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Yeo GHT, Lin L, Qi CY, Cha M, Gifford DK, Sherwood RI. A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation. Cell Stem Cell 2020; 26:938-950.e6. [PMID: 32459995 PMCID: PMC7398619 DOI: 10.1016/j.stem.2020.04.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/10/2019] [Accepted: 04/27/2020] [Indexed: 01/08/2023]
Abstract
Empirical optimization of stem cell differentiation protocols is time consuming, is laborintensive, and typically does not comprehensively interrogate all relevant signaling pathways. Here we describe barcodelet single-cell RNA sequencing (barRNA-seq), which enables systematic exploration of cellular perturbations by tagging individual cells with RNA "barcodelets" to identify them on the basis of the treatments they receive. We apply barRNA-seq to simultaneously manipulate up to seven developmental pathways and study effects on embryonic stem cell (ESC) germ layer specification and mesodermal specification, uncovering combinatorial effects of signaling pathway activation on gene expression. We further develop a data-driven framework for identifying combinatorial signaling perturbations that drive cells toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, and use this approach to guide ESC differentiation into a notochord-like population. We expect that barRNA-seq will have broad utility for investigating and understanding how cooperative signaling pathways drive cell fate acquisition.
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Affiliation(s)
- Grace Hui Ting Yeo
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lin Lin
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Celine Yueyue Qi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Minsun Cha
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David K Gifford
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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Characterization of gonad differentially expressed SoxB2 genes in mud crab Scylla paramamosain. Gene 2020; 740:144507. [DOI: 10.1016/j.gene.2020.144507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/26/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022]
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Lin J, Yuan Y, Shi X, Fang S, Zhang Y, Guan M, Xie Z, Ma H, Lin F. Molecular cloning, characterization and expression profiles of a SoxB2 gene related to gonadal development in mud crab (Scylla paramamosain). INVERTEBR REPROD DEV 2020. [DOI: 10.1080/07924259.2020.1726515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiali Lin
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Yuying Yuan
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Xi Shi
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Shaobin Fang
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Yin Zhang
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Mengyun Guan
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Zhuofang Xie
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Hongyu Ma
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
| | - Fan Lin
- Institute of Marine Sciences, Shantou University, Shantou, China
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China
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Zhang S, Chen X, Wang M, Zhang W, Pan J, Qin Q, Zhong L, Shao J, Sun M, Jiang H, Bian W. Genome-wide identification, phylogeny and expressional profile of the Sox gene family in channel catfish (Ictalurus punctatus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:17-26. [DOI: 10.1016/j.cbd.2018.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 12/11/2017] [Accepted: 03/05/2018] [Indexed: 01/10/2023]
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Balta EA, Wittmann MT, Jung M, Sock E, Haeberle BM, Heim B, von Zweydorf F, Heppt J, von Wittgenstein J, Gloeckner CJ, Lie DC. Phosphorylation Modulates the Subcellular Localization of SOX11. Front Mol Neurosci 2018; 11:211. [PMID: 29973868 PMCID: PMC6020773 DOI: 10.3389/fnmol.2018.00211] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/29/2018] [Indexed: 12/24/2022] Open
Abstract
SOX11 is a key Transcription Factor (TF) in the regulation of embryonic and adult neurogenesis, whose mutation has recently been linked to an intellectual disability syndrome in humans. SOX11's transient activity during neurogenesis is critical to ensure the precise execution of the neurogenic program. Here, we report that SOX11 displays differential subcellular localizations during the course of neurogenesis. Western-Blot analysis of embryonic mouse brain lysates indicated that SOX11 is post-translationally modified by phosphorylation. Using Mass Spectrometry, we found 10 serine residues in the SOX11 protein that are putatively phosphorylated. Systematic analysis of phospho-mutant SOX11 resulted in the identification of the S30 residue, whose phosphorylation promotes nuclear over cytoplasmic localization of SOX11. Collectively, these findings uncover phosphorylation as a novel layer of regulation of the intellectual disability gene Sox11.
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Affiliation(s)
- Elli-Anna Balta
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marie-Theres Wittmann
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Jung
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elisabeth Sock
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Birgit Heim
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Jana Heppt
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Julia von Wittgenstein
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Johannes Gloeckner
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany.,DZNE-German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Dieter Chichung Lie
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Function of translationally controlled tumor protein (TCTP) in Eudrilus eugeniae regeneration. PLoS One 2017; 12:e0175319. [PMID: 28403226 PMCID: PMC5389791 DOI: 10.1371/journal.pone.0175319] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/23/2017] [Indexed: 01/07/2023] Open
Abstract
TCTP (Translationally Controlled Tumour Protein) is a multifunctional protein that plays a role in the development, immune system, tumour reversion, and maintenance of stem cells. The mRNA of the Tpt1 gene is over-expressed during liver regeneration. But, the function of the protein in regeneration is not known. To study the role of the protein in regeneration, the earthworm Eudrilus eugeniae was chosen. First, the full length cDNA of the Tpt1 gene was sequenced. The size of the cDNA is 504 bp and the protein has 167 amino acids. The highest level of TCTP expression was documented in the worm after three days of regeneration. The protein was found to be expressed specifically in the epithelial layer of the skin. During regeneration, the protein expression was found to be the highest at the tip of blastema. The pharmacological suppression of TCTP using nutlin-3 and TCTP RNAi experiments resulted in the failure of the regeneration process. The suppression of TCTP caused the arrest of proliferation in posterior amputated worms. The severe cell death was documented in the amputated region of nutlin-3 injected worm. The silencing of TCTP has blocked the modification of clitellar segments. The experiments confirm that TCTP has major functions in the upstream signalling of cell proliferation in the early regeneration process in E. eugeniae.
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Pauls S, Goode DK, Petrone L, Oliveri P, Elgar G. Evolution of lineage-specific functions in ancient cis-regulatory modules. Open Biol 2016; 5:rsob.150079. [PMID: 26538567 PMCID: PMC4680567 DOI: 10.1098/rsob.150079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Morphological evolution is driven both by coding sequence variation and by changes in regulatory sequences. However, how cis-regulatory modules (CRMs) evolve to generate entirely novel expression domains is largely unknown. Here, we reconstruct the evolutionary history of a lens enhancer located within a CRM that not only predates the lens, a vertebrate innovation, but bilaterian animals in general. Alignments of orthologous sequences from different deuterostomes sub-divide the CRM into a deeply conserved core and a more divergent flanking region. We demonstrate that all deuterostome flanking regions, including invertebrate sequences, activate gene expression in the zebrafish lens through the same ancient cluster of activator sites. However, levels of gene expression vary between species due to the presence of repressor motifs in flanking region and core. These repressor motifs are responsible for the relatively weak enhancer activity of tetrapod flanking regions. Ray-finned fish, however, have gained two additional lineage-specific activator motifs which in combination with the ancient cluster of activators and the core constitute a potent lens enhancer. The exploitation and modification of existing regulatory potential in flanking regions but not in the highly conserved core might represent a more general model for the emergence of novel regulatory functions in complex CRMs.
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Affiliation(s)
- Stefan Pauls
- Division of Systems Biology, Francis Crick Institute, Mill Hill laboratories, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Debbie K Goode
- Cambridge Institute for Medical Research and the Wellcome Trust/MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 OXY, UK
| | - Libero Petrone
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1 E6BT, UK
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1 E6BT, UK
| | - Greg Elgar
- Division of Systems Biology, Francis Crick Institute, Mill Hill laboratories, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Jiang Y, Han K, Chen S, Hong W, Wang Y, Zhang Z. Molecular cloning, characterization and expression of Lc-Sox11a in large yellow croaker Larimichthys crocea. Gene 2015; 574:287-301. [PMID: 26275936 DOI: 10.1016/j.gene.2015.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 08/08/2015] [Accepted: 08/09/2015] [Indexed: 12/30/2022]
Abstract
Sox genes play important roles in various developmental processes such as sex determination, embryogenesis, oogenesis, neurogenesis, and larval development. In order to clarify the roles of Sox genes in the developmental process of large yellow croaker, the full-length cDNA of the Sox11a gene (Lc-Sox11a) was cloned for the first time. Bioinformatics analysis indicated that Lc-Sox11a contains a protein of 366 amino acids with a Ser-rich region, a C-terminal conserved region, and a high mobility group box. The expression of Lc-Sox11a in different tissues of both sexes and in different developmental embryonic stages revealed that Lc-Sox11a were expressed with tissue and gender specificity, of which the expression level in female was ovary>brain>eye>gill; in male was brain>testis>gill. The gender differences occurred in the brain and eye with the male brain>female brain, female eye>male eye. Moreover, the expression of Lc-Sox11a in the gonad and brain at different growth stages was detected. Significant up-regulated expression of Lc-Sox11a was found in the ovary and the male brain at 1000dph (days post hatching) compared with 270dph and 635dph. However, significant down-regulated expression of Lc-Sox11a occurred in the testis with growth. Besides, the expression of Lc-Sox11a in the female brain showed a trend of first rising then falling, with the highest peak in 635dph. The results of in situ hybridization displayed that Lc-Sox11a was widely distributed only in cytoplasm of oocytes at each stage in oogenesis. In early stage of oocytes, Lc-Sox11a was expressed weakly and evenly. As the appearance of vacuoles and synthesis of yolks, positive signals of Lc-Sox11a distributed intensively in the residual cytoplasm. In spermatogenesis, Lc-Sox11a was distributed in cytoplasm of all male germ cells except spermatozoon with spermatogonium>spermatocyte>spermatid. During embryogenesis, Lc-Sox11a was expressed in most embryonic stages, the highest expression occurred in the formation-of-eye-lens stage, closely followed by the closure-of-blastopore stage, then the beginning-of-heart-pulsation stage. The results of whole mount in situ hybridization showed that the expression of Lc-Sox11a began to increase beginning with the multiple-cell stage, with the major distribution of Lc-Sox11a in the brain and eye areas in the pre-hatching stage.
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Affiliation(s)
- Yonghua Jiang
- College of Ocean & Earth Science, Xiamen University, Xiamen 361005, China; Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Kunhuang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Large Yellow Croaker, Ningde Fufa Fisheries Company Limited, Ningde 352103, China
| | - Shihai Chen
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China
| | - Wanshu Hong
- College of Ocean & Earth Science, Xiamen University, Xiamen 361005, China
| | - Yilei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Fisheries College, Jimei University, Xiamen 361021, China.
| | - Ziping Zhang
- Department of Natural Sciences and Mathematics, State University of New York at Cobleskill, NY 12043, United States
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Whittington N, Cunningham D, Le TK, De Maria D, Silva EM. Sox21 regulates the progression of neuronal differentiation in a dose-dependent manner. Dev Biol 2015; 397:237-47. [PMID: 25448693 PMCID: PMC4325979 DOI: 10.1016/j.ydbio.2014.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/12/2014] [Indexed: 12/27/2022]
Abstract
Members of the SoxB transcription factor family play critical roles in the regulation of neurogenesis. The SoxB1 proteins are required for the induction and maintenance of a proliferating neural progenitor population in numerous vertebrates, however the role of the SoxB2 protein, Sox21, is less clear due to conflicting results. To clarify the role of Sox21 in neurogenesis, we examined its function in the Xenopus neural plate. Here we report that misexpression of Sox21 expands the neural progenitor domain, and represses neuron formation by binding to Neurogenin (Ngn2) and blocking its function. Conversely, we found that Sox21 is also required for neuron formation, as cells lacking Sox21 undergo cell death and thus are unable to differentiate. Together our data indicate that Sox21 plays more than one role in neurogenesis, where a threshold level is required for cell viability and normal differentiation of neurons, but a higher concentration of Sox21 inhibits neuron formation and instead promotes progenitor maintenance.
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Affiliation(s)
- Niteace Whittington
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Doreen Cunningham
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Thien-Kim Le
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - David De Maria
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
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Can the ‘neuron theory’ be complemented by a universal mechanism for generic neuronal differentiation. Cell Tissue Res 2014; 359:343-84. [DOI: 10.1007/s00441-014-2049-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 12/19/2022]
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12
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Study of promoter DNA methylation of Sox11 and its correlation with tissue-specific expression in the laboratory mouse. Gene 2014; 552:133-9. [DOI: 10.1016/j.gene.2014.09.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/05/2014] [Accepted: 09/13/2014] [Indexed: 02/05/2023]
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Ariza-Cosano A, Bensimon-Brito A, Gómez-Skarmeta JL, Bessa J. sox21a directs lateral line patterning by modulating FGF signaling. Dev Neurobiol 2014; 75:80-92. [PMID: 25044975 DOI: 10.1002/dneu.22211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 01/19/2023]
Abstract
The development of organs composed by repeated functional units is, in many cases, accomplished by the transition of cells from a progenitor to a differentiation domain, triggering a reiterated developmental program. Yet, how these discrete fields are formed during development is still a largely unresolved question. The posterior lateral line (pLL), a sensory organ present in fish and amphibians, develops from a primordium that migrates along the flanks of the animal periodically depositing neuromasts, the pLL functional units. In zebrafish (Danio rerio), the developmental program of the pLL is triggered by the transit of progenitor cells from a Wnt to a Fgf signaling domain. It has been proposed that these two fields are defined by the antagonistic activity of these two signaling pathways, but how they are formed and maintained is still an open question in the development of the pLL. In this work, we show that sox21a, an HMG -box transcription factor, is expressed within the Fgf domain. We demonstrate that, while the Fgf signaling pathway do not control sox21a, knockdown of sox21a causes impairment of Fgf signaling, expansion of the Wnt signaling domain and disruption of neuromast development. These results suggest that sox21a is a key player in the pLL primordium patterning, fine-tuning the border of the Fgf and Wnt signaling domains.
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Affiliation(s)
- Ana Ariza-Cosano
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Ctra. Utrera Km 1, Seville, 41013, Spain
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Pillai-Kastoori L, Wen W, Wilson SG, Strachan E, Lo-Castro A, Fichera M, Musumeci SA, Lehmann OJ, Morris AC. Sox11 is required to maintain proper levels of Hedgehog signaling during vertebrate ocular morphogenesis. PLoS Genet 2014; 10:e1004491. [PMID: 25010521 PMCID: PMC4091786 DOI: 10.1371/journal.pgen.1004491] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 05/21/2014] [Indexed: 11/29/2022] Open
Abstract
Ocular coloboma is a sight-threatening malformation caused by failure of the choroid fissure to close during morphogenesis of the eye, and is frequently associated with additional anomalies, including microphthalmia and cataracts. Although Hedgehog signaling is known to play a critical role in choroid fissure closure, genetic regulation of this pathway remains poorly understood. Here, we show that the transcription factor Sox11 is required to maintain specific levels of Hedgehog signaling during ocular development. Sox11-deficient zebrafish embryos displayed delayed and abnormal lens formation, coloboma, and a specific reduction in rod photoreceptors, all of which could be rescued by treatment with the Hedgehog pathway inhibitor cyclopamine. We further demonstrate that the elevated Hedgehog signaling in Sox11-deficient zebrafish was caused by a large increase in shha transcription; indeed, suppressing Shha expression rescued the ocular phenotypes of sox11 morphants. Conversely, over-expression of sox11 induced cyclopia, a phenotype consistent with reduced levels of Sonic hedgehog. We screened DNA samples from 79 patients with microphthalmia, anophthalmia, or coloboma (MAC) and identified two novel heterozygous SOX11 variants in individuals with coloboma. In contrast to wild type human SOX11 mRNA, mRNA containing either variant failed to rescue the lens and coloboma phenotypes of Sox11-deficient zebrafish, and both exhibited significantly reduced transactivation ability in a luciferase reporter assay. Moreover, decreased gene dosage from a segmental deletion encompassing the SOX11 locus resulted in microphthalmia and related ocular phenotypes. Therefore, our study reveals a novel role for Sox11 in controlling Hedgehog signaling, and suggests that SOX11 variants contribute to pediatric eye disorders.
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Affiliation(s)
- Lakshmi Pillai-Kastoori
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Wen Wen
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stephen G. Wilson
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Erin Strachan
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Adriana Lo-Castro
- Department of Neuroscience, Pediatric Neurology Unit, “Tor Vergata” University of Rome, Rome, Italy
| | - Marco Fichera
- Laboratory of Medical Genetics, IRCCS Associazione Oasi Maria Santissima, Troina, Italy, and Medical Genetics, University of Catania, Catania, Italy
| | | | - Ordan J. Lehmann
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ann C. Morris
- Department of Biology, University of Kentucky, Lexington, Kentucky, United States of America
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Tsurusaki Y, Koshimizu E, Ohashi H, Phadke S, Kou I, Shiina M, Suzuki T, Okamoto N, Imamura S, Yamashita M, Watanabe S, Yoshiura KI, Kodera H, Miyatake S, Nakashima M, Saitsu H, Ogata K, Ikegawa S, Miyake N, Matsumoto N. De novo SOX11 mutations cause Coffin-Siris syndrome. Nat Commun 2014; 5:4011. [PMID: 24886874 DOI: 10.1038/ncomms5011] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 04/30/2014] [Indexed: 11/09/2022] Open
Abstract
Coffin-Siris syndrome (CSS) is a congenital disorder characterized by growth deficiency, intellectual disability, microcephaly, characteristic facial features and hypoplastic nails of the fifth fingers and/or toes. We previously identified mutations in five genes encoding subunits of the BAF complex, in 55% of CSS patients. Here we perform whole-exome sequencing in additional CSS patients, identifying de novo SOX11 mutations in two patients with a mild CSS phenotype. sox11a/b knockdown in zebrafish causes brain abnormalities, potentially explaining the brain phenotype of CSS. SOX11 is the downstream transcriptional factor of the PAX6-BAF complex, highlighting the importance of the BAF complex and SOX11 transcriptional network in brain development.
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Affiliation(s)
- Yoshinori Tsurusaki
- 1] Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan [2]
| | - Eriko Koshimizu
- 1] Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan [2]
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, 2100 Magome, Iwatsuki 339-8551, Japan
| | - Shubha Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Raebareli Rd, Lucknow 226014, India
| | - Ikuyo Kou
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Shiina
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Toshifumi Suzuki
- 1] Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan [2] Department of Obstetrics and Gynecology, Juntendo University, Hongo 3-1-3, Bunkyo-ku, Tokyo 113-8431, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho, Izumi 594-1101, Japan
| | - Shintaro Imamura
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Japan
| | - Michiaki Yamashita
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Japan
| | - Satoshi Watanabe
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Koh-ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Hirofumi Kodera
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
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16
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Range R. Specification and positioning of the anterior neuroectoderm in deuterostome embryos. Genesis 2014; 52:222-34. [PMID: 24549984 DOI: 10.1002/dvg.22759] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/10/2014] [Accepted: 02/14/2014] [Indexed: 02/01/2023]
Abstract
The molecular mechanisms used by deuterostome embryos (vertebrates, urochordates, cephalochordates, hemichordates, and echinoderms) to specify and then position the anterior neuroectoderm (ANE) along the anterior-posterior axis are incompletely understood. Studies in several deuterostome embryos suggest that the ANE is initially specified by an early, broad regulatory state. Then, a posterior-to-anterior wave of respecification restricts this broad ANE potential to the anterior pole. In vertebrates, sea urchins and hemichordates a posterior-anterior gradient of Wnt/β-catenin signaling plays an essential and conserved role in this process. Recent data collected from the basal deuterostome sea urchin embryo suggests that positioning the ANE to the anterior pole involves more than the Wnt/β-catenin pathway, instead relying on the integration of information from the Wnt/β-catenin, Wnt/JNK, and Wnt/PKC pathways. Moreover, comparison of functional and expression data from the ambulacrarians, invertebrate chordates, and vertebrates strongly suggests that this Wnt network might be an ANE positioning mechanism shared by all deuterostomes.
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Affiliation(s)
- Ryan Range
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi
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17
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Moore DL, Goldberg JL. Multiple transcription factor families regulate axon growth and regeneration. Dev Neurobiol 2012; 71:1186-211. [PMID: 21674813 DOI: 10.1002/dneu.20934] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Understanding axon regenerative failure remains a major goal in neuroscience, and reversing this failure remains a major goal for clinical neurology. Although an inhibitory central nervous system environment clearly plays a role, focus on molecular pathways within neurons has begun to yield fruitful insights. Initial steps forward investigated the receptors and signaling pathways immediately downstream of environmental cues, but recent work has also shed light on transcriptional control mechanisms that regulate intrinsic axon growth ability, presumably through whole cassettes of gene target regulation. Here we will discuss transcription factors that regulate neurite growth in vitro and in vivo, including p53, SnoN, E47, cAMP-responsive element binding protein (CREB), signal transducer and activator of transcription 3 (STAT3), nuclear factor of activated T cell (NFAT), c-Jun activating transcription factor 3 (ATF3), sex determining region Ybox containing gene 11 (Sox11), nuclear factor κ-light chain enhancer of activated B cells (NFκB), and Krüppel-like factors (KLFs). Revealing the similarities and differences among the functions of these transcription factors may further our understanding of the mechanisms of transcriptional regulation in axon growth and regeneration.
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Affiliation(s)
- Darcie L Moore
- Bascom Palmer Eye Institute and the Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Florida, USA
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18
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Pauls S, Smith SF, Elgar G. Lens development depends on a pair of highly conserved Sox21 regulatory elements. Dev Biol 2012; 365:310-8. [PMID: 22387845 PMCID: PMC3480646 DOI: 10.1016/j.ydbio.2012.02.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/16/2012] [Accepted: 02/18/2012] [Indexed: 02/03/2023]
Abstract
Highly conserved non-coding elements (CNEs) linked to genes involved in embryonic development have been hypothesised to correspond to cis-regulatory modules due to their ability to induce tissue-specific expression patterns. However, attempts to prove their requirement for normal development or for the correct expression of the genes they are associated with have yielded conflicting results. Here, we show that CNEs at the vertebrate Sox21 locus are crucial for Sox21 expression in the embryonic lens and that loss of Sox21 function interferes with normal lens development. Using different expression assays in zebrafish we find that two CNEs linked to Sox21 in all vertebrates contain lens enhancers and that their removal from a reporter BAC abolishes lens expression. Furthermore inhibition of Sox21 function after the injection of a sox21b morpholino into zebrafish leads to defects in lens development. These findings identify a direct link between sequence conservation and genomic function of regulatory sequences. In addition to this we provide evidence that putative Sox binding sites in one of the CNEs are essential for induction of lens expression as well as enhancer function in the CNS. Our results show that CNEs identified in pufferfish-mammal whole-genome comparisons are crucial developmental enhancers and hence essential components of gene regulatory networks underlying vertebrate embryogenesis.
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19
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Lan X, Wen L, Li K, Liu X, Luo B, Chen F, Xie D, Kung HF. Comparative analysis of duplicated sox21 genes in zebrafish. Dev Growth Differ 2011; 53:347-56. [PMID: 21492149 DOI: 10.1111/j.1440-169x.2010.01239.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sox21 is thought to function as a counteracting partner of SoxB1 (Sox1, 2, 3) genes and is involved in cell fate determination. In this study, we comparatively analyzed the expression patterns and conserved cis-regulatory elements of the duplicated sox21 genes in zebrafish. In embryogenesis, sox21b is predominantly expressed in the telencephalon, hypothalamus, mesencephalon and lens, and sox21a is solely expressed in the midbrain-hindbrain boundary, olfactory placode and lateral line, while both genes are expressed in the hindbrain, spinal cord and ear. In adult, sox21a is expressed in the brain, skin, ovary and intestine, while sox21b is expressed in the brain and testis. Interestingly, all 16 pan-vertebrate conserved non-coding elements (CNEs) are asymmetrically preserved in the sox21b locus, whereas two fish-specific elements are kept in the sox21a locus, and this is correlated with increased evolutionary rate of the sox21a protein sequence. Transient transgenic reporter analysis revealed that six sox21b CNEs and two sox21a CNEs drove green fluorescent protein (GFP) expression in tissues correlated with the partitioning of expression in two orthologues. These results indicate that sox21a and sox21b have reciprocally lost expression domains of the ancestral gene reflected by degeneration of certain CNEs in their genomic loci and provide clear evidence for evolution of the duplicated sox21 genes by subfunctionalization. In addition, our data suggest that some CNEs-based regulatory pathways have been predominantly preserved in the sox21b locus.
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Affiliation(s)
- Xianjiang Lan
- Laboratory of Integrated Biosciences, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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20
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Cui J, Shen X, Zhao H, Nagahama Y. Genome-Wide Analysis of Sox Genes in Medaka (Oryzias latipes) and Their Expression Pattern in Embryonic Development. Cytogenet Genome Res 2011; 134:283-94. [DOI: 10.1159/000329480] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2011] [Indexed: 12/23/2022] Open
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21
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Webb KJ, Coolen M, Gloeckner CJ, Stigloher C, Bahn B, Topp S, Ueffing M, Bally-Cuif L. The Enhancer of split transcription factor Her8a is a novel dimerisation partner for Her3 that controls anterior hindbrain neurogenesis in zebrafish. BMC DEVELOPMENTAL BIOLOGY 2011; 11:27. [PMID: 21586122 PMCID: PMC3125270 DOI: 10.1186/1471-213x-11-27] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 05/17/2011] [Indexed: 12/31/2022]
Abstract
Background Neurogenesis control and the prevention of premature differentiation in the vertebrate embryo are crucial processes, allowing the formation of late-born cell types and ensuring the correct shape and cytoarchitecture of the brain. Members of the Hairy/Enhancer of Split (Hairy/E(spl)) family of bHLH-Orange transcription factors, such as zebrafish Her3, 5, 9 and 11, are implicated in the local inhibition of neurogenesis to maintain progenitor pools within the early neural plate. To better understand how these factors exert their inhibitory function, we aimed to isolate some of their functional interactors. Results We used a yeast two-hybrid screen with Her5 as bait and recovered a novel zebrafish Hairy/E(spl) factor - Her8a. Using phylogenetic and synteny analyses, we demonstrate that her8a evolved from an ancient duplicate of Hes6 that was recently lost in the mammalian lineage. We show that her8a is expressed across the mid- and anterior hindbrain from the start of segmentation. Through knockdown and misexpression experiments, we demonstrate that Her8a is a negative regulator of neurogenesis and plays an essential role in generating progenitor pools within rhombomeres 2 and 4 - a role resembling that of Her3. Her8a co-purifies with Her3, suggesting that Her8a-Her3 heterodimers may be relevant in this domain of the neural plate, where both proteins are co-expressed. Finally, we demonstrate that her8a expression is independent of Notch signaling at the early neural plate stage but that SoxB factors play a role in its expression, linking patterning information to neurogenesis control. Overall, the regulation and function of Her8a differ strikingly from those of its closest relative in other vertebrates - the Hes6-like proteins. Conclusions Our results characterize the phylogeny, expression and functional interactions involving a new Her factor, Her8a, and highlight the complex interplay of E(spl) proteins that generates the neurogenesis pattern of the zebrafish early neural plate.
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Affiliation(s)
- Katharine J Webb
- Zebrafish Neurogenetics Department, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr, 1, D-85764 Neuherberg, Germany.
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22
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Abstract
For more than a decade, the zebrafish has proven to be an excellent model organism to investigate the mechanisms of neurogenesis during development. The often cited advantages, namely external development, genetic, and optical accessibility, have permitted direct examination and experimental manipulations of neurogenesis during development. Recent studies have begun to investigate adult neurogenesis, taking advantage of its widespread occurrence in the mature zebrafish brain to investigate the mechanisms underlying neural stem cell maintenance and recruitment. Here we provide a comprehensive overview of the tools and techniques available to study neurogenesis in zebrafish both during development and in adulthood. As useful resources, we provide tables of available molecular markers, transgenic, and mutant lines. We further provide optimized protocols for studying neurogenesis in the adult zebrafish brain, including in situ hybridization, immunohistochemistry, in vivo lipofection and electroporation methods to deliver expression constructs, administration of bromodeoxyuridine (BrdU), and finally slice cultures. These currently available tools have put zebrafish on par with other model organisms used to investigate neurogenesis.
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Affiliation(s)
- Prisca Chapouton
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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23
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Lin Y, Chen D, Fan Q, Zhang H. Characterization of SoxB2 and SoxC genes in amphioxus (Branchiostoma belcheri): implications for their evolutionary conservation. ACTA ACUST UNITED AC 2009; 52:813-22. [PMID: 19802739 DOI: 10.1007/s11427-009-0111-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Accepted: 04/02/2009] [Indexed: 10/20/2022]
Abstract
Most Sox genes directly affect cell fate determination and differentiation. In this study, we isolated two Sox genes: SoxB2 and SoxC from amphioxus (Branchiostoma belcheri), the closest living invertebrate relative of the vertebrates. Alignments of SoxB2 and SoxC protein sequences and their vertebrate homologs show high conservation of their HMG domains. Phylogenic analysis shows that amphioxus SoxB2 and SoxC fall out of the vertebrate branches, suggesting that vertebrate homologs might arise from gene duplications during evolution. The two genes possess similar spatial and temporal expression patterns during embryogenesis and in adults. They are both maternally inherited. During neurulation, they are expressed in the neural ectoderm and archenterons. In adults, they are expressed not only in the nerve cord, but also in the gut, midgut diverticulum, gill and oocytes. These results suggest that amphioxus SoxB2 and SoxC might co-function and have conserved functions in the nervous system and gonads as their vertebrate homologs.
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Affiliation(s)
- YuShuang Lin
- Institute of Developmental Biology, Life Science College, Key Lab of Experimental Teratology of Ministry of Education, Shandong University, Jinan 250100, China
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24
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Sox12 deletion in the mouse reveals nonreciprocal redundancy with the related Sox4 and Sox11 transcription factors. Mol Cell Biol 2008; 28:4675-87. [PMID: 18505825 DOI: 10.1128/mcb.00338-08] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcription factors Sox4 and Sox11 are important regulators of diverse developmental processes including heart, lung, pancreas, spleen, and B-cell development. Here we have studied the role of the related Sox12 as the third protein of the SoxC group both in vivo and in vitro. Despite widespread Sox12 expression during embryonic development, Sox12-deficient mice developed surprisingly normally, so that they were born alive, showed no gross phenotypic abnormalities, and were fertile in both sexes. Comparison with the related Sox4 and Sox11 revealed extensive overlap in the embryonic expression pattern but more uniform expression levels for Sox12, without sites of particularly high expression. All three Sox proteins furthermore exhibited comparable DNA-binding characteristics and functioned as transcriptional activators. Sox12 was, however, a relatively weak transactivator in comparison to Sox11. We conclude that Sox4 and Sox11 function redundantly with Sox12 and can compensate its loss during mouse development. Because of differences in expression levels and transactivation rates, however, functional compensation is not reciprocal.
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25
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Zhang L, Lin D, Zhang Y, Ma G, Zhang W. A homologue of Sox11 predominantly expressed in the ovary of the orange-spotted grouper Epinephelus coioides. Comp Biochem Physiol B Biochem Mol Biol 2007; 149:345-53. [PMID: 18032080 DOI: 10.1016/j.cbpb.2007.10.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 10/10/2007] [Accepted: 10/11/2007] [Indexed: 10/22/2022]
Abstract
Sox, a family of genes related to the mammalian sex-determining region Y (SRY) gene, are found throughout the animal kingdom and regulate diverse developmental processes including sex determination. The full-length Sox11b cDNA was cloned from the ovary of the orange-spotted grouper Epinephelus coioides. This sequence is highly homologous to SOX11 of other species and contained the signature features of mammalian SOX11 homologues, except for the absence of Pro-Glu rich region and presence of two Ser-rich regions. Southern blot analysis suggested that there is likely a single copy of Sox11b gene in the genome of this fish. The mRNA expression of Sox11b was detected in a wide range of tissues except the blood cells, and its expression is especially abundant in the ovary. During embryogenesis and larval development, the mRNA levels of Sox11b were high except at the eyed stage. During 17alpha-methyltestosterone (MT)-induced precocious sex change, the mRNA levels of Sox11b in the gonads were decreased significantly. Together, these results indicated that Sox11b may be involved in the oogenesis, embryogenesis, larval development, and sex change of the orange-spotted grouper.
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Affiliation(s)
- Lihong Zhang
- State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou 510275, PR China
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26
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Santos EM, Workman VL, Paull GC, Filby AL, Van Look KJW, Kille P, Tyler CR. Molecular basis of sex and reproductive status in breeding zebrafish. Physiol Genomics 2007; 30:111-22. [PMID: 17374843 DOI: 10.1152/physiolgenomics.00284.2006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The zebrafish ( Danio rerio) is used extensively as a model species for studies on vertebrate development and for assessing chemical effects on reproduction. Despite this, the molecular mechanisms controlling zebrafish reproduction are poorly understood. We analyzed the transcriptomic profiles of the gonads of individual zebrafish, using a 17k oligonucleotide microarray, to define the molecular basis of sex and reproductive status in sexually mature fish. The gonadal transcriptome differed substantially between sexes. Among the genes overexpressed in females, 11 biological processes were overrepresented including mitochondrion organization and biogenesis, and cell growth and/or maintenance. Among the genes overexpressed in males, six biological processes were overrepresented including protein biosynthesis and protein metabolism. Analysis of the expression of gene families known to be involved in reproduction identified a number of genes differentially expressed between ovaries and testes including a number of sox genes and genes belonging to the insulin-like growth factor and the activin-inhibin pathways. Real-time quantitative PCR confirmed the expression profiles for nine of the most differentially expressed genes and indicated that many transcripts are likely to be switched off in one of the sexes in the gonads of adult fish. Significant differences were seen between the gonad transcriptomes of individual reproductively active females reflecting their stage of maturation, whereas the testis transcriptomes were remarkably similar between individuals. In summary, we have identified molecular processes associated with (gonadal) sex specificity in breeding zebrafish and established a strong relationship between individual ovarian transcriptomes and reproductive status in females.
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Affiliation(s)
- E M Santos
- School of Biosciences, University of Exeter, Exeter, UK.
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27
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McEwen GK, Woolfe A, Goode D, Vavouri T, Callaway H, Elgar G. Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. Genome Res 2006; 16:451-65. [PMID: 16533910 PMCID: PMC1457030 DOI: 10.1101/gr.4143406] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most of these elements share little sequence identity to each other, a small number are remarkably similar and appear to be the product of duplication events. Here, we searched for duplicated conserved noncoding elements in the human genome, using comparisons with Fugu to select putative cis-regulatory sequences. We identified 124 families of duplicated elements, each containing between two and five members, that are highly conserved within and between vertebrate genomes. In 74% of cases, we were able to assign a specific set of paralogous genes with annotation relating to transcriptional regulation and/or development to each family, thus removing much of the ambiguity in identifying associated genes. We find that duplicate elements have the potential to up-regulate reporter gene expression in a tissue-specific manner and that expression domains often overlap, but are not necessarily identical, between family members. Over two thirds of the families are conserved in duplicate in fish and appear to predate the large-scale duplication events thought to have occurred at the origin of vertebrates. We propose a model whereby gene duplication and the evolution of cis-regulatory elements can be considered in the context of increased morphological diversity and the emergence of the modern vertebrate body plan.
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Affiliation(s)
- Gayle K. McEwen
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, United Kingdom
- MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, United Kingdom
| | - Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, United Kingdom
| | - Debbie Goode
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Tanya Vavouri
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, United Kingdom
| | - Heather Callaway
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
- Corresponding author.E-mail ; fax 0044 207 882 3000
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28
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Ellingsen S, Laplante MA, König M, Kikuta H, Furmanek T, Hoivik EA, Becker TS. Large-scale enhancer detection in the zebrafish genome. Development 2005; 132:3799-811. [PMID: 16049110 DOI: 10.1242/dev.01951] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Murine retroviral vectors carrying an enhancer detection cassette were used to generate 95 transgenic lines of fish in which reporter expression is observed in distinct patterns during embryonic development. We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. Many integrations map close to previously known developmental genes, including transcription factors of the Pax, Hox, Sox, Pou, Otx, Emx, zinc-finger and bHLH gene families. In most cases, the activated provirus is located in, or within a 15 kb interval around, the corresponding transcriptional unit. The exceptions include four insertions into a gene desert on chromosome 20 upstream of sox11b, and an insertion upstream of otx1. In these cases, the activated insertions are found at a distance of between 32 kb and 132 kb from the coding region. These as well as seven other insertions described here identify genes that have recently been associated with ultra conserved non-coding elements found in all vertebrate genomes.
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Affiliation(s)
- Staale Ellingsen
- Sars International Centre for Marine Molecular Biology at the University of Bergen, Thormoehlensgate 55, 5008 Bergen, Norway
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29
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Abstract
Among the families of transcription factors expressed at the neural plate border in response to neural crest-inducing signals, Sox proteins have emerged as important players in regulating multiple aspects of neural crest development. Here, we summarize the expression of six Sox genes, namely Sox8, Sox9, Sox10, LSox5, Sox4 and Sox11, in neural crest progenitors and their derivatives, and review some aspects of their function pertaining to neural crest development in several species.
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Affiliation(s)
- Chang-Soo Hong
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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30
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Hoegg S, Brinkmann H, Taylor JS, Meyer A. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J Mol Evol 2005; 59:190-203. [PMID: 15486693 DOI: 10.1007/s00239-004-2613-z] [Citation(s) in RCA: 427] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Accepted: 02/13/2004] [Indexed: 10/26/2022]
Abstract
For many genes, ray-finned fish (Actinopterygii) have two paralogous copies, where only one ortholog is present in tetrapods. The discovery of an additional, almost-complete set of Hox clusters in teleosts (zebrafish, pufferfish, medaka, and cichlid) but not in basal actinopterygian lineages ( Polypterus) led to the formulation of the fish-specific genome duplication hypothesis. The phylogenetic timing of this genome duplication during the evolution of ray-finned fish is unknown, since only a few species of basal fish lineages have been investigated so far. In this study, three nuclear genes ( fzd8, sox11, tyrosinase) were sequenced from sturgeons (Acipenseriformes), gars (Semionotiformes), bony tongues (Osteoglossomorpha), and a tenpounder (Elopomorpha). For these three genes, two copies have been described previously teleosts (e.g., zebrafish, pufferfish), but only one orthologous copy is found in tetrapods. Individual gene trees for these three genes and a concatenated dataset support the hypothesis that the fish-specific genome duplication event took place after the split of the Acipenseriformes and the Semionotiformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes. If these three genes were duplicated during the proposed fish-specific genome duplication event, then this event separates the species-poor early-branching lineages from the species-rich teleost lineage. The additional number of genes resulting from this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish.
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Affiliation(s)
- Simone Hoegg
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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31
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Leung AYH, Mendenhall EM, Kwan TTF, Liang R, Eckfeldt C, Chen E, Hammerschmidt M, Grindley S, Ekker SC, Verfaillie CM. Characterization of expanded intermediate cell mass in zebrafish chordin morphant embryos. Dev Biol 2005; 277:235-54. [PMID: 15572152 DOI: 10.1016/j.ydbio.2004.09.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 08/30/2004] [Accepted: 09/24/2004] [Indexed: 11/30/2022]
Abstract
We investigated the mechanisms of intermediate cell mass (ICM) expansion in zebrafish chordin (Chd) morphant embryos and examined the role of BMPs in relation to this phenotype. At 24 h post-fertilization (hpf), the expanded ICM of embryos injected with chd morpholino (MO) (ChdMO embryos) contained a monotonous population of hematopoietic progenitors. In situ hybridization showed that hematopoietic transcription factors were ubiquitously expressed in the ICM whereas vascular gene expression was confined to the periphery. BMP4 (but not BMP2b or 7) and smad5 mRNA were ectopically expressed in the ChdMO ICM. At 48 hpf, monocytic cells were evident in both the ICM and circulation of ChdMO but not WT embryos. While injection of BMP4 MO had no effect on WT hematopoiesis, co-injecting BMP4 with chd MOs significantly reduced ICM expansion. Microarray studies revealed a number of genes that were differentially expressed in ChdMO and WT embryos and their roles in hematopoiesis has yet to be determined. In conclusion, the expanded ICM in ChdMO embryos represented an expansion of embryonic hematopoiesis that was skewed towards a monocytic lineage. BMP4, but not BMP2b or 7, was involved in this process. The results provide ground for further research into the mechanisms of embryonic hematopoietic cell expansion.
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Affiliation(s)
- Anskar Y H Leung
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
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32
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Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W, Edwards YJK, Cooke JE, Elgar G. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 2005; 3:e7. [PMID: 15630479 PMCID: PMC526512 DOI: 10.1371/journal.pbio.0030007] [Citation(s) in RCA: 674] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 10/21/2004] [Indexed: 02/06/2023] Open
Abstract
In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH), in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development.
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Affiliation(s)
- Adam Woolfe
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Martin Goodson
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Debbie K Goode
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Phil Snell
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Gayle K McEwen
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Tanya Vavouri
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Sarah F Smith
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Phil North
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Heather Callaway
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Krys Kelly
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Klaudia Walter
- 2Medical Research Council Biostatistics Unit, Institute of Public Health, Addenbrookes HospitalCambridgeUnited Kingdom
| | - Irina Abnizova
- 2Medical Research Council Biostatistics Unit, Institute of Public Health, Addenbrookes HospitalCambridgeUnited Kingdom
| | - Walter Gilks
- 2Medical Research Council Biostatistics Unit, Institute of Public Health, Addenbrookes HospitalCambridgeUnited Kingdom
| | - Yvonne J. K Edwards
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Julie E Cooke
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
| | - Greg Elgar
- 1Medical Research Council Rosalind Franklin Centre for Genomics ResearchHinxton, CambridgeUnited Kingdom
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Argenton F, Giudici S, Deflorian G, Cimbro S, Cotelli F, Beltrame M. Ectopic expression and knockdown of a zebrafish sox21 reveal its role as a transcriptional repressor in early development. Mech Dev 2004; 121:131-42. [PMID: 15037315 DOI: 10.1016/j.mod.2004.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2003] [Revised: 12/31/2003] [Accepted: 01/04/2004] [Indexed: 11/17/2022]
Abstract
Sox proteins are DNA-binding proteins belonging to the HMG box superfamily and they play key roles in animal embryonic development. Zebrafish Sox21a is part of group B Sox proteins and its chicken and mouse orthologs have been described as transcriptional repressor and activator, respectively, in two different target gene contexts. Zebrafish sox21a is present as a maternal transcript in the oocyte and is mainly expressed at the developing midbrain-hindbrain boundary from the onset of neurulation. In order to understand its role in vivo, we ectopically expressed sox21a by microinjection. Ectopic expression of full length sox21a leads to dorsalization of the embryos. A subset of the dorsalized embryos shows a partial axis splitting, and hence an ectopic neural tube, as an additional phenotype. At gastrulation, injected embryos show expansion of the expression domains of organizer-specific genes, such as chordin and goosecoid. Molecular markers used in somitogenesis highlight that sox21a-injected embryos have shortened AP axis, undulating axial structures, enlarged or even radialized paraxial territory. The developmental abnormalities caused by ectopic expression of sox21a are suggestive of defects in convergence-extension morphogenetic movements. Antisense morpholino oligonucleotides, designed to functionally knockdown sox21a, cause ventralization of the embryos. Moreover, gain-of-function experiments with chimeric constructs, where Sox21a DNA-binding domain is fused to a transcriptional activator (VP16) or repressor (EnR) domain, suggests that zebrafish Sox21a acts as a repressor in dorso-ventral patterning.
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34
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Zhang C, Basta T, Hernandez-Lagunas L, Simpson P, Stemple DL, Artinger KB, Klymkowsky MW. Repression of nodal expression by maternal B1-type SOXs regulates germ layer formation in Xenopus and zebrafish. Dev Biol 2004; 273:23-37. [PMID: 15302595 DOI: 10.1016/j.ydbio.2004.05.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Revised: 05/24/2004] [Accepted: 05/26/2004] [Indexed: 10/26/2022]
Abstract
B1-type SOXs (SOXs 1, 2, and 3) are the most evolutionarily conserved subgroup of the SOX transcription factor family. To study their maternal functions, we used the affinity-purified antibody antiSOX3c, which inhibits the binding of Xenopus SOX3 to target DNA sequences [Development. 130(2003)5609]. The antibody also cross-reacts with zebrafish embryos. When injected into fertilized Xenopus or zebrafish eggs, antiSOX3c caused a profound gastrulation defect; this defect could be rescued by the injection of RNA encoding SOX3DeltaC-EnR, a SOX3-engrailed repression domain chimera. In antiSOX3c-injected Xenopus embryos, normal animal-vegetal patterning of mesodermal and endodermal markers was disrupted, expression domains were shifted toward the animal pole, and the levels of the endodermal markers SOX17 and endodermin increased. In Xenopus, SOX3 acts as a negative regulator of Xnr5, which encodes a nodal-related TGFbeta-family protein. Two nodal-related proteins are expressed in the early zebrafish embryo, squint and cyclops; antiSOX3c-injection leads to an increase in the level of cyclops expression. In both Xenopus and zebrafish, the antiSOX3c phenotype was rescued by the injection of RNA encoding the nodal inhibitor Cerberus-short (CerS). In Xenopus, antiSOX3c's effects on endodermin expression were suppressed by injection of RNA encoding a dominant negative version of Mixer or a morpholino against SOX17alpha2, both of which act downstream of nodal signaling in the endoderm specification pathway. Based on these data, it appears that maternal B1-type SOX functions together with the VegT/beta-catenin system to regulate nodal expression and to establish the normal pattern of germ layer formation in Xenopus. A mechanistically conserved system appears to act in a similar manner in the zebrafish.
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Affiliation(s)
- Chi Zhang
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, 80309-0347, USA
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35
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Sock E, Rettig SD, Enderich J, Bösl MR, Tamm ER, Wegner M. Gene targeting reveals a widespread role for the high-mobility-group transcription factor Sox11 in tissue remodeling. Mol Cell Biol 2004; 24:6635-44. [PMID: 15254231 PMCID: PMC444853 DOI: 10.1128/mcb.24.15.6635-6644.2004] [Citation(s) in RCA: 220] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The high-mobility-group domain-containing transcription factor Sox11 is expressed transiently during embryonic development in many tissues that undergo inductive remodeling. Here we have analyzed the function of Sox11 by gene deletion in the mouse. Sox11-deficient mice died at birth from congenital cyanosis, likely resulting from heart defects. These included ventricular septation defects and outflow tract malformations that ranged from arterial common trunk to a condition known as double outlet right ventricle. Many other organs that normally express Sox11 also exhibited severe developmental defects. We observed various craniofacial and skeletal malformations, asplenia, and hypoplasia of the lung, stomach, and pancreas. Eyelids and the abdominal wall did not close properly in some Sox11-deficient mice. This phenotype suggests a prime function for Sox11 in tissue remodeling and identifies SOX11 as a potentially mutated gene in corresponding human malformation syndromes.
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Affiliation(s)
- Elisabeth Sock
- Institut für Biochemie, Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
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36
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Ohba H, Chiyoda T, Endo E, Yano M, Hayakawa Y, Sakaguchi M, Darnell RB, Okano HJ, Okano H. Sox21 is a repressor of neuronal differentiation and is antagonized by YB-1. Neurosci Lett 2004; 358:157-60. [PMID: 15039105 DOI: 10.1016/j.neulet.2004.01.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 01/08/2004] [Accepted: 01/09/2004] [Indexed: 10/26/2022]
Abstract
Sox21, a high-mobility group box transcription factor, is expressed throughout the immature neural stem/progenitor population in ventricular zone but not in the cortical plate in embryonic mouse brain and its expression is restricted to the subventricular zone in the adult brain. In undifferentiated PC12 cells, endogenous Sox21 expression is detected but its expression ceases during the nerve growth factor (NGF)-induced neuronal differentiation. Overexpression of Sox21 results in a substantial repression of NGF-induced neurite outgrowth in PC12 cells. Further, we biochemically identified a Sox21-associating protein, Y-box binding protein 1 which not only binds to Sox21 but also partially restores NGF-induced neurite outgrowth of PC12 cells inhibited by Sox21. These results suggest that Sox21 is a repressor of neuronal differentiation in the developing nervous system.
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Affiliation(s)
- Hiroyuki Ohba
- CREST-JST and Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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37
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38
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Abstract
Neural progenitors of the vertebrate CNS are defined by generic cellular characteristics, including their pseudoepithelial morphology and their ability to divide and differentiate. SOXB1 transcription factors, including the three closely related genes Sox1, Sox2, and Sox3, universally mark neural progenitor and stem cells throughout the vertebrate CNS. We show here that constitutive expression of SOX2 inhibits neuronal differentiation and results in the maintenance of progenitor characteristics. Conversely, inhibition of SOX2 signaling results in the delamination of neural progenitor cells from the ventricular zone and exit from cell cycle, which is associated with a loss of progenitor markers and the onset of early neuronal differentiation markers. The phenotype elicited by inhibition of SOX2 signaling can be rescued by coexpression of SOX1, providing evidence for redundant SOXB1 function in CNS progenitors. Taken together, these data indicate that SOXB1 signaling is both necessary and sufficient to maintain panneural properties of neural progenitor cells.
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Affiliation(s)
- Victoria Graham
- Neuroscience Center, Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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39
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Hwang CK, Wu X, Wang G, Kim CS, Loh HH. Mouse mu opioid receptor distal promoter transcriptional regulation by SOX proteins. J Biol Chem 2003; 278:3742-50. [PMID: 12446692 DOI: 10.1074/jbc.m208780200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified transcription factors that bind to specific sequences in 5'-distal promoter regulatory sequences of the mouse mu opioid receptor (mor) promoter using the yeast one-hybrid system. The sequence between -746 and -707 in mor distal promoter was used as the bait because it acts as a functional promoter element and binds several DNA-binding proteins. From an adult mouse brain cDNA library, five cDNA clones encoding three Sox gene family (Sry like high mobility group (HMG) box gene) transcriptional factors, mSOX18, mSOX21, and mSOX6, were isolated. Electrophoretic mobility shift assays confirmed the presence of a binding site for SOX proteins in the -731/-725 region. Additionally, we have also established that the flanking regions outside the core Sox-binding site play an essential role in high affinity binding. DNase I footprint analysis indicates that proteins from mouse brain interact with the Sox-binding site within the mor distal promoter. Finally, we demonstrated that overexpression of mSOX18 and/or mSOX21 was able to up-regulate mouse mor distal promoter activity in mor-expressing neuronal cells (NMB). These data indicate that SOX proteins might contribute to the transcriptional activity of the mor gene and suggest that mu opioid receptor could mediate some of the developmental processes in which SOX proteins are included.
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Affiliation(s)
- Cheol Kyu Hwang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis 55455, USA.
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40
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Taguchi S, Tagawa K, Humphreys T, Satoh N. Group B sox genes that contribute to specification of the vertebrate brain are expressed in the apical organ and ciliary bands of hemichordate larvae. Zoolog Sci 2002; 19:57-66. [PMID: 12025405 DOI: 10.2108/zsj.19.57] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have identified and characterized the sequence and expression of two Group B Sox genes in the acorn worm, Ptychodera flava. One sequence represents a Group B1 Sox gene and is designated Pf-SoxB1; the other is a Group B2 Sox gene and is designated Pf-SoxB2. Both genes encode polypeptides with an HMG domain in the N-terminal half. Whole-mount in situ hybridization to embryonic and larval stages of P. flava shows that the two genes are expressed in rather similar patterns at these stages. Expression is first detected in the cells of the blastula and subsequently localizes to the ectoderm during gastrulation. As the mouth forms, expression becomes concentrated in the stomodeum region. During morphogenesis of the tornaria larva, expression in the stomodeal ectoderm remains prominent around the mouth and under the oral hood. Later the genes are prominently upregulated in the ciliary bands and the apical organ. These results provide additional evidence that genes playing essential roles in the formation of the chordate dorsal central nervous system function in the development of the ciliary bands and apical organ, neural structures of this non-chordate deuterostome larva.
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Affiliation(s)
- Shunsuke Taguchi
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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41
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Girard F, Crémazy F, Berta P, Renucci A. Expression pattern of the Sox31 gene during zebrafish embryonic development. Mech Dev 2001; 100:71-3. [PMID: 11118886 DOI: 10.1016/s0925-4773(00)00491-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have identified a novel Sox gene in zebrafish (Danio rerio), Sox31, closely related to mammalian group B Sox genes. The gene is maternally expressed. Zygotic transcription starts at gastrulation, in the presumptive neuroectoderm. Later, expression is restricted to the developing central nervous system, including forebrain, midbrain, hindbrain and spinal cord.
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Affiliation(s)
- F Girard
- Institut de Génétique Humaine, 141 rue de la Cardonille, 34033 Montpellier, France.
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42
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Bowles J, Schepers G, Koopman P. Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev Biol 2000; 227:239-55. [PMID: 11071752 DOI: 10.1006/dbio.2000.9883] [Citation(s) in RCA: 691] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Members of the SOX family of transcription factors are found throughout the animal kingdom, are characterized by the presence of a DNA-binding HMG domain, and are involved in a diverse range of developmental processes. Previous attempts to group SOX genes and deduce their structural, functional, and evolutionary relationships have relied largely on complete or partial HMG box sequence of a limited number of genes. In this study, we have used complete HMG domain sequence, full-length protein structure, and gene organization data to study the pattern of evolution within the family. For the first time, a substantial number of invertebrate SOX sequences have been included in the analysis. We find support for subdivision of the family into groups A-H, as has been suggested in some previous studies, and for the assignment of two new groups, I and J. For vertebrate genes, it appears that relatedness as suggested by HMG domain sequence is congruent with relatedness as indicated by overall structure of the full-length protein and intron-exon structure of the genes. Most of the SOX groups identified in vertebrates were represented by a single SOX sequence in each invertebrate species studied. We have named anonymous sequences and, where appropriate, have suggested systematic names for some previously identified sequences. In addition, we identify an HMG domain signature motif which may be considered representative of the SOX family. Based on our data, we propose a robust phylogeny of SOX genes that reflects their evolutionary history in metazoans.
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Affiliation(s)
- J Bowles
- Institute for Molecular Bioscience, University of Queensland, Brisbane, 4072, Australia
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