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Arenas-Mena C, Akin S. Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus. Genetics 2023; 225:iyad145. [PMID: 37551428 PMCID: PMC10789315 DOI: 10.1093/genetics/iyad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Transcriptional regulatory elements (TREs) are the primary nodes that control developmental gene regulatory networks. In embryo stages, larvae, and adult differentiated red spherule cells of the sea urchin Strongylocentrotus purpuratus, transcriptionally engaged TREs are detected by Precision Run-On Sequencing (PRO-seq), which maps genome-wide at base pair resolution the location of paused or elongating RNA polymerase II (Pol II). In parallel, TRE accessibility is estimated by the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq). Our analysis identifies surprisingly early and widespread TRE accessibility in 4-cell cleavage embryos that is not necessarily followed by concurrent or subsequent transcription. TRE transcriptional differences identified by PRO-seq provide more contrast among embryonic stages than ATAC-seq accessibility differences, in agreement with the apparent excess of accessible but inactive TREs during embryogenesis. Global TRE accessibility reaches a maximum around the 20-hour late blastula stage, which coincides with the consolidation of major embryo regionalizations and peak histone variant H2A.Z expression. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during embryogenesis. However, our results would not reconcile well with labile nucleosome models based on simple A/T sequence enrichment. In addition, a large number of distal TREs become transcriptionally disengaged during developmental progression, in support of an early Pol II paused model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. Thus, developmental potency in early embryos may be facilitated by incipient accessibility and transcriptional pause at TREs.
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Affiliation(s)
- Cesar Arenas-Mena
- Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA
- PhD Programs in Biology and Biochemistry at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA
| | - Serhat Akin
- Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA
- PhD Program in Biology at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA
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2
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Feuda R. The temporal dynamics of the sea urchin regulome. Biol Open 2022; 11:276353. [PMID: 36094151 PMCID: PMC9493716 DOI: 10.1242/bio.059216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/14/2022] [Indexed: 12/04/2022] Open
Abstract
In this work, we used Nanostring N-counter technology, to evaluate the mRNA expression level of more than 330 regulatory genes over 34 time points covering the first three days of development of the sea urchin larvae. The hierarchical clustering of the mRNAs expression levels has identified groups corresponding to the major developmental landmarks (e.g. maternal to zygotic transition and gastrulation). Furthermore, comparison with previous experiments indicates high reproducibility of mRNA level temporal dynamics across batches. Finally, we generated an online tool to visualise gene expression during sea urchin larval development. The site can be accessed at and https://www621.lamp.le.ac.uk/nanostring_app/nanostring/. Summary: This study uses Nanostring N-counter technology to evaluate the mRNA expression level of more than 330 regulatory genes over 34 time points covering the first three days of development of the sea urchin larvae.
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Affiliation(s)
- Roberto Feuda
- Division of Biology and Biological Engineering, MC156-29, California Institute of Technology, Pasadena, CA 91125, USA
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3
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Hogan JD, Keenan JL, Luo L, Ibn-Salem J, Lamba A, Schatzberg D, Piacentino ML, Zuch DT, Core AB, Blumberg C, Timmermann B, Grau JH, Speranza E, Andrade-Navarro MA, Irie N, Poustka AJ, Bradham CA. The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes. Dev Biol 2019; 460:139-154. [PMID: 31816285 DOI: 10.1016/j.ydbio.2019.12.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 10/25/2022]
Abstract
Embryonic development is arguably the most complex process an organism undergoes during its lifetime, and understanding this complexity is best approached with a systems-level perspective. The sea urchin has become a highly valuable model organism for understanding developmental specification, morphogenesis, and evolution. As a non-chordate deuterostome, the sea urchin occupies an important evolutionary niche between protostomes and vertebrates. Lytechinus variegatus (Lv) is an Atlantic species that has been well studied, and which has provided important insights into signal transduction, patterning, and morphogenetic changes during embryonic and larval development. The Pacific species, Strongylocentrotus purpuratus (Sp), is another well-studied sea urchin, particularly for gene regulatory networks (GRNs) and cis-regulatory analyses. A well-annotated genome and transcriptome for Sp are available, but similar resources have not been developed for Lv. Here, we provide an analysis of the Lv transcriptome at 11 timepoints during embryonic and larval development. Temporal analysis suggests that the gene regulatory networks that underlie specification are well-conserved among sea urchin species. We show that the major transitions in variation of embryonic transcription divide the developmental time series into four distinct, temporally sequential phases. Our work shows that sea urchin development occurs via sequential intervals of relatively stable gene expression states that are punctuated by abrupt transitions.
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Affiliation(s)
- John D Hogan
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Lingqi Luo
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Jonas Ibn-Salem
- Evolution and Development Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany; Faculty of Biology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Arjun Lamba
- Biology Department, Boston University, Boston, MA, USA
| | | | - Michael L Piacentino
- Program in Molecular and Cellular Biology and Biochemistry, Boston University, Boston, MA, USA
| | - Daniel T Zuch
- Program in Molecular and Cellular Biology and Biochemistry, Boston University, Boston, MA, USA
| | - Amanda B Core
- Biology Department, Boston University, Boston, MA, USA
| | | | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - José Horacio Grau
- Dahlem Centre for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Berlin, Germany; Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Emily Speranza
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | | | - Naoki Irie
- Department of Biological Sciences, University of Tokyo, Tokyo, Japan
| | - Albert J Poustka
- Evolution and Development Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany; Dahlem Centre for Genome Research and Medical Systems Biology, Environmental and Phylogenomics Group, Berlin, Germany
| | - Cynthia A Bradham
- Program in Bioinformatics, Boston University, Boston, MA, USA; Biology Department, Boston University, Boston, MA, USA; Program in Molecular and Cellular Biology and Biochemistry, Boston University, Boston, MA, USA.
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4
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A Survey on Tubulin and Arginine Methyltransferase Families Sheds Light on P. lividus Embryo as Model System for Antiproliferative Drug Development. Int J Mol Sci 2019; 20:ijms20092136. [PMID: 31052191 PMCID: PMC6539552 DOI: 10.3390/ijms20092136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/27/2019] [Indexed: 01/18/2023] Open
Abstract
Tubulins and microtubules (MTs) represent targets for taxane-based chemotherapy. To date, several lines of evidence suggest that effectiveness of compounds binding tubulin often relies on different post-translational modifications on tubulins. Among them, methylation was recently associated to drug resistance mechanisms impairing taxanes binding. The sea urchin is recognized as a research model in several fields including fertilization, embryo development and toxicology. To date, some α- and β-tubulin genes have been identified in P. lividus, while no data are available in echinoderms for arginine methyl transferases (PRMT). To evaluate the exploiting of the sea urchin embryo in the field of antiproliferative drug development, we carried out a survey of the expressed α- and β-tubulin gene sets, together with a comprehensive analysis of the PRMT gene family and of the methylable arginine residues in P. lividus tubulins. Because of their specificities, the sea urchin embryo may represent an interesting tool for dissecting mechanisms of tubulin targeting drug action. Therefore, results herein reported provide evidences supporting the P. lividus embryo as animal system for testing antiproliferative drugs.
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Peter IS. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins. Methods Cell Biol 2018; 151:89-113. [PMID: 30948033 DOI: 10.1016/bs.mcb.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The discovery of gene regulatory networks (GRNs) has opened a gate to access the genomic mechanisms controlling development. GRNs are systems of transcriptional regulatory circuits that control the differential specification of cell fates during development by regulating gene expression. The experimental analysis of GRNs involves a collection of methods, each revealing aspects of the overall control process. This review provides an overview of experimental and computational methods that have been successfully applied for solving developmental GRNs in the sea urchin embryo. The key in this approach is to obtain experimental evidence for functional interactions between transcription factors and regulatory DNA. In the second part of this review, a more generally applicable strategy is discussed that shows a path from experimental evidence to annotation of regulatory linkages to the generation of GRN models.
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Affiliation(s)
- Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
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6
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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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7
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Kudtarkar P, Cameron RA. Echinobase: an expanding resource for echinoderm genomic information. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:4157993. [PMID: 29220460 PMCID: PMC5737241 DOI: 10.1093/database/bax074] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/23/2017] [Indexed: 11/21/2022]
Abstract
Echinobase, a web accessible information system of diverse genomics and biological data for the echinoderm clade, grew out of SpBase, the first echinoderm genome project for sea urchin, Strongylocentrotus purpuratus. Sea urchins and their relatives are utilitarian research models in fields ranging from marine biology to developmental biology and gene regulatory systems. Echinobase is a user-friendly web interface that links an array of biological data that would otherwise have been tedious and frustrating for researchers to extract and organize. The system hosts a powerful gene search engine, genomics browser and other bioinformatics tools to investigate genomics and high throughput data. The Echinobase information system now serves genomic information for eight echinoderm species: S. purpuratus, Strongylocentrotus fransciscanus, Allocentrotus fragilis, Lytechinus variegatus, Patiria miniata, Parastichopus parvimensis and Ophiothrix spiculata, Eucidaris tribuloides. Herein lies a description of the web information system, genomics data types and content hosted by Echinobase.org. The goal of Echinobase is to connect genomic information to various experimental data and accelerate the research in field of molecular biology, developmental process, gene regulatory networks and more recently engineering biological systems0. Database URL:http://www.echinobase.org
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Affiliation(s)
- Parul Kudtarkar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R. Andrew Cameron
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Corresponding author: Tel: 626 395 8421;
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8
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Abstract
A growing body of evidence shows that gene expression in multicellular organisms is controlled by the combinatorial function of multiple transcription factors. This indicates that not the individual transcription factors or signaling molecules, but the combination of expressed regulatory molecules, the regulatory state, should be viewed as the functional unit in gene regulation. Here, I discuss the concept of the regulatory state and its proposed role in the genome-wide control of gene expression. Recent analyses of regulatory gene expression in sea urchin embryos have been instrumental for solving the genomic control of cell fate specification in this system. Some of the approaches that were used to determine the expression of regulatory states during sea urchin embryogenesis are reviewed. Significant developmental changes in regulatory state expression leading to the distinct specification of cell fates are regulated by gene regulatory network circuits. How these regulatory state transitions are encoded in the genome is illuminated using the sea urchin endoderm-mesoderms cell fate decision circuit as an example. These observations highlight the importance of considering developmental gene regulation, and the function of individual transcription factors, in the context of regulatory states.
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9
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Dylus DV, Czarkwiani A, Blowes LM, Elphick MR, Oliveri P. Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution. Genome Biol 2018; 19:26. [PMID: 29490679 PMCID: PMC5831733 DOI: 10.1186/s13059-018-1402-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Background Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm—the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. Results We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, rather than when cells initiate differentiation. Conclusions Our findings indicate that there has been a high degree of gene regulatory network rewiring and clade-specific gene duplication, supporting the hypothesis of a convergent evolution of larval skeleton development in echinoderms. Electronic supplementary material The online version of this article (10.1186/s13059-018-1402-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David V Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.,CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT, UK.,Present address: Department of Computational Biology, UNIL, Genopode, 1005, Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Liisa M Blowes
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,Present address: Centre for Cell Biology & Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK. .,Centre for Life's Origins and Evolution (CLOE), UCL, Gower Street, London, WC1E 6BT, UK.
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10
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Abstract
The control processes that underlie the progression of development can be summarized in maps of gene regulatory networks (GRNs). A critical step in their assembly is the systematic perturbation of network candidates. In sea urchins the most important method for interfering with expression in a gene-specific way is application of morpholino antisense oligonucleotides (MOs). MOs act by binding to their sequence complement in transcripts resulting in a block in translation or a change in splicing and thus result in a loss of function. Despite the tremendous success of this technology, recent comparisons to mutants generated by genome editing have led to renewed criticism and challenged its reliability. As with all methods based on sequence recognition, MOs are prone to off-target binding that may result in phenotypes that are erroneously ascribed to the loss of the intended target. However, the slow progression of development in sea urchins has enabled extremely detailed studies of gene activity in the embryo. This wealth of knowledge paired with the simplicity of the sea urchin embryo enables careful analysis of MO phenotypes through a variety of methods that do not rely on terminal phenotypes. This article summarizes the use of MOs in probing GRNs and the steps that should be taken to assure their specificity.
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11
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Hinman VF, Burke RD. Embryonic neurogenesis in echinoderms. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e316. [PMID: 29470839 DOI: 10.1002/wdev.316] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 01/09/2023]
Abstract
The phylogenetic position of echinoderms is well suited to revealing shared features of deuterostomes that distinguish them from other bilaterians. Although echinoderm neurobiology remains understudied, genomic resources, molecular methods, and systems approaches have enabled progress in understanding mechanisms of embryonic neurogenesis. Even though the morphology of echinoderm larvae is diverse, larval nervous systems, which arise during gastrulation, have numerous similarities in their organization. Diverse neural subtypes and specialized sensory neurons have been identified and details of neuroanatomy using neuron-specific labels provide hypotheses for neural function. The early patterning of ectoderm and specification of axes has been well studied in several species and underlying gene regulatory networks have been established. The cells giving rise to central and peripheral neural components have been identified in urchins and sea stars. Neurogenesis includes typical metazoan features of asymmetric division of neural progenitors and in some cases limited proliferation of neural precursors. Delta/Notch signaling has been identified as having critical roles in regulating neural patterning and differentiation. Several transcription factors functioning in pro-neural phases of specification, neural differentiation, and sub-type specification have been identified and structural or functional components of neurons are used as differentiation markers. Several methods for altering expression in embryos have revealed aspects of a regulatory hierarchy of transcription factors in neurogenesis. Interfacing neurogenic gene regulatory networks to the networks regulating ectodermal domains and identifying the spatial and temporal inputs that pattern the larval nervous system is a major challenge that will contribute substantially to our understanding of the evolution of metazoan nervous systems. This article is categorized under: Comparative Development and Evolution > Model Systems Comparative Development and Evolution > Body Plan Evolution Early Embryonic Development > Gastrulation and Neurulation.
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Affiliation(s)
- Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
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12
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Moundoyi H, Demouy J, Le Panse S, Morales J, Sarels B, Cormier P. Toward Multiscale Modeling of Molecular and Biochemical Events Occurring at Fertilization Time in Sea Urchins. Results Probl Cell Differ 2018; 65:69-89. [DOI: 10.1007/978-3-319-92486-1_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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13
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Abstract
The echinoderms are a phylum of invertebrate deuterostome animals that constitute important research models for a number of biological disciplines. EchinoBase ( www.echinobase.org ) is an echinoderm-specific genome database and web information system that provides a platform for the interrogation and exploration of echinoderm genomic data. This chapter outlines the datasets available on EchinoBase; from assembled genomes and genome annotations, to spatial and quantitative expression data, as well as functional genomics datasets. We also highlight the bioinformatic tools available on the website to facilitate rapid inquiries using these data (genome browsers, precompiled BLAST databases, etc.), and suggest optimized strategies for performing these inquiries. We conclude with a perspective on how one could integrate various genomic resources to predict putative noncoding regulatory regions. The available datasets and analyses they permit provide the basic components required for developing an understanding of how echinoderm genomes are regulated, especially during early development, and provides a platform for comparative genomic inquiries among species in this phylum.
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14
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Dylus DV, Czarkwiani A, Stångberg J, Ortega-Martinez O, Dupont S, Oliveri P. Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. EvoDevo 2016; 7:2. [PMID: 26759711 PMCID: PMC4709884 DOI: 10.1186/s13227-015-0039-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 11/20/2022] Open
Abstract
Background The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin. Results We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformispplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states. Conclusion Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0039-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David Viktor Dylus
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; CoMPLEX/SysBio, UCL, Gower Street, London, WC1E 6BT UK ; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anna Czarkwiani
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
| | - Josefine Stångberg
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK ; Research Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Olga Ortega-Martinez
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden
| | - Sam Dupont
- Department of Biological and Environmental Sciences, Sven Lovén Centre for Marine Sciences, University of Gothenburg, Kristineberg 566, 451 78 Fiskebäckskil, Sweden
| | - Paola Oliveri
- Research Department of Genetics, Evolution and Environment, University College London, Room 426, Darwin Building, Gower Street, London, WC1E 6BT UK
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15
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Kapsenberg L, Hofmann GE. Signals of resilience to ocean change: high thermal tolerance of early stage Antarctic sea urchins (Sterechinus neumayeri) reared under present-day and future pCO2 and temperature. Polar Biol 2014. [DOI: 10.1007/s00300-014-1494-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Holland LZ. Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:342-52. [DOI: 10.1002/jez.b.22569] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Linda Z. Holland
- Marine Biology Research Division; Scripps Institution of Oceanography; University of California San Diego; La Jolla California 92093-0202 USA
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17
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Tu Q, Cameron RA, Davidson EH. Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev Biol 2013; 385:160-7. [PMID: 24291147 DOI: 10.1016/j.ydbio.2013.11.019] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/13/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
Development depends on the precise control of gene expression in time and space. A critical step towards understanding the global gene regulatory networks underlying development is to obtain comprehensive information on gene expression. In this study, we measured expression profiles for the entire expressed gene set during sea urchin embryonic development. We confirmed the reliability of these profiles by comparison with NanoString measurements for a subset of genes and with literature values. The data show that ~16,500 genes have been activated by the end of embryogenesis, and for half of them the transcript abundance changes more than 10-fold during development. From this genome scale expression survey, we show that complex patterns of expression by many genes underlie embryonic development, particularly during the early stages before gastrulation. An intuitive web application for data query and visualization is presented to facilitate use of this large dataset.
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Affiliation(s)
- Qiang Tu
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - R Andrew Cameron
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Eric H Davidson
- Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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Kober KM, Bernardi G. Phylogenomics of strongylocentrotid sea urchins. BMC Evol Biol 2013; 13:88. [PMID: 23617542 PMCID: PMC3637829 DOI: 10.1186/1471-2148-13-88] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/09/2013] [Indexed: 11/10/2022] Open
Abstract
Background Strongylocentrotid sea urchins have a long tradition as model organisms for studying many fundamental processes in biology including fertilization, embryology, development and genome regulation but the phylogenetic relationships of the group remain largely unresolved. Although the differing isolating mechanisms of vicariance and rapidly evolving gamete recognition proteins have been proposed, a stable and robust phylogeny is unavailable. Results We used a phylogenomic approach with mitochondrial and nuclear genes taking advantage of the whole-genome sequencing of nine species in the group to establish a stable (i.e. concordance in tree topology among multiple lies of evidence) and robust (i.e. high nodal support) phylogenetic hypothesis for the family Strongylocentrotidae. We generated eight draft mitochondrial genome assemblies and obtained 13 complete mitochondrial genes for each species. Consistent with previous studies, mitochondrial sequences failed to provide a reliable phylogeny. In contrast, we obtained a very well-supported phylogeny from 2301 nuclear genes without evidence of positive Darwinian selection both from the majority of most-likely gene trees and the concatenated fourfold degenerate sites: ((P. depressus, (M. nudus, M. franciscanus), (H. pulcherrimus, (S. purpuratus, (S. fragilis, (S. pallidus, (S. droebachiensis, S. intermedius)). This phylogeny was consistent with a single invasion of deep-water environments followed by a holarctic expansion by Strongylocentrotus. Divergence times for each species estimated with reference to the divergence times between the two major clades of the group suggest a correspondence in the timing with the opening of the Bering Strait and the invasion of the holarctic regions. Conclusions Nuclear genome data contains phylogenetic signal informative for understanding the evolutionary history of this group. However, mitochondrial genome data does not. Vicariance can explain major patterns observed in the phylogeny. Other isolating mechanisms are appropriate to explore in this system to help explain divergence patterns not well supported by vicariance, such as the effects of rapidly evolving gamete recognition proteins on isolating populations. Our findings of a stable and robust phylogeny, with the increase in mitochondrial and nuclear comparative genomic data, provide a system in which we can enhance our understanding of molecular evolution and adaptation in this group of sea urchins.
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Affiliation(s)
- Kord M Kober
- Department of Ecology & Evolutionary Biology, University Of California Santa Cruz, Santa Cruz, CA, USA.
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Tu Q, Cameron RA, Worley KC, Gibbs RA, Davidson EH. Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis. Genome Res 2012; 22:2079-87. [PMID: 22709795 PMCID: PMC3460201 DOI: 10.1101/gr.139170.112] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/16/2012] [Indexed: 11/25/2022]
Abstract
A comprehensive transcriptome analysis has been performed on protein-coding RNAs of Strongylocentrotus purpuratus, including 10 different embryonic stages, six feeding larval and metamorphosed juvenile stages, and six adult tissues. In this study, we pooled the transcriptomes from all of these sources and focused on the insights they provide for gene structure in the genome of this recently sequenced model system. The genome had initially been annotated by use of computational gene model prediction algorithms. A large fraction of these predicted genes were recovered in the transcriptome when the reads were mapped to the genome and appropriately filtered and analyzed. However, in a manually curated subset, we discovered that more than half the computational gene model predictions were imperfect, containing errors such as missing exons, prediction of nonexistent exons, erroneous intron/exon boundaries, fusion of adjacent genes, and prediction of multiple genes from single genes. The transcriptome data have been used to provide a systematic upgrade of the gene model predictions throughout the genome, very greatly improving the research usability of the genomic sequence. We have constructed new public databases that incorporate information from the transcriptome analyses. The transcript-based gene model data were used to define average structural parameters for S. purpuratus protein-coding genes. In addition, we constructed a custom sea urchin gene ontology, and assigned about 7000 different annotated transcripts to 24 functional classes. Strong correlations became evident between given functional ontology classes and structural properties, including gene size, exon number, and exon and intron size.
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Affiliation(s)
- Qiang Tu
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - R. Andrew Cameron
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Kim C. Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric H. Davidson
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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Ben-Tabou de-Leon S, Davidson EH. Experimentally based sea urchin gene regulatory network and the causal explanation of developmental phenomenology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 1:237-246. [PMID: 20228891 DOI: 10.1002/wsbm.24] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene regulatory networks for development underlie cell fate specification and differentiation. Network topology, logic and dynamics can be obtained by thorough experimental analysis. Our understanding of the gene regulatory network controlling endomesoderm specification in the sea urchin embryo has attained an advanced level such that it explains developmental phenomenology. Here we review how the network explains the mechanisms utilized in development to control the formation of dynamic expression patterns of transcription factors and signaling molecules. The network represents the genomic program controlling timely activation of specification and differentiation genes in the correct embryonic lineages. It can also be used to study evolution of body plans. We demonstrate how comparing the sea urchin gene regulatory network to that of the sea star and to that of later developmental stages in the sea urchin, reveals mechanisms underlying the origin of evolutionary novelty. The experimentally based gene regulatory network for endomesoderm specification in the sea urchin embryo provides unique insights into the system level properties of cell fate specification and its evolution.
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Affiliation(s)
| | - Eric H Davidson
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
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Nam J, Dong P, Tarpine R, Istrail S, Davidson EH. Functional cis-regulatory genomics for systems biology. Proc Natl Acad Sci U S A 2010; 107:3930-5. [PMID: 20142491 PMCID: PMC2840491 DOI: 10.1073/pnas.1000147107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Gene expression is controlled by interactions between trans-regulatory factors and cis-regulatory DNA sequences, and these interactions constitute the essential functional linkages of gene regulatory networks (GRNs). Validation of GRN models requires experimental cis-regulatory tests of predicted linkages to authenticate their identities and proposed functions. However, cis-regulatory analysis is, at present, at a severe bottleneck in genomic system biology because of the demanding experimental methodologies currently in use for discovering cis-regulatory modules (CRMs), in the genome, and for measuring their activities. Here we demonstrate a high-throughput approach to both discovery and quantitative characterization of CRMs. The unique aspect is use of DNA sequence tags to "barcode" CRM expression constructs, which can then be mixed, injected together into sea urchin eggs, and subsequently deconvolved. This method has increased the rate of cis-regulatory analysis by >100-fold compared with conventional one-by-one reporter assays. The utility of the DNA-tag reporters was demonstrated by the rapid discovery of 81 active CRMs from 37 previously unexplored sea urchin genes. We then obtained simultaneous high-resolution temporal characterization of the regulatory activities of more than 80 CRMs. On average 2-3 CRMs were discovered per gene. Comparison of endogenous gene expression profiles with those of the CRMs recovered from each gene showed that, for most cases, at least one CRM is active in each phase of endogenous expression, suggesting that CRM recovery was comprehensive. This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology.
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Affiliation(s)
- Jongmin Nam
- Division of Biology, California Institute of Technology, Pasadena, CA 91125; and
| | - Ping Dong
- Division of Biology, California Institute of Technology, Pasadena, CA 91125; and
| | - Ryan Tarpine
- Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912
| | - Sorin Istrail
- Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912
| | - Eric H. Davidson
- Division of Biology, California Institute of Technology, Pasadena, CA 91125; and
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García-Arrarás JE, Dolmatov IY. Echinoderms: potential model systems for studies on muscle regeneration. Curr Pharm Des 2010; 16:942-55. [PMID: 20041824 PMCID: PMC2933377 DOI: 10.2174/138161210790883426] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 12/06/2009] [Indexed: 11/22/2022]
Abstract
Organisms of the phylum Echinodermata show some of the most impressive regenerative feats within the animal kingdom. Following injury or self-induced autotomy, species in this phylum can regenerate most tissues and organs, being the regeneration of the muscular systems one of the best studied. Even though echinoderms are closely related to chordates, they are little known in the biomedical field, and therefore their uses to study pharmacological effects on muscle formation and/or regeneration have been extremely limited. In order to rectify this lack of knowledge, we describe here the echinoderm muscular systems, particularly the somatic and visceral muscle components. In addition, we provide details of the processes that are known to take place during muscle regeneration, namely dedifferentiation, myogenesis and new muscle formation. Finally, we provide the available information on molecular and pharmacological studies that involve echinoderm muscle regeneration. We expect that by making this information accessible, researchers consider the use of echinoderms as model systems for pharmacological studies in muscle development and regeneration.
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Cameron RA, Davidson EH. Flexibility of transcription factor target site position in conserved cis-regulatory modules. Dev Biol 2009; 336:122-35. [DOI: 10.1016/j.ydbio.2009.09.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 09/09/2009] [Accepted: 09/10/2009] [Indexed: 10/20/2022]
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Peter IS, Davidson EH. The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage. Dev Biol 2009; 340:188-99. [PMID: 19895806 DOI: 10.1016/j.ydbio.2009.10.037] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2009] [Revised: 10/27/2009] [Accepted: 10/27/2009] [Indexed: 12/20/2022]
Abstract
As the result of early specification processes, sea urchin embryos eventually form various mesodermal cell lineages and a gut consisting of fore-, mid- and hindgut. The progression of specification as well as the overall spatial organization of the organism is encoded in its gene regulatory networks (GRNs). We have analyzed the GRN driving endoderm specification up to the onset of gastrulation and present in this paper the mechanisms which determine this process up to mid-blastula stage. At this stage, the embryo consists of two separate lineages of endoderm precursor cells with distinct regulatory states. One of these lineages, the veg2 cell lineage, gives rise to endoderm and mesoderm cell types. The separation of these cell fates is initiated by the spatially confined activation of the mesoderm GRN superimposed on a generally activated endoderm GRN within veg2 descendants. Here we integrate the architecture of regulatory interactions with the spatial restriction of regulatory gene expression to model the logic control of endoderm development.
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Affiliation(s)
- Isabelle S Peter
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
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26
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Deplancke B. Experimental advances in the characterization of metazoan gene regulatory networks. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:12-27. [PMID: 19324929 DOI: 10.1093/bfgp/elp001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene regulatory networks (GRNs) play a vital role in metazoan development and function, and deregulation of these networks is often implicated in disease. GRNs depict the dynamic interactions between genomic and regulatory state components. The genomic components comprise genes and their associated cis-regulatory elements. The regulatory state components consist primarily of transcriptional complexes that bind the latter elements. With the availability of complete genome sequences, several approaches have recently been developed which promise to significantly enhance our ability to identify either the genomic or regulatory state components, or the interactions between these two. In this review, I provide an in-depth overview of these approaches and detail how each contributes to a more comprehensive understanding of GRN composition and function.
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Affiliation(s)
- Bart Deplancke
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.
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27
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Bolouri H, Davidson EH. The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example. Dev Biol 2009; 340:170-8. [PMID: 19523466 DOI: 10.1016/j.ydbio.2009.06.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/20/2009] [Accepted: 06/05/2009] [Indexed: 10/20/2022]
Abstract
The "Community Effect" denotes intra-territorial signaling amongst cells which constitute a particular tissue or embryonic progenitor field. The cells of the territory express the same transcriptional regulatory state, and the intra-territorial signaling is essential to maintenance of this specific regulatory state. The structure of the underlying gene regulatory network (GRN) subcircuitry explains the genomically wired mechanism by which community effect signaling is linked to the continuing transcriptional generation of the territorial regulatory state. A clear example is afforded by the oral ectoderm GRN of the sea urchin embryo where cis-regulatory evidence, experimental embryology, and network analysis combine to provide a complete picture. We review this example and consider less well known but similar cases in other developing systems where the same subcircuit GRN topology is present. To resolve mechanistic issues that arise in considering how community effect signaling could operate to produce its observed effects, we construct and analyze the behavior of a quantitative model of community effect signaling in the sea urchin embryo oral ectoderm. Community effect network topology could constitute part of the genomic regulatory code that defines transcriptional function in multicellular tissues composed of cells in contact, and hence may have arisen as a metazoan developmental strategy.
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Affiliation(s)
- Hamid Bolouri
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Cameron RA, Samanta M, Yuan A, He D, Davidson E. SpBase: the sea urchin genome database and web site. Nucleic Acids Res 2009; 37:D750-4. [PMID: 19010966 PMCID: PMC2686435 DOI: 10.1093/nar/gkn887] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Accepted: 10/20/2008] [Indexed: 11/29/2022] Open
Abstract
SpBase is a system of databases focused on the genomic information from sea urchins and related echinoderms. It is exposed to the public through a web site served with open source software (http://spbase.org/). The enterprise was undertaken to provide an easily used collection of information to directly support experimental work on these useful research models in cell and developmental biology. The information served from the databases emerges from the draft genomic sequence of the purple sea urchin, Strongylocentrotus purpuratus and includes sequence data and genomic resource descriptions for other members of the echinoderm clade which in total span 540 million years of evolutionary time. This version of the system contains two assemblies of the purple sea urchin genome, associated expressed sequences, gene annotations and accessory resources. Search mechanisms for the sequences and the gene annotations are provided. Because the system is maintained along with the Sea Urchin Genome resource, a database of sequenced clones is also provided.
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Affiliation(s)
- R Andrew Cameron
- Center for Computational Regulatory Genomics, Beckman Institute 139-74, California Institute of Technology, Pasadena, CA 91104, USA.
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Halley JD, Winkler DA, Burden FR. Toward a Rosetta stone for the stem cell genome: Stochastic gene expression, network architecture, and external influences. Stem Cell Res 2008; 1:157-68. [DOI: 10.1016/j.scr.2008.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Revised: 03/17/2008] [Accepted: 03/21/2008] [Indexed: 02/05/2023] Open
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MATERNA STEFANC, CAMERON RANDREW. The sea urchin genome as a window on function. THE BIOLOGICAL BULLETIN 2008; 214:266-73. [PMID: 18574103 PMCID: PMC3981829 DOI: 10.2307/25470668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The emphasis on the sequencing of genomes seems to make this task an end in itself. However, genome sequences and the genes that are predicted from them are really an opportunity to examine the biological function of the organism constructed by that genome. This point is illustrated here by examples in which the newly annotated gene complement reveals surprises about the way Strongylocentrotus purpuratus, the purple sea urchin, goes about its business. The three topics considered here are the nature of the innate immune system; the unexpected complexity of sensory function implied by genes encoding sensory proteins; and the remarkable intricacy of the regulatory gene complement in embryogenesis.
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Affiliation(s)
- STEFAN C. MATERNA
- Division of Biology 156-29, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125
| | - R. ANDREW CAMERON
- Division of Biology 156-29, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125
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Smith J, Davidson EH. A new method, using cis-regulatory control, for blocking embryonic gene expression. Dev Biol 2008; 318:360-5. [PMID: 18423438 DOI: 10.1016/j.ydbio.2008.02.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 02/29/2008] [Accepted: 02/29/2008] [Indexed: 11/17/2022]
Abstract
Many genes, and particularly regulatory genes, are utilized multiple times in unrelated phases of development. For studies of gene function during embryogenesis, there is often need of a method for interfering with expression only at a specific developmental time or place. Here we show that in sea urchin embryos cis-regulatory control systems which operate only at specific times and places can be used to drive expression of short designed sequences targeting given primary transcripts, thereby effectively taking out the function of the target genes. The active sequences are designed to be complementary to intronic sequences of the primary transcript of the target genes. In this work, the target genes were the transcription factors alx1 and ets1, both required for skeletogenesis, and the regulatory drivers were from the sm30 and tbr genes. The sm30 gene is expressed only after skeletogenic cell ingression. When its regulatory apparatus was used as driver, the alx1 and ets1 repression constructs had the effect of preventing postgastrular skeletogenesis, while not interfering with earlier alx1 and ets1 function in promoting skeletogenic mesenchyme ingression. In contrast, repression constructs using the tbr driver, which is active in blastula stage, block ingression. This method thus provides the opportunity to study regulatory requirements of skeletogenesis after ingression, and may be similarly useful in many other developmental contexts.
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Affiliation(s)
- Joel Smith
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA.
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Ducibella T, Fissore R. The roles of Ca2+, downstream protein kinases, and oscillatory signaling in regulating fertilization and the activation of development. Dev Biol 2008; 315:257-79. [PMID: 18255053 DOI: 10.1016/j.ydbio.2007.12.012] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/12/2007] [Accepted: 12/13/2007] [Indexed: 12/12/2022]
Abstract
Reviews in Developmental Biology have covered the pathways that generate the all-important intracellular calcium (Ca(2+)) signal at fertilization [Miyazaki, S., Shirakawa, H., Nakada, K., Honda, Y., 1993a. Essential role of the inositol 1,4,5-trisphosphate receptor/Ca(2+) release channel in Ca(2+) waves and Ca(2+) oscillations at fertilization of mammalian eggs. Dev. Biol. 158, 62-78; Runft, L., Jaffe, L., Mehlmann, L., 2002. Egg activation at fertilization: where it all begins. Dev. Biol. 245, 237-254] and the different temporal responses of Ca(2+) in many organisms [Stricker, S., 1999. Comparative biology of calcium signaling during fertilization and egg activation in animals. Dev. Biol. 211, 157-176]. Those reviews raise the importance of identifying how Ca(2+) causes the events of egg activation (EEA) and to what extent these temporal Ca(2+) responses encode developmental information. This review covers recent studies that have analyzed how these Ca(2+) signals are interpreted by specific proteins, and how these proteins regulate various EEA responsible for the onset of development. Many of these proteins are protein kinases (CaMKII, PKC, MPF, MAPK, MLCK) whose activity is directly or indirectly regulated by Ca(2+), and whose amount increases during late oocyte maturation. We cover biochemical progress in defining the signaling pathways between Ca(2+) and the EEA, as well as discuss how oscillatory or multiple Ca(2+) signals are likely to have specific advantages biochemically and/or developmentally. These emerging concepts are put into historical context, emphasizing that key contributions have come from many organisms. The intricate interdependence of Ca(2+), Ca(2+)-dependent proteins, and the EEA raise many new questions for future investigations that will provide insight into the extent to which fertilization-associated signaling has long-range implications for development. In addition, answers to these questions should be beneficial to establishing parameters of egg quality for human and animal IVF, as well as improving egg activation protocols for somatic cell nuclear transfer to generate stem cells and save endangered species.
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Affiliation(s)
- Tom Ducibella
- Department of OB/GYN, Tufts-New England Medical Center, Boston, MA 02111, USA.
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Song JL, Wessel GM. Genes involved in the RNA interference pathway are differentially expressed during sea urchin development. Dev Dyn 2007; 236:3180-90. [DOI: 10.1002/dvdy.21353] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Materna SC, Davidson EH. Logic of gene regulatory networks. Curr Opin Biotechnol 2007; 18:351-4. [PMID: 17689240 PMCID: PMC2031216 DOI: 10.1016/j.copbio.2007.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 07/12/2007] [Indexed: 11/21/2022]
Abstract
Regulatory networks of transcription factors and signaling molecules lie at the heart of development. Their architecture implements logic functions whose execution propels cells from one regulatory state to the next, thus driving development forward. As an example of a subcircuit that translates transcriptional input into developmental output, we consider a particularly simple case, the regulatory processes underlying pigment cell formation in sea urchin embryos. The regulatory events in this process can be represented as elementary logic functions.
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Affiliation(s)
- Stefan C Materna
- California Institute of Technology, Division of Biology, m/c 156-29, 1200 E. California Blvd., Pasadena, CA 91125, USA
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Revilla-i-Domingo R, Oliveri P, Davidson EH. A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres. Proc Natl Acad Sci U S A 2007; 104:12383-8. [PMID: 17636127 PMCID: PMC1941478 DOI: 10.1073/pnas.0705324104] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Specification of sea urchin embryo micromeres occurs early in cleavage, with the establishment of a well defined regulatory state. The architecture of the gene regulatory network controlling the specification process indicates that transcription of the initial tier of control genes depends on a double-negative gate. A gene encoding a transcriptional repressor, pmar1, is activated specifically in micromeres, where it represses transcription of a second repressor that is otherwise active globally. Thus, the micromere-specific control genes, which are the target of the second repressor, are expressed exclusively in this lineage. The double-negative specification gate was logically required from the results of numerous prior experiments, but the identity of the gene encoding the second repressor remained elusive. Here we show that hesC is this gene, and we demonstrate experimentally all of its predicted functions, including global repression of micromere-specific regulatory genes. As logically required, blockade of hesC mRNA translation and global overexpression of pmar1 mRNA have the same effect, which is to cause all of the cells of the embryo to express micromere-specific genes.
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Affiliation(s)
| | - Paola Oliveri
- Division of Biology 156–29, California Institute of Technology, Pasadena, CA 91125
| | - Eric H. Davidson
- Division of Biology 156–29, California Institute of Technology, Pasadena, CA 91125
- *To whom correspondence should be addressed. E-mail:
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Kobayashi A, Watanabe Y, Akasaka K, Kokubo T. Real-time monitoring of functional interactions between upstream and core promoter sequences in living cells of sea urchin embryos. Nucleic Acids Res 2007; 35:4882-94. [PMID: 17626044 PMCID: PMC1950538 DOI: 10.1093/nar/gkm519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There are some functional compatibilities between upstream and core promoter sequences for transcriptional activation in yeast, Drosophila and mammalian cells. Here we examined whether similar compatibilities exist in sea urchin embryos, and if so, whether they are dynamically regulated during early development. Two reporter plasmids, each containing a test promoter conjugated to either CFP or YFP, were concurrently introduced into embryos, and their expression patterns were studied by fluorescence microscopy. The upstream sequence of the Hemicentrotus pulcherrimus (Hp) OtxE promoter drives the expression of its own core promoter and that of Strongylocentrotus purpuratus (Sp) Spec2a in different embryonic regions, especially at the late gastrula stage. Interestingly, when the four putative transcription factor binding sites of this upstream sequence were individually mutated, the resulting sequences directed different spatiotemporal expression from the same set of two core promoters, indicating that combinations of upstream factors may determine core promoter usage in sea urchin embryos. In addition, the insertion or deletion of consensus or nonconsensus TATA sequences changed the expression profile significantly, irrespective of whether the upstream sequence was intact or mutated. Thus, the TATA sequence may serve as a primary determinant for core promoter selection in these cells.
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Affiliation(s)
- Akiko Kobayashi
- Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan and Misaki Marine Biological Station, Graduate School of Sciences, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Youko Watanabe
- Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan and Misaki Marine Biological Station, Graduate School of Sciences, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Koji Akasaka
- Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan and Misaki Marine Biological Station, Graduate School of Sciences, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Tetsuro Kokubo
- Division of Molecular and Cellular Biology, International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Kanagawa, 230-0045, Japan and Misaki Marine Biological Station, Graduate School of Sciences, University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
- *To whom correspondence should be addressed.045-508-7237; Fax: 045-508-7369
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Tu Q, Brown CT, Davidson EH, Oliveri P. Sea urchin Forkhead gene family: Phylogeny and embryonic expression. Dev Biol 2006; 300:49-62. [PMID: 17081512 DOI: 10.1016/j.ydbio.2006.09.031] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 09/14/2006] [Accepted: 09/15/2006] [Indexed: 11/21/2022]
Abstract
Transcription factors of the Forkhead (Fox) family have been identified in many metazoans, and play important roles in diverse biological processes. Here we define the set of fox genes present in the sea urchin genome, and survey their usage during development. This genome includes 22 fox genes, only three of which were previously known. Of the 23 fox gene subclasses identified in vertebrate genomes, the Strongylocentrotus purpuratus genome has orthologues of all but four (E, H, R and S). Phylogenetic analysis suggests that one S. purpuratus fox gene is equally related to foxA and foxB of vertebrates; this gene defines a new class. Two other genes appear to be specific to the sea urchin, with respect to the genomes so far sequenced. Fox genes orthologous with those of vertebrates but lacking in arthropod or nematode genomes may be deuterostome-specific (subclasses I, J1, J2, L1, M and Q1), while the majority are pan-bilaterian. All but one of the S. purpuratus fox genes (SpfoxQ1) are expressed during embryogenesis, most in a very specific temporal and spatial manner. The sea urchin fox genes clearly execute many different regulatory functions, and almost all of them participate in the process of embryonic development.
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Affiliation(s)
- Qiang Tu
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
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Samanta MP, Tongprasit W, Istrail S, Cameron RA, Tu Q, Davidson EH, Stolc V. The Transcriptome of the Sea Urchin Embryo. Science 2006; 314:960-2. [PMID: 17095694 DOI: 10.1126/science.1131898] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.
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