems biology. We conclude by discussing some important challenges in ascidian imaging and image analysis that remain to be solved.
Collapse
Affiliation(s)
- Michael Veeman
- Division of Biology, Kansas State University, Manhattan KS, USA
| | - Wendy Reeves
- Division of Biology, Kansas State University, Manhattan KS, USA
| |
Collapse
|
46
|
Ohtsuka Y, Matsumoto J, Katsuyama Y, Okamura Y. Nodal signaling regulates specification of ascidian peripheral neurons through control of the BMP signal. Development 2014; 141:3889-99. [PMID: 25231764 DOI: 10.1242/dev.110213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The neural crest and neurogenic placodes are thought to be a vertebrate innovation that gives rise to much of the peripheral nervous system (PNS). Despite their importance for understanding chordate evolution and vertebrate origins, little is known about the evolutionary origin of these structures. Here, we investigated the mechanisms underlying the development of ascidian trunk epidermal sensory neurons (ESNs), which are thought to function as mechanosensory neurons in the rostral-dorsal trunk epidermis. We found that trunk ESNs are derived from the anterior and lateral neural plate border, as is the case in the vertebrate PNS. Pharmacological experiments indicated that intermediate levels of bone morphogenetic protein (BMP) signal induce formation of ESNs from anterior ectodermal cells. Gene knockdown experiments demonstrated that HrBMPa (60A-subclass BMP) and HrBMPb (dpp-subclass BMP) act to induce trunk ESNs at the tailbud stage and that anterior trunk ESN specification requires Chordin-mediated antagonism of the BMP signal, but posterior trunk ESN specification does not. We also found that Nodal functions as a neural plate border inducer in ascidians. Nodal signaling regulates expression of HrBMPs and HrChordin in the lateral neural plate, and consequently specifies trunk ESNs. Collectively, these findings show that BMP signaling that is regulated spatiotemporally by Nodal signaling is required for trunk ESN specification, which clearly differs from the BMP gradient model proposed for vertebrate neural induction.
Collapse
Affiliation(s)
- Yukio Ohtsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Jun Matsumoto
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - You Katsuyama
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Yasushi Okamura
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| |
Collapse
|
47
|
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
| |
Collapse
|
48
|
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.
Collapse
|
49
|
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.
Collapse
Affiliation(s)
- Tatsuro Ikeda
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | | | | |
Collapse
|
50
|
Schlosser G, Patthey C, Shimeld SM. The evolutionary history of vertebrate cranial placodes II. Evolution of ectodermal patterning. Dev Biol 2014; 389:98-119. [PMID: 24491817 DOI: 10.1016/j.ydbio.2014.01.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/21/2014] [Accepted: 01/24/2014] [Indexed: 12/12/2022]
Abstract
Cranial placodes are evolutionary innovations of vertebrates. However, they most likely evolved by redeployment, rewiring and diversification of preexisting cell types and patterning mechanisms. In the second part of this review we compare vertebrates with other animal groups to elucidate the evolutionary history of ectodermal patterning. We show that several transcription factors have ancient bilaterian roles in dorsoventral and anteroposterior regionalisation of the ectoderm. Evidence from amphioxus suggests that ancestral chordates then concentrated neurosecretory cells in the anteriormost non-neural ectoderm. This anterior proto-placodal domain subsequently gave rise to the oral siphon primordia in tunicates (with neurosecretory cells being lost) and anterior (adenohypophyseal, olfactory, and lens) placodes of vertebrates. Likewise, tunicate atrial siphon primordia and posterior (otic, lateral line, and epibranchial) placodes of vertebrates probably evolved from a posterior proto-placodal region in the tunicate-vertebrate ancestor. Since both siphon primordia in tunicates give rise to sparse populations of sensory cells, both proto-placodal domains probably also gave rise to some sensory receptors in the tunicate-vertebrate ancestor. However, proper cranial placodes, which give rise to high density arrays of specialised sensory receptors and neurons, evolved from these domains only in the vertebrate lineage. We propose that this may have involved rewiring of the regulatory network upstream and downstream of Six1/2 and Six4/5 transcription factors and their Eya family cofactors. These proteins, which play ancient roles in neuronal differentiation were first recruited to the dorsal non-neural ectoderm in the tunicate-vertebrate ancestor but subsequently probably acquired new target genes in the vertebrate lineage, allowing them to adopt new functions in regulating proliferation and patterning of neuronal progenitors.
Collapse
Affiliation(s)
- Gerhard Schlosser
- Department of Zoology, School of Natural Sciences & Regenerative Medicine Institute (REMEDI), National University of Ireland, University Road, Galway, Ireland.
| | - Cedric Patthey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Sebastian M Shimeld
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| |
Collapse
|