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Feuda R, Peter IS. Homologous gene regulatory networks control development of apical organs and brains in Bilateria. SCIENCE ADVANCES 2022; 8:eabo2416. [PMID: 36322649 PMCID: PMC9629743 DOI: 10.1126/sciadv.abo2416] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Apical organs are relatively simple larval nervous systems. The extent to which apical organs are evolutionarily related to the more complex nervous systems of other animals remains unclear. To identify common developmental mechanisms, we analyzed the gene regulatory network (GRN) controlling the development of the apical organ in sea urchins. We characterized the developmental expression of 30 transcription factors and identified key regulatory functions for FoxQ2, Hbn, Delta/Notch signaling, and SoxC in the patterning of the apical organ and the specification of neurons. Almost the entire set of apical transcription factors is expressed in the nervous system of worms, flies, zebrafish, frogs, and mice. Furthermore, a regulatory module controlling the axial patterning of the vertebrate brain is expressed in the ectoderm of sea urchin embryos. We conclude that GRNs controlling the formation of bilaterian nervous systems share a common origin and that the apical GRN likely resembles an ancestral regulatory program.
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Adonin L, Drozdov A, Barlev NA. Sea Urchin as a Universal Model for Studies of Gene Networks. Front Genet 2021; 11:627259. [PMID: 33552139 PMCID: PMC7854572 DOI: 10.3389/fgene.2020.627259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.
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Affiliation(s)
- Leonid Adonin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nickolai A Barlev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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Slota LA, Miranda EM, McClay DR. Spatial and temporal patterns of gene expression during neurogenesis in the sea urchin Lytechinus variegatus. EvoDevo 2019; 10:2. [PMID: 30792836 PMCID: PMC6371548 DOI: 10.1186/s13227-019-0115-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/30/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The sea urchin is a basal deuterostome that is more closely related to vertebrates than many organisms traditionally used to study neurogenesis. This phylogenetic position means that the sea urchin can provide insights into the evolution of the nervous system by helping resolve which developmental processes are deuterostome innovations, which are innovations in other clades, and which are ancestral. However, the nervous system of echinoderms is one of the least understood of all major metazoan phyla. To gain insights into echinoderm neurogenesis, spatial and temporal gene expression data are essential. Then, functional data will enable the building of a detailed gene regulatory network for neurogenesis in the sea urchin that can be compared across metazoans to resolve questions about how nervous systems evolved. RESULTS Here, we analyze spatiotemporal gene expression during sea urchin neurogenesis for genes that have been shown to be neurogenic in one or more species. We report the expression of 21 genes expressed in areas of neurogenesis in the sea urchin embryo from blastula stage (just before neural progenitors begin their specification sequence) through pluteus larval stage (when much of the nervous system has been patterned). Among those 21 gene expression patterns, we report expression of 11 transcription factors and 2 axon guidance genes, each expressed in discrete domains in the neuroectoderm or in the endoderm. Most of these genes are expressed in and around the ciliary band. Some including the transcription factors Lv-mbx, Lv-dmrt, Lv-islet, and Lv-atbf1, the nuclear protein Lv-prohibitin, and the guidance molecule Lv-semaa are expressed in the endoderm where they are presumably involved in neurogenesis in the gut. CONCLUSIONS This study builds a foundation to study how neurons are specified and evolved by analyzing spatial and temporal gene expression during neurogenesis in a basal deuterostome. With these expression patterns, we will be able to understand what genes are required for neural development in the sea urchin. These data can be used as a starting point to (1) build a spatial gene regulatory network for sea urchin neurogenesis, (2) identify how subtypes of neurons are specified, (3) perform comparative studies with the sea urchin, protostome, and vertebrate organisms.
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Affiliation(s)
- Leslie A. Slota
- Department of Biology, Duke University, 124 Science Dr., Box 90338, Durham, NC 27708 USA
| | - Esther M. Miranda
- Department of Biology, Duke University, 124 Science Dr., Box 90338, Durham, NC 27708 USA
| | - David R. McClay
- Department of Biology, Duke University, 124 Science Dr., Box 90338, Durham, NC 27708 USA
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Reference assembly and gene expression analysis of Apostichopus japonicus larval development. Sci Rep 2019; 9:1131. [PMID: 30718912 PMCID: PMC6362246 DOI: 10.1038/s41598-018-37755-5] [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: 04/27/2018] [Accepted: 12/13/2018] [Indexed: 01/31/2023] Open
Abstract
The transcriptome of the holothurian Apostichopus japonicus was sequenced at four developmental stages—blastula, gastrula, auricularia, pentactula—on an Illumina sequencer. Based on our RNA-seq data and the paired-end reads from 16 libraries obtained by other researchers earlier, we have achieved the currently most complete transcriptome assembly for A. japonicus with the best basic statistical parameters. An analysis of the obtained transcriptome has revealed 174 differentially expressed transcription factors, as well as stage-specific transcription factors that are most promising for further study. In addition, a total of 1,174,999 high-quality single nucleotide polymorphisms have been identified, including 58,932 indels. A GO enrichment analysis of contigs containing polymorphic loci shows the predominance of GO terms associated with immune response. The data obtained by us provide an additional basis for a deeper study of the mechanisms of the planktotrophic-type development in holothurians and can be used in commercial sea cucumber breeding programs.
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McClay DR, Miranda E, Feinberg SL. Neurogenesis in the sea urchin embryo is initiated uniquely in three domains. Development 2018; 145:dev167742. [PMID: 30413529 PMCID: PMC6240313 DOI: 10.1242/dev.167742] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/25/2018] [Indexed: 12/23/2022]
Abstract
Many marine larvae begin feeding within a day of fertilization, thus requiring rapid development of a nervous system to coordinate feeding activities. Here, we examine the patterning and specification of early neurogenesis in sea urchin embryos. Lineage analysis indicates that neurons arise locally in three regions of the embryo. Perturbation analyses showed that when patterning is disrupted, neurogenesis in the three regions is differentially affected, indicating distinct patterning requirements for each neural domain. Six transcription factors that function during proneural specification were identified and studied in detail. Perturbations of these proneural transcription factors showed that specification occurs differently in each neural domain prior to the Delta-Notch restriction signal. Though gene regulatory network state changes beyond the proneural restriction are largely unresolved, the data here show that the three neural regions already differ from each other significantly early in specification. Future studies that define the larval nervous system in the sea urchin must therefore separately characterize the three populations of neurons that enable the larva to feed, to navigate, and to move food particles through the gut.
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Affiliation(s)
- David R McClay
- Department of Biology, 124 Science Drive, Duke University, Durham, NC 27708, USA
| | - Esther Miranda
- Department of Biology, 124 Science Drive, Duke University, Durham, NC 27708, USA
| | - Stacy L Feinberg
- Department of Biology, 124 Science Drive, Duke University, Durham, NC 27708, USA
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Anishchenko E, Arnone MI, D'Aniello S. SoxB2 in sea urchin development: implications in neurogenesis, ciliogenesis and skeletal patterning. EvoDevo 2018; 9:5. [PMID: 29479411 PMCID: PMC5817722 DOI: 10.1186/s13227-018-0094-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/01/2018] [Indexed: 11/21/2022] Open
Abstract
Background Current studies in evolutionary developmental biology are focused on the reconstruction of gene regulatory networks in target animal species. From decades, the scientific interest on genetic mechanisms orchestrating embryos development has been increasing in consequence to the fact that common features shared by evolutionarily distant phyla are being clarified. In 2011, a study across eumetazoan species showed for the first time the existence of a highly conserved non-coding element controlling the SoxB2 gene, which is involved in the early specification of the nervous system. This discovery raised several questions about SoxB2 function and regulation in deuterostomes from an evolutionary point of view. Results Due to the relevant phylogenetic position within deuterostomes, the sea urchin Strongylocentrotus purpuratus represents an advantageous animal model in the field of evolutionary developmental biology. Herein, we show a comprehensive study of SoxB2 functions in sea urchins, in particular its expression pattern in a wide range of developmental stages, and its co-localization with other neurogenic markers, as SoxB1, SoxC and Elav. Moreover, this work provides a detailed description of the phenotype of sea urchin SoxB2 knocked-down embryos, confirming its key function in neurogenesis and revealing, for the first time, its additional roles in oral and aboral ectoderm cilia and skeletal rod morphology. Conclusions We concluded that SoxB2 in sea urchins has a neurogenic function; however, this gene could have multiple roles in sea urchin embryogenesis, expanding its expression in non-neurogenic cells. We showed that SoxB2 is functionally conserved among deuterostomes and suggested that in S. purpuratus this gene acquired additional functions, being involved in ciliogenesis and skeletal patterning. Electronic supplementary material The online version of this article (10.1186/s13227-018-0094-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgeniya Anishchenko
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Naples, Italy
| | - Maria Ina Arnone
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Naples, Italy
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, 80121 Naples, Italy
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Bentovim L, Harden TT, DePace AH. Transcriptional precision and accuracy in development: from measurements to models and mechanisms. Development 2017; 144:3855-3866. [PMID: 29089359 PMCID: PMC5702068 DOI: 10.1242/dev.146563] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During development, genes are transcribed at specific times, locations and levels. In recent years, the emergence of quantitative tools has significantly advanced our ability to measure transcription with high spatiotemporal resolution in vivo. Here, we highlight recent studies that have used these tools to characterize transcription during development, and discuss the mechanisms that contribute to the precision and accuracy of the timing, location and level of transcription. We attempt to disentangle the discrepancies in how physicists and biologists use the term ‘precision' to facilitate interactions using a common language. We also highlight selected examples in which the coupling of mathematical modeling with experimental approaches has provided important mechanistic insights, and call for a more expansive use of mathematical modeling to exploit the wealth of quantitative data and advance our understanding of animal transcription. Summary: This Review highlights how high-resolution quantitative tools and theoretical models have formed our current view of the mechanisms determining precision and accuracy in the timing, location and level of transcription in the Drosophila embryo.
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Affiliation(s)
- Lital Bentovim
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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An Intronic cis-Regulatory Element Is Crucial for the Alpha Tubulin Pl-Tuba1a Gene Activation in the Ciliary Band and Animal Pole Neurogenic Domains during Sea Urchin Development. PLoS One 2017; 12:e0170969. [PMID: 28141828 PMCID: PMC5283682 DOI: 10.1371/journal.pone.0170969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/13/2017] [Indexed: 12/12/2022] Open
Abstract
In sea urchin development, structures derived from neurogenic territory control the swimming and feeding responses of the pluteus as well as the process of metamorphosis. We have previously isolated an alpha tubulin family member of Paracentrotus lividus (Pl-Tuba1a, formerly known as Pl-Talpha2) that is specifically expressed in the ciliary band and animal pole neurogenic domains of the sea urchin embryo. In order to identify cis-regulatory elements controlling its spatio-temporal expression, we conducted gene transfer experiments, transgene deletions and site specific mutagenesis. Thus, a genomic region of about 2.6 Kb of Pl-Tuba1a, containing four Interspecifically Conserved Regions (ICRs), was identified as responsible for proper gene expression. An enhancer role was ascribed to ICR1 and ICR2, while ICR3 exerted a pivotal role in basal expression, restricting Tuba1a expression to the proper territories of the embryo. Additionally, the mutation of the forkhead box consensus sequence binding site in ICR3 prevented Pl-Tuba1a expression.
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Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins. Proc Natl Acad Sci U S A 2016; 113:E7202-E7211. [PMID: 27810959 DOI: 10.1073/pnas.1612820113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Developmental gene regulatory networks (GRNs) are assemblages of gene regulatory interactions that direct ontogeny of animal body plans. Studies of GRNs operating in the early development of euechinoid sea urchins have revealed that little appreciable change has occurred since their divergence ∼90 million years ago (mya). These observations suggest that strong conservation of GRN architecture was maintained in early development of the sea urchin lineage. Testing whether this holds for all sea urchins necessitates comparative analyses of echinoid taxa that diverged deeper in geological time. Recent studies highlighted extensive divergence of skeletogenic mesoderm specification in the sister clade of euechinoids, the cidaroids, suggesting that comparative analyses of cidaroid GRN architecture may confer a greater understanding of the evolutionary dynamics of developmental GRNs. Here I report spatiotemporal patterning of 55 regulatory genes and perturbation analyses of key regulatory genes involved in euechinoid oral-aboral patterning of nonskeletogenic mesodermal and ectodermal domains in early development of the cidaroid Eucidaris tribuloides These results indicate that developmental GRNs directing mesodermal and ectodermal specification have undergone marked alterations since the divergence of cidaroids and euechinoids. Notably, statistical and clustering analyses of echinoid temporal gene expression datasets indicate that regulation of mesodermal genes has diverged more markedly than regulation of ectodermal genes. Although research on indirect-developing euechinoid sea urchins suggests strong conservation of GRN circuitry during early embryogenesis, this study indicates that since the divergence of cidaroids and euechinoids, developmental GRNs have undergone significant, cell type-biased alterations.
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Arnone MI, Andrikou C, Annunziata R. Echinoderm systems for gene regulatory studies in evolution and development. Curr Opin Genet Dev 2016; 39:129-137. [DOI: 10.1016/j.gde.2016.05.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/07/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
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Israel JW, Martik ML, Byrne M, Raff EC, Raff RA, McClay DR, Wray GA. Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. PLoS Biol 2016; 14:e1002391. [PMID: 26943850 PMCID: PMC4778923 DOI: 10.1371/journal.pbio.1002391] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/26/2016] [Indexed: 01/08/2023] Open
Abstract
The ecologically significant shift in developmental strategy from planktotrophic (feeding) to lecithotrophic (nonfeeding) development in the sea urchin genus Heliocidaris is one of the most comprehensively studied life history transitions in any animal. Although the evolution of lecithotrophy involved substantial changes to larval development and morphology, it is not known to what extent changes in gene expression underlie the developmental differences between species, nor do we understand how these changes evolved within the context of the well-defined gene regulatory network (GRN) underlying sea urchin development. To address these questions, we used RNA-seq to measure expression dynamics across development in three species: the lecithotroph Heliocidaris erythrogramma, the closely related planktotroph H. tuberculata, and an outgroup planktotroph Lytechinus variegatus. Using well-established statistical methods, we developed a novel framework for identifying, quantifying, and polarizing evolutionary changes in gene expression profiles across the transcriptome and within the GRN. We found that major changes in gene expression profiles were more numerous during the evolution of lecithotrophy than during the persistence of planktotrophy, and that genes with derived expression profiles in the lecithotroph displayed specific characteristics as a group that are consistent with the dramatically altered developmental program in this species. Compared to the transcriptome, changes in gene expression profiles within the GRN were even more pronounced in the lecithotroph. We found evidence for conservation and likely divergence of particular GRN regulatory interactions in the lecithotroph, as well as significant changes in the expression of genes with known roles in larval skeletogenesis. We further use coexpression analysis to identify genes of unknown function that may contribute to both conserved and derived developmental traits between species. Collectively, our results indicate that distinct evolutionary processes operate on gene expression during periods of life history conservation and periods of life history divergence, and that this contrast is even more pronounced within the GRN than across the transcriptome as a whole.
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Affiliation(s)
- Jennifer W. Israel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Megan L. Martik
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Maria Byrne
- Schools of Medical and Biological Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Elizabeth C. Raff
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Rudolf A. Raff
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - David R. McClay
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
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Martik ML, Lyons DC, McClay DR. Developmental gene regulatory networks in sea urchins and what we can learn from them. F1000Res 2016; 5. [PMID: 26962438 PMCID: PMC4765714 DOI: 10.12688/f1000research.7381.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 12/21/2022] Open
Abstract
Sea urchin embryos begin zygotic transcription shortly after the egg is fertilized. Throughout the cleavage stages a series of transcription factors are activated and, along with signaling through a number of pathways, at least 15 different cell types are specified by the beginning of gastrulation. Experimentally, perturbation of contributing transcription factors, signals and receptors and their molecular consequences enabled the assembly of an extensive gene regulatory network model. That effort, pioneered and led by Eric Davidson and his laboratory, with many additional insights provided by other laboratories, provided the sea urchin community with a valuable resource. Here we describe the approaches used to enable the assembly of an advanced gene regulatory network model describing molecular diversification during early development. We then provide examples to show how a relatively advanced authenticated network can be used as a tool for discovery of how diverse developmental mechanisms are controlled and work.
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Affiliation(s)
- Megan L Martik
- Biology Department, Duke University, Durham, North Carolina, 27708, USA
| | - Deirdre C Lyons
- Biology Department, Duke University, Durham, North Carolina, 27708, USA
| | - David R McClay
- Biology Department, Duke University, Durham, North Carolina, 27708, USA
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Wei Z, Angerer LM, Angerer RC. Neurogenic gene regulatory pathways in the sea urchin embryo. Development 2016; 143:298-305. [PMID: 26657764 PMCID: PMC4725339 DOI: 10.1242/dev.125989] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/26/2015] [Indexed: 01/18/2023]
Abstract
During embryogenesis the sea urchin early pluteus larva differentiates 40-50 neurons marked by expression of the pan-neural marker synaptotagmin B (SynB) that are distributed along the ciliary band, in the apical plate and pharyngeal endoderm, and 4-6 serotonergic neurons that are confined to the apical plate. Development of all neurons has been shown to depend on the function of Six3. Using a combination of molecular screens and tests of gene function by morpholino-mediated knockdown, we identified SoxC and Brn1/2/4, which function sequentially in the neurogenic regulatory pathway and are also required for the differentiation of all neurons. Misexpression of Brn1/2/4 at low dose caused an increase in the number of serotonin-expressing cells and at higher dose converted most of the embryo to a neurogenic epithelial sphere expressing the Hnf6 ciliary band marker. A third factor, Z167, was shown to work downstream of the Six3 and SoxC core factors and to define a branch specific for the differentiation of serotonergic neurons. These results provide a framework for building a gene regulatory network for neurogenesis in the sea urchin embryo.
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Affiliation(s)
- Zheng Wei
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lynne M Angerer
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert C Angerer
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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Piacentino ML, Zuch DT, Fishman J, Rose S, Speranza EE, Li C, Yu J, Chung O, Ramachandran J, Ferrell P, Patel V, Reyna A, Hameeduddin H, Chaves J, Hewitt FB, Bardot E, Lee D, Core AB, Hogan JD, Keenan JL, Luo L, Coulombe-Huntington J, Blute TA, Oleinik E, Ibn-Salem J, Poustka AJ, Bradham CA. RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins. Development 2016; 143:703-14. [PMID: 26755701 DOI: 10.1242/dev.129312] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 01/05/2016] [Indexed: 12/12/2022]
Abstract
The sea urchin larval skeleton offers a simple model for formation of developmental patterns. The calcium carbonate skeleton is secreted by primary mesenchyme cells (PMCs) in response to largely unknown patterning cues expressed by the ectoderm. To discover novel ectodermal cues, we performed an unbiased RNA-Seq-based screen and functionally tested candidates; we thereby identified several novel skeletal patterning cues. Among these, we show that SLC26a2/7 is a ventrally expressed sulfate transporter that promotes a ventral accumulation of sulfated proteoglycans, which is required for ventral PMC positioning and skeletal patterning. We show that the effects of SLC perturbation are mimicked by manipulation of either external sulfate levels or proteoglycan sulfation. These results identify novel skeletal patterning genes and demonstrate that ventral proteoglycan sulfation serves as a positional cue for sea urchin skeletal patterning.
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Affiliation(s)
- Michael L Piacentino
- Department of Biology, Boston University, Boston, MA 02215, USA Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Daniel T Zuch
- Department of Biology, Boston University, Boston, MA 02215, USA Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Julie Fishman
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Sviatlana Rose
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Emily E Speranza
- Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Christy Li
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Jia Yu
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Oliver Chung
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Patrick Ferrell
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Vijeta Patel
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Arlene Reyna
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - James Chaves
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Evan Bardot
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - David Lee
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Amanda B Core
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - John D Hogan
- Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Jessica L Keenan
- Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Lingqi Luo
- Program in Bioinformatics, Boston University, Boston, MA 02215, USA
| | | | - Todd A Blute
- Department of Biology, Boston University, Boston, MA 02215, USA Proteomics and Imaging Core Facility, Boston University, Boston, MA 02215, USA
| | - Ekaterina Oleinik
- Scientific Computing and Visualization Group, Boston University, Boston, MA 02215 USA
| | - Jonas Ibn-Salem
- Max-Planck Institute for Molecular Genetics, Evolution and Development Group, Ihnestrasse 73, Berlin 14195, Germany
| | - Albert J Poustka
- Max-Planck Institute for Molecular Genetics, Evolution and Development Group, Ihnestrasse 73, Berlin 14195, Germany Dahlem Center for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Fabeckstraße 60-62, Berlin 14195, Germany
| | - Cynthia A Bradham
- Department of Biology, Boston University, Boston, MA 02215, USA Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA Program in Bioinformatics, Boston University, Boston, MA 02215, USA
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Barsi JC, Davidson EH. cis -Regulatory control of the initial neurogenic pattern of onecut gene expression in the sea urchin embryo. Dev Biol 2016; 409:310-318. [DOI: 10.1016/j.ydbio.2015.10.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/01/2015] [Accepted: 10/16/2015] [Indexed: 01/05/2023]
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Garner S, Zysk I, Byrne G, Kramer M, Moller D, Taylor V, Burke RD. Neurogenesis in sea urchin embryos and the diversity of deuterostome neurogenic mechanisms. Development 2015; 143:286-97. [PMID: 26511925 DOI: 10.1242/dev.124503] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 10/19/2015] [Indexed: 01/08/2023]
Abstract
A single origin to the diverse mechanisms of metazoan neurogenesis is suggested by the involvement of common signaling components and similar classes of transcription factors. However, in many forms we lack details of where neurons arise, patterns of cell division, and specific differentiation pathway components. The sea urchin larval nervous system is composed of an apical organ, which develops from neuroepithelium and functions as a central nervous system, and peripheral neurons, which differentiate in the ciliary band and project axons to the apical organ. To reveal developmental mechanisms of neurogenesis in this basal deuterostome, we developed antibodies to SoxC, SoxB2, ELAV and Brn1/2/4 and used neurons that develop at specific locations to establish a timeline for neurogenesis. Neural progenitors express, in turn, SoxB2, SoxC, and Brn1/2/4, before projecting neurites and expressing ELAV and SynB. Using pulse-chase labeling of cells with a thymidine analog to identify cells in S-phase, we establish that neurons identified by location are in their last mitotic cycle at the time of hatching, and S-phase is coincident with expression of SoxC. The number of cells expressing SoxC and differentiating as neurons is reduced in embryos injected with antisense morpholino oligonucleotides to SoxC, SoxB2 or Six3. Injection of RNA encoding SoxC into eggs does not enhance neurogenesis. In addition, inhibition of FGF receptors (SU5402) or a morpholino to FGFR1 reduces expression of SoxC. These data indicate that there are common features of neurogenesis in deuterostomes, and that sea urchins employ developmental mechanisms that are distinct from other ambulacraria.
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Affiliation(s)
- Sarah Garner
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Ivona Zysk
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Glynis Byrne
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Marabeth Kramer
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Daniel Moller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Valerie Taylor
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
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Lapraz F, Haillot E, Lepage T. A deuterostome origin of the Spemann organiser suggested by Nodal and ADMPs functions in Echinoderms. Nat Commun 2015; 6:8434. [PMID: 26423516 PMCID: PMC4600745 DOI: 10.1038/ncomms9434] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 08/20/2015] [Indexed: 01/05/2023] Open
Abstract
During development of chordates, establishment of the body plan relies on the activity of an organizing centre located on the dorsal side of the embryo that patterns the embryo and induces neural tissue. Intriguingly, the evolutionary origin of this crucial signalling centre remains unclear and whether analogous organizers regulate D/V patterning in other deuterostome or protostome phyla is not known. Here we provide evidence that the ventral ectoderm of the sea urchin embryo is a long-range organizing centre that shares several fundamental properties with the Spemann organizer: the ability to induce duplicated embryonic axes when ectopically induced, the ability to induce neural fate in neighbouring tissues and the ability to finely regulate the level of BMP signalling by using an autoregulatory expansion–repression mechanism. These findings suggest that the evolutionary origin of the Spemann organizer is more ancient than previously thought and that it may possibly be traced back to the common ancestor of deuterostomes. Establishment of the body plan in chordates is determined by an organizing centre located on the dorsal side of the embryo. Here, the authors show that the ventral ectoderm of the sea urchin embryo is an organizing centre that shares several fundamental properties with the amphibian Spemann organizer.
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Affiliation(s)
- François Lapraz
- Institut de Biologie Valrose, iBV, UMR 7277 CNRS, Inserm U1091, UNS, University of Nice Sophia Antipolis Nice 06108, 2 France
| | - Emmanuel Haillot
- Institut de Biologie Valrose, iBV, UMR 7277 CNRS, Inserm U1091, UNS, University of Nice Sophia Antipolis Nice 06108, 2 France
| | - Thierry Lepage
- Institut de Biologie Valrose, iBV, UMR 7277 CNRS, Inserm U1091, UNS, University of Nice Sophia Antipolis Nice 06108, 2 France
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