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Nurcombe ZW, Hehr CL, McFarlane S. Plexina4 and cell survival in the developing zebrafish hindbrain. Dev Dyn 2023; 252:1323-1337. [PMID: 37283310 DOI: 10.1002/dvdy.633] [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: 11/20/2022] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Growth factors are important in the developing and mature nervous system to support the survival of neurons. Developmental signaling molecules are known for their roles in controlling neurogenesis and neural circuit formation. Whether or not these molecules also have roles in cell survival in the developing nervous system is poorly understood. Plexins are a family of transmembrane receptors that bind Semaphorin ligands and are known to function in the guidance of developing axons and blood vessels. RESULTS In embryonic zebrafish, plexina4 is expressed widely in the brain, becoming largely restricted to the hindbrain as neurogenesis and differentiation proceed. Apoptosis is increased in the embryonic hindbrain of a plexina4ca307/ca307 CRISPR mutant. Based on the literature, we tested the secreted heat shock protein, Clusterin, as a candidate ligand to mediate cell survival through Plexina4. clusterin is expressed by the floor plate of the embryonic zebrafish hindbrain, in proximity to plexina4-expressing hindbrain cells. Morpholino-mediated knockdown of Clusterin increases cell apoptosis in the hindbrain, with additional cell death observed in epistasis experiments where Clusterin is knocked down in a plexina4 mutant background. CONCLUSIONS Our data suggest that Plexina4 promotes cell survival in the developing zebrafish hindbrain, likely through a pathway independent of Clusterin.
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Affiliation(s)
- Zachary W Nurcombe
- Department Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
- Graduate Program in Neuroscience, University of Calgary, Calgary, Alberta, Canada
| | - Carrie Lynn Hehr
- Department Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarah McFarlane
- Department Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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Meyers EA, Kessler JA. TGF-β Family Signaling in Neural and Neuronal Differentiation, Development, and Function. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a022244. [PMID: 28130363 DOI: 10.1101/cshperspect.a022244] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signaling by the transforming growth factor β (TGF-β) family is necessary for proper neural development and function throughout life. Sequential waves of activation, inhibition, and reactivation of TGF-β family members regulate numerous elements of the nervous system from the earliest stages of embryogenesis through adulthood. This review discusses the expression, regulation, and function of TGF-β family members in the central nervous system at various developmental stages, beginning with induction and patterning of the nervous system to their importance in the adult as modulators of inflammatory response and involvement in degenerative diseases.
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Affiliation(s)
- Emily A Meyers
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - John A Kessler
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
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3
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Foxa2 and Hif1ab regulate maturation of intestinal goblet cells by modulating agr2 expression in zebrafish embryos. Biochem J 2016; 473:2205-18. [PMID: 27222589 DOI: 10.1042/bcj20160392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/24/2016] [Indexed: 12/12/2022]
Abstract
Mammalian anterior gradient 2 (AGR2), an endoplasmic reticulum (ER) protein disulfide-isomerase (PDI), is involved in cancer cell growth and metastasis, asthma and inflammatory bowel disease (IBD). Mice lacking Agr2 exhibit decreased Muc2 protein in intestinal goblet cells, abnormal Paneth cell development, ileitis and colitis. Despite its importance in cancer biology and inflammatory diseases, the mechanisms regulating agr2 expression in the gastrointestinal tract remain unclear. In the present study, we investigated the mechanisms that control agr2 expression in the pharynx and intestine of zebrafish by transient/stable transgenesis, coupled with motif mutation, morpholino knockdown, mRNA rescue and ChIP. A 350 bp DNA sequence with a hypoxia-inducible response element (HRE) and forkhead-response element (FHRE) within a region -4.5 to -4.2 kbp upstream of agr2 directed EGFP expression specifically in the pharynx and intestine. No EGFP expression was detected in the intestinal goblet cells of Tg(HREM:EGFP) or Tg(FHREM:EGFP) embryos with mutated HRE or FHRE, whereas EGFP was expressed in the pharynx of Tg(HREM:EGFP), but not Tg(FHREM:EGFP), embryos. Morpholino knockdown of foxa1 (forkhead box A1) reduced agr2 levels in the pharynx, whereas knockdown of foxa2 or hif1ab decreased intestinal agr2 expression and affected the differentiation and maturation of intestinal goblet cells. These results demonstrate that Foxa1 regulates agr2 expression in the pharynx, whereas both Foxa2 and Hif1ab control agr2 expression in intestinal goblet cells to regulate maturation of these cells.
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Rastegar S, Strähle U. The Zebrafish as Model for Deciphering the Regulatory Architecture of Vertebrate Genomes. GENETICS, GENOMICS AND FISH PHENOMICS 2016; 95:195-216. [DOI: 10.1016/bs.adgen.2016.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Puelles L, Rubenstein JLR. A new scenario of hypothalamic organization: rationale of new hypotheses introduced in the updated prosomeric model. Front Neuroanat 2015; 9:27. [PMID: 25852489 PMCID: PMC4365718 DOI: 10.3389/fnana.2015.00027] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/23/2015] [Indexed: 01/12/2023] Open
Abstract
In this essay, we aim to explore in depth the new concept of the hypothalamus that was presented in the updated prosomeric model (Puelles et al., 2012b; Allen Developing Mouse Brain Atlas). Initial sections deal with the antecedents of prosomeric ideas represented by the extensive literature centered on the alternative columnar model of Herrick (1910), Kuhlenbeck (1973) and Swanson (1992, 2003); a detailed critique explores why the columnar model is not helpful in the search for causal developmental explanations. In contrast, the emerging prosomeric scenario visibly includes many possibilities to propose causal explanations of hypothalamic structure relative to both anteroposterior and dorsoventral patterning mechanisms, and insures the possibility to compare hypothalamic histogenesis with that of more caudal parts of the brain. Next the four major changes introduced in the organization of the hypothalamus on occasion of the updated model are presented, and our rationale for these changes is explored in detail. It is hoped that this example of morphological theoretical analysis may be useful for readers interested in brain models, or in understanding why models may need to change in the quest for higher consistency.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy, School of Medicine, University Murcia and Instituto Murciano de Investigación BiosanitariaMurcia, Spain
| | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, University of California, San FranciscoSan Francisco, CA, USA
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6
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Zarin AA, Asadzadeh J, Labrador JP. Transcriptional regulation of guidance at the midline and in motor circuits. Cell Mol Life Sci 2014; 71:419-32. [PMID: 23917723 PMCID: PMC11113760 DOI: 10.1007/s00018-013-1434-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 07/01/2013] [Accepted: 07/22/2013] [Indexed: 12/16/2022]
Abstract
Axon navigation through the developing body of an embryo is a challenging and exquisitely precise process. Axonal processes within the nervous system harbor extremely complicated internal regulatory mechanisms that enable each of them to respond to environmental cues in a unique way, so that every single neuron has an exact stereotypical localization and axonal projection pattern. Receptors and adhesion molecules expressed on axonal membranes will determine their guidance properties. Axon guidance is thought to be controlled to a large extent through transcription factor codes. These codes would be responsible for the deployment of specific guidance receptors and adhesion molecules on axonal membranes to allow them to reach their targets. Although families of transcriptional regulators as well as families of guidance molecules have been conserved across evolution, their relationships seem to have developed independently. This review focuses on the midline and the neuromuscular system in both vertebrates and Drosophila in which such relationships have been particularly well studied.
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Affiliation(s)
- Aref Arzan Zarin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Jamshid Asadzadeh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Juan-Pablo Labrador
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
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7
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Role of Shh in the development of molecularly characterized tegmental nuclei in mouse rhombomere 1. Brain Struct Funct 2013; 219:777-92. [PMID: 23494735 DOI: 10.1007/s00429-013-0534-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
Hindbrain rhombomeres in general are differentially specified molecularly by unique combinations of Hox genes with other developmental genes. Rhombomere 1 displays special features, including absence of Hox gene expression. It lies within the hindbrain range of the Engrailed genes (En1, En2), controlled by the isthmic organizer via diffusion of FGF8. It is limited rostrally by the isthmus territory, and caudally by rhombomere 2. It is double the normal size of any other rhombomere. Its dorsal part generates the cerebellar hemispheres and its ventral part gives rise to several populations, such as some raphe nuclei, the interpeduncular nucleus, the rhabdoid nucleus, anterior, dorsal, ventral and posterodorsal tegmental nuclei, the cholinergic pedunculopontine and laterodorsal tegmental nuclei, rostral parts of the hindbrain reticular formation, the locus coeruleus, and part of the lateral lemniscal and paralemniscal nuclei, among other formations. Some of these populations migrate tangentially before reaching their final positions. The morphogen Sonic Hedgehog (Shh) is normally released from the local floor plate and underlying notochord. In the present report we explore, first, whether Shh is required in the specification of these r1 populations, and, second, its possible role in the guidance of tangentially migrating neurons that approach the midline. Our results indicate that when Shh function is altered selectively in a conditional mutant mouse strain, most populations normally generated in the medial basal plate of r1 are completely absent. Moreover, the relocation of some neurons that normally originate in the alar plate and migrate tangentially into the medial basal plate is variously altered. In contrast, neurons that migrate radially (or first tangentially and then radially) into the lateral basal plate were not significantly affected.
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8
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Bayly RD, Brown CY, Agarwala S. A novel role for FOXA2 and SHH in organizing midbrain signaling centers. Dev Biol 2012; 369:32-42. [PMID: 22750257 DOI: 10.1016/j.ydbio.2012.06.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 06/06/2012] [Accepted: 06/20/2012] [Indexed: 02/04/2023]
Abstract
The floor plate (FP) is a midline signaling center, known to direct ventral cell fates and axon guidance in the neural tube. The recent identification of midbrain FP as a source of dopaminergic neurons has renewed interest in its specification and organization, which remain poorly understood. In this study, we have examined the chick midbrain and spinal FP and show that both can be partitioned into medial (MFP) and lateral (LFP) subdivisions. Although Hedgehog (HH) signaling is necessary and sufficient for LFP specification, it is not sufficient for MFP induction. By contrast, the transcription factor FOXA2 can execute the full midbrain and spinal cord FP program via HH-independent and dependent mechanisms. Interestingly, although HH-independent FOXA2 activity is necessary and sufficient for inducing MFP-specific gene expression (e.g., LMX1B, BMP7), it cannot confer ventral identity to midline cells without also turning on Sonic hedgehog (SHH). We also note that the signaling centers of the midbrain, the FP, roof plate (RP) and the midbrain-hindbrain boundary (MHB) are physically contiguous, with each expressing LMX1B and BMP7. Possibly as a result, SHH or FOXA2 misexpression can transform the MHB into FP and also suppress RP induction. Conversely, HH or FOXA2 knockdown expands the endogenous RP and transforms the MFP into a RP and/or MHB fate. Finally, combined HH blockade and FOXA2 misexpression in ventral midbrain induces LMX1B expression, which triggers the specification of the RP, rather than the MFP. Thus we identify HH-independent and dependent roles for FOXA2 in specifying the FP. In addition, we elucidate for the first time, a novel role for SHH in determining whether a midbrain signaling center will become the FP, MHB or RP.
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Affiliation(s)
- Roy D Bayly
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712-0248, USA
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9
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Yagami K, Sadaoka S, Nakamura M, Nakamura H, Maki S, Yagasaki T, Udagawa N. Neural-inducing Factor Netrin-1 is Regulated in Chondrogenesis and Osteogenesis by BMP or Noggin. J HARD TISSUE BIOL 2012. [DOI: 10.2485/jhtb.21.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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10
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Williams PG, Wetherbee JJ, Rosenfeld JA, Hersh JH. 20p11 deletion in a female child with panhypopituitarism, cleft lip and palate, dysmorphic facial features, global developmental delay and seizure disorder. Am J Med Genet A 2011; 155A:186-91. [PMID: 21204230 DOI: 10.1002/ajmg.a.33763] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deletions of 20p are rare with the majority of reported cases involving individuals with 20p12 deletions associated with Alagille syndrome. We report on a child with a de novo mosaic 20p11 deletion who presents with panhypopituitarism; hypoplastic pituitary gland and ectopic posterior pituitary gland on MRI of the brain; cleft lip and palate; kyphosis with anterior beaking of L1 and L2 vertebral bodies; pulmonic stenosis; dysmorphic facial features including flat nasal bridge, hypoplastic premaxilla, hypotelorism, preauricular pit, and cupped ears; seizure disorder; variable muscle tone; and global developmental delay. Array comparative genomic hybridization revealed this deletion to be approximately 5.4 Mb in size, containing 35 genes. Previously, an infant with 20p11.22 deletion who had panhypopituitarism, craniofacial, and genital abnormalities was reported, but the precise parameters of that deletion are unavailable. Several other reported cases of 20p11 deletions also have phenotypic overlap with our case. The similarities in clinical features of these patients suggest that the genes at 20p11 have a critical role in development of midline brain structures.
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Affiliation(s)
- P G Williams
- Department of Pediatrics, University of Louisville, Kentucky.
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11
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Mansour AA, Nissim-Eliraz E, Zisman S, Golan-Lev T, Schatz O, Klar A, Ben-Arie N. Foxa2 regulates the expression of Nato3 in the floor plate by a novel evolutionarily conserved promoter. Mol Cell Neurosci 2010; 46:187-99. [PMID: 20849957 DOI: 10.1016/j.mcn.2010.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 08/29/2010] [Accepted: 09/01/2010] [Indexed: 11/24/2022] Open
Abstract
The development of the neural tube into a complex central nervous system involves morphological, cellular and molecular changes, all of which are tightly regulated. The floor plate (FP) is a critical organizing center located at the ventral-most midline of the neural tube. FP cells regulate dorsoventral patterning, differentiation and axon guidance by secreting morphogens. Here we show that the bHLH transcription factor Nato3 (Ferd3l) is specifically expressed in the spinal FP of chick and mouse embryos. Using in ovo electroporation to understand the regulation of the FP-specific expression of Nato3, we have identified an evolutionarily conserved 204 bp genomic region, which is necessary and sufficient to drive expression to the chick FP. This promoter contains two Foxa2-binding sites, which are highly conserved among distant phyla. The two sites can bind Foxa2 in vitro, and are necessary for the expression in the FP in vivo. Gain and loss of Foxa2 function in vivo further emphasize its role in Nato3 promoter activity. Thus, our data suggest that Nato3 is a direct target of Foxa2, a transcription activator and effector of Sonic hedgehog, the hallmark regulator of FP induction and spinal cord development. The identification of the FP-specific promoter is an important step towards a better understanding of the molecular mechanisms through which Nato3 transcription is regulated and for uncovering its function during nervous system development. Moreover, the promoter provides us with a powerful tool for conditional genetic manipulations in the FP.
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Affiliation(s)
- Abed AlFatah Mansour
- Department of Cell and Developmental Biology, Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
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12
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Ribes V, Balaskas N, Sasai N, Cruz C, Dessaud E, Cayuso J, Tozer S, Yang LL, Novitch B, Marti E, Briscoe J. Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube. Genes Dev 2010; 24:1186-200. [PMID: 20516201 PMCID: PMC2878655 DOI: 10.1101/gad.559910] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 04/07/2010] [Indexed: 12/14/2022]
Abstract
The secreted ligand Sonic Hedgehog (Shh) organizes the pattern of cellular differentiation in the ventral neural tube. For the five neuronal subtypes, increasing levels and durations of Shh signaling direct progenitors to progressively more ventral identities. Here we demonstrate that this mode of action is not applicable to the generation of the most ventral cell type, the nonneuronal floor plate (FP). In chick and mouse embryos, FP specification involves a biphasic response to Shh signaling that controls the dynamic expression of key transcription factors. During gastrulation and early somitogenesis, FP induction depends on high levels of Shh signaling. Subsequently, however, prospective FP cells become refractory to Shh signaling, and this is a prerequisite for the elaboration of their identity. This prompts a revision to the model of graded Shh signaling in the neural tube, and provides insight into how the dynamics of morphogen signaling are deployed to extend the patterning capacity of a single ligand. In addition, we provide evidence supporting a common scheme for FP specification by Shh signaling that reconciles mechanisms of FP development in teleosts and amniotes.
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Affiliation(s)
- Vanessa Ribes
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Nikolaos Balaskas
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Noriaki Sasai
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Catarina Cruz
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Eric Dessaud
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Jordi Cayuso
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Samuel Tozer
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Lin Lin Yang
- Department of Neurobiology, Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Ben Novitch
- Department of Neurobiology, Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Elisa Marti
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - James Briscoe
- Developmental Neurobiology, Medical Research Council-National Institute for Medical Research, London NW7 1AA, United Kingdom
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Rosenfeld JA, Ballif BC, Martin DM, Aylsworth AS, Bejjani BA, Torchia BS, Shaffer LG. Clinical characterization of individuals with deletions of genes in holoprosencephaly pathways by aCGH refines the phenotypic spectrum of HPE. Hum Genet 2010; 127:421-40. [PMID: 20066439 DOI: 10.1007/s00439-009-0778-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 12/14/2009] [Indexed: 12/31/2022]
Abstract
Holoprosencephaly (HPE) is the most common developmental forebrain anomaly in humans. Both environmental and genetic factors have been identified to play a role in the HPE phenotype. Previous studies of the genetic bases of HPE have taken a phenotype-first approach by examining groups of patients with HPE for specific mutations or deletions in known or candidate HPE genes. In this study, we characterized the presence or absence of HPE or a microform in 136 individuals in which microarray-based comparative genomic hybridization (aCGH) identified a deletion of one of 35 HPE loci. Frank holoprosencephaly was present in 11 individuals with deletions of one of the common HPE genes SHH, ZIC2, SIX3, and TGIF1, in one individual with a deletion of the HPE8 locus at 14q13, and in one individual with a deletion of FGF8, whereas deletions of other HPE loci and candidate genes (FOXA2 and LRP2) expressed microforms of HPE. Although individuals with deletions of other HPE candidates (DISP1, LSS, HHIP, SMO, BMP4, CDON, CDC42, ACVR2A, OTX2, and WIF1) had clinically significant features, none had frank HPE or a microform. A search for significant aCGH findings in individuals referred for testing for HPE revealed a novel association of a duplication involving GSK3B at 3q13.33 with HPE or a microform, seen in two unrelated individuals.
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Chan TM, Longabaugh W, Bolouri H, Chen HL, Tseng WF, Chao CH, Jang TH, Lin YI, Hung SC, Wang HD, Yuh CH. Developmental gene regulatory networks in the zebrafish embryo. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:279-98. [PMID: 18992377 DOI: 10.1016/j.bbagrm.2008.09.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 08/21/2008] [Accepted: 09/22/2008] [Indexed: 01/12/2023]
Abstract
The genomic developmental program operates mainly through the regulated expression of genes encoding transcription factors and signaling pathways. Complex networks of regulatory genetic interactions control developmental cell specification and fates. Development in the zebrafish, Danio rerio, has been studied extensively and large amounts of experimental data, including information on spatial and temporal gene expression patterns, are available. A wide variety of maternal and zygotic regulatory factors and signaling pathways have been discovered in zebrafish, and these provide a useful starting point for reconstructing the gene regulatory networks (GRNs) underlying development. In this review, we describe in detail the genetic regulatory subcircuits responsible for dorsoanterior-ventroposterior patterning and endoderm formation. We describe a number of regulatory motifs, which appear to act as the functional building blocks of the GRNs. Different positive feedback loops drive the ventral and dorsal specification processes. Mutual exclusivity in dorsal-ventral polarity in zebrafish is governed by intra-cellular cross-inhibiting GRN motifs, including vent/dharma and tll1/chordin. The dorsal-ventral axis seems to be determined by competition between two maternally driven positive-feedback loops (one operating on Dharma, the other on Bmp). This is the first systematic approach aimed at developing an integrated model of the GRNs underlying zebrafish development. Comparison of GRNs' organizational motifs between different species will provide insights into developmental specification and its evolution. The online version of the zebrafish GRNs can be found at http://www.zebrafishGRNs.org.
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Affiliation(s)
- Tzu-Min Chan
- Division of Molecular and Genomic Medicine, National Health Research Institute, Taiwan, Republic of China
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15
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The words of the regulatory code are arranged in a variable manner in highly conserved enhancers. Dev Biol 2008; 318:366-77. [PMID: 18455719 DOI: 10.1016/j.ydbio.2008.03.034] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 03/17/2008] [Accepted: 03/20/2008] [Indexed: 01/29/2023]
Abstract
The cis-regulatory regions of many developmental regulators and transcription factors are believed to be highly conserved in the genomes of vertebrate species, suggesting specific regulatory mechanisms for these gene classes. We functionally characterized five notochord enhancers, whose sequence is highly conserved, and systematically mutated two of them. Two subregions were identified to be essential for expression in the notochord of the zebrafish embryo. Synthetic enhancers containing the two essential regions in front of a TATA-box drive expression in the notochord while concatemerization of the subregions alone is not sufficient, indicating that the combination of the two sequence elements is required for notochord expression. Both regions are present in the five functionally characterized notochord enhancers. However, the position, the distance and relative orientation of the two sequence motifs can vary substantially within the enhancer sequences. This suggests that the regulatory grammar itself does not dictate the high evolutionary conservation between these orthologous cis-regulatory sequences. Rather, it represents a less well-conserved layer of sequence organization within these sequences.
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16
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Sequential and cooperative action of Fgfs and Shh in the zebrafish retina. Dev Biol 2008; 314:200-14. [DOI: 10.1016/j.ydbio.2007.11.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 11/19/2007] [Accepted: 11/27/2007] [Indexed: 11/23/2022]
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17
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Sanges R, Kalmar E, Claudiani P, D'Amato M, Muller F, Stupka E. Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome Biol 2007; 7:R56. [PMID: 16859531 PMCID: PMC1779573 DOI: 10.1186/gb-2006-7-7-r56] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2006] [Revised: 04/05/2006] [Accepted: 06/27/2006] [Indexed: 02/06/2023] Open
Abstract
Alignment of orthologous vertebrate loci reveals that a significant proportion of conserved cis-regulatory elements have undergone shuffling during evolution. Background All vertebrates share a remarkable degree of similarity in their development as well as in the basic functions of their cells. Despite this, attempts at unearthing genome-wide regulatory elements conserved throughout the vertebrate lineage using BLAST-like approaches have thus far detected noncoding conservation in only a few hundred genes, mostly associated with regulation of transcription and development. Results We used a unique combination of tools to obtain regional global-local alignments of orthologous loci. This approach takes into account shuffling of regulatory regions that are likely to occur over evolutionary distances greater than those separating mammalian genomes. This approach revealed one order of magnitude more vertebrate conserved elements than was previously reported in over 2,000 genes, including a high number of genes found in the membrane and extracellular regions. Our analysis revealed that 72% of the elements identified have undergone shuffling. We tested the ability of the elements identified to enhance transcription in zebrafish embryos and compared their activity with a set of control fragments. We found that more than 80% of the elements tested were able to enhance transcription significantly, prevalently in a tissue-restricted manner corresponding to the expression domain of the neighboring gene. Conclusion Our work elucidates the importance of shuffling in the detection of cis-regulatory elements. It also elucidates how similarities across the vertebrate lineage, which go well beyond development, can be explained not only within the realm of coding genes but also in that of the sequences that ultimately govern their expression.
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Affiliation(s)
- Remo Sanges
- Telethon Institute of Genetics and Medicine, Via P. Castellino, 80131 Napoli, Italy
| | - Eva Kalmar
- Institute of Toxicology and Genetics, Forschungzenbrum, Karlsruhe, Postfach 3640, D-76021 Karlsruhe, Germany
| | - Pamela Claudiani
- Telethon Institute of Genetics and Medicine, Via P. Castellino, 80131 Napoli, Italy
| | - Maria D'Amato
- Telethon Institute of Genetics and Medicine, Via P. Castellino, 80131 Napoli, Italy
| | - Ferenc Muller
- Institute of Toxicology and Genetics, Forschungzenbrum, Karlsruhe, Postfach 3640, D-76021 Karlsruhe, Germany
| | - Elia Stupka
- Telethon Institute of Genetics and Medicine, Via P. Castellino, 80131 Napoli, Italy
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18
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Dubourg C, Bendavid C, Pasquier L, Henry C, Odent S, David V. Holoprosencephaly. Orphanet J Rare Dis 2007; 2:8. [PMID: 17274816 PMCID: PMC1802747 DOI: 10.1186/1750-1172-2-8] [Citation(s) in RCA: 263] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 02/02/2007] [Indexed: 12/14/2022] Open
Abstract
Holoprosencephaly (HPE) is a complex brain malformation resulting from incomplete cleavage of the prosencephalon, occurring between the 18th and the 28th day of gestation and affecting both the forebrain and the face. It is estimated to occur in 1/16,000 live births and 1/250 conceptuses. Three ranges of increasing severity are described: lobar, semi-lobar and alobar HPE. Another milder subtype of HPE called middle interhemispheric variant (MIHF) or syntelencephaly is also reported. In most of the cases, facial anomalies are observed in HPE, like cyclopia, proboscis, median or bilateral cleft lip/palate in severe forms, ocular hypotelorism or solitary median maxillary central incisor in minor forms. These latter midline defects can occur without the cerebral malformations and then are called microforms. Children with HPE have many medical problems: developmental delay and feeding difficulties, epilepsy, instability of temperature, heart rate and respiration. Endocrine disorders like diabetes insipidus, adrenal hypoplasia, hypogonadism, thyroid hypoplasia and growth hormone deficiency are frequent. To date, seven genes have been positively implicated in HPE: Sonic hedgehog (SHH), ZIC2, SIX3, TGIF, PTCH, GLI2 and TDGF1. A molecular diagnosis can be performed by gene sequencing and allele quantification for the four main genes SHH, ZIC2, SIX3 and TGIF. Major rearrangements of the subtelomeres can also be identified by multiplex ligation-dependent probe amplification (MLPA). Nevertheless, in about 70% of cases, the molecular basis of the disease remains unknown, suggesting the existence of several other candidate genes or environmental factors. Consequently, a "multiple-hit hypothesis" of genetic and/or environmental factors (like maternal diabetes) has been proposed to account for the extreme clinical variability. In a practical approach, prenatal diagnosis is based on ultrasound and magnetic resonance imaging (MRI) rather than on molecular diagnosis. Treatment is symptomatic and supportive, and requires a multidisciplinary management. Child outcome depends on the HPE severity and the medical and neurological complications associated. Severely affected children have a very poor prognosis. Mildly affected children may exhibit few symptoms and may live a normal life.
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Affiliation(s)
- Christèle Dubourg
- UMR 6061 CNRS, Institut de Génétique et Développement de Rennes, Université de Rennes1, IFR 140 GFAS, Faculté de Médecine, Rennes, 35000, France
- Laboratoire de Génétique Moléculaire et Hormonologie, Centre Hospitalier et Universitaire de Pontchaillou, Rennes, 35000, France
| | - Claude Bendavid
- UMR 6061 CNRS, Institut de Génétique et Développement de Rennes, Université de Rennes1, IFR 140 GFAS, Faculté de Médecine, Rennes, 35000, France
- Laboratoire de Génétique Moléculaire et Hormonologie, Centre Hospitalier et Universitaire de Pontchaillou, Rennes, 35000, France
| | - Laurent Pasquier
- Service de Génétique Médicale, Hôpital Sud, Rennes, 35000, France
| | - Catherine Henry
- Laboratoire de Cytogénétique, Centre Hospitalier et Universitaire de Pontchaillou, Rennes, 35000, France
| | - Sylvie Odent
- Service de Génétique Médicale, Hôpital Sud, Rennes, 35000, France
| | - Véronique David
- UMR 6061 CNRS, Institut de Génétique et Développement de Rennes, Université de Rennes1, IFR 140 GFAS, Faculté de Médecine, Rennes, 35000, France
- Laboratoire de Génétique Moléculaire et Hormonologie, Centre Hospitalier et Universitaire de Pontchaillou, Rennes, 35000, France
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19
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Chiou MJ, Chao TT, Wu JL, Kuo CM, Chen JY. The physiological role of CTGF/CCN2 in zebrafish notochond development and biological analysis of the proximal promoter region. Biochem Biophys Res Commun 2006; 349:750-8. [PMID: 16950203 DOI: 10.1016/j.bbrc.2006.08.095] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2006] [Accepted: 08/17/2006] [Indexed: 11/16/2022]
Abstract
During mouse embryogenesis, CTGF/CCN2 is expressed in zones containing hypertrophic chondroctyes and calcifying cartilage such as long bones, ribs, vertebral column, and phalanges. But in fish, its expression is yet unclear. Development of the vertebrae is morphologically similar among vertebrates, indicating that the underlying mechanism regulating the process is highly conserved during evolution. Analysis of 3.2kb of the CTGF/CCN2 proximal promoter sequence revealed a consensus TATAA box, putative AP1, Brn-2, CdxA, C/EBP alpha, C/EBP beta, C-Ets-, delta E, HFH-2, and HSF2 binding sites. Transient expression experiments with a 5'-deletion revealed at least 4 regulatory regions in the zebrafish CTGF/CCN2 gene, 2 with a stimulatory effect on transcription and 2 with an apparent inhibitory effect after IGF-I treatment in the ZFL cell line. To study the promoter-specific expression, we constructed a series of CTGF/CCN2 (3.0-, 2.5-, 2.0-, 1.5-, 1.0-, and 0.4-kb) promoter-driven green fluorescent protein (GFP) fragments encoding the GFP cDNA transgene which was microinjected into zebrafish embryos. Morphological studies of transgenic zebrafish indicated that the CTGF/CCN2 promoter-driven GFP transcripts appeared in the notochord. Targeted knockdown of the CTGF/CCN2 gene by two antisense morpholino oligonucleotides resulted in disruptions to notochord development. From a comparative point of view, this study of the CTGF/CCN2 gene in zebrafish may correlate well with those previously published on the mouse. These molecular results suggest that CTGF/CCN2 plays an important role in notochord development and is required for general embryonic development.
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Affiliation(s)
- Ming-Jyun Chiou
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Jiaushi, Ilan 262, Taiwan, ROC
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20
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Ezin AM, Skoglund P, Keller R. The presumptive floor plate (notoplate) induces behaviors associated with convergent extension in medial but not lateral neural plate cells of Xenopus. Dev Biol 2006; 300:670-86. [PMID: 17034782 DOI: 10.1016/j.ydbio.2006.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2006] [Revised: 08/03/2006] [Accepted: 09/05/2006] [Indexed: 10/24/2022]
Abstract
In previous work (Elul, T., Keller, R., 2000. Monopolar protrusive activity: a new morphogenic cell behavior in the neural plate dependent on vertical interactions with the mesoderm in Xenopus. Dev. Biol. 224, 3-19; Ezin, A.M., Skoglund, P. Keller, R. 2003. The midline (notochord and notoplate) patterns the cell motility underlying convergence and extension of the Xenopus neural plate. Dev. Biol. 256, 100-114), the midline tissues of notochord and overlying notoplate were found to induce the monopolar, medially directed protrusive activity of deep neural cells. This behavior is thought to drive the mediolateral intercalation and convergent extension of the neural plate in Xenopus. Here we address the issue of whether the notochord, the notoplate, or both is essential for this induction. Our strategy was to remove the notochord, leaving the overlying notoplate intact, and determine whether it alone can induce the monopolar, medially directed cell behavior. We first establish that the notoplate (presumptive floor plate), when separated from the underlying notochord in the early neurula (stages 13-14), will independently mature into a floor plate as assayed three criteria: (1) continued expression of an early marker, sonic hedgehog, and a later, marker, F-spondin; (2) the display of the notoplate/floor plate-specific randomly oriented protrusive activity; (3) the characteristic lack of mixing of cells between the notoplate and lateral neural plate. Under these conditions, in the presence of a mature notoplate/floor plate and in the absence of the notochord, the characteristic monopolar, medially directed behavior occurred, but only locally near the midline. These results show that the notoplate/floor plate capacity to induce the medially directed motility is limited in range, and they suggest that the notochord is necessary for the normally observed longer range induction in lateral neural plate cells. This work helps to further the understanding of molecular and tissue interactions required for convergent extension.
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Affiliation(s)
- Akouavi M Ezin
- Department of Biology, Gilmer Hall, University of Virginia, Charlottesville, VA 22903, USA.
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21
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Chatterjee B, Chin AJ, Valdimarsson G, Finis C, Sonntag JM, Choi BY, Tao L, Balasubramanian K, Bell C, Krufka A, Kozlowski DJ, Johnson RG, Lo CW. Developmental regulation and expression of the zebrafish connexin43 gene. Dev Dyn 2005; 233:890-906. [PMID: 15895415 DOI: 10.1002/dvdy.20426] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We cloned and sequenced the zebrafish (Danio rerio) connexin43 (Cx43alpha1) gene. The predicted protein sequence shows a high degree of sequence conservation. Transcript analyses revealed multiple transcription start sites and a potential alternative transcript encoding a N-terminally truncated Cx43alpha1 protein. Maternal Cx43alpha1 transcripts were detected, with zygotic expression initiated before gastrulation. In situ hybridization revealed many Cx43alpha1 expression domains, including the notochord and brain, heart and vasculature, many resembling patterns seen in mammalian embryos. Of interest, a reporter construct under control of the mouse Cx43alpha1 promoter was observed to drive green fluorescent protein expression in zebrafish embryos in domains mimicking the native Cx43alpha1 expression pattern in fish and mice. Sequence comparison between the mouse and zebrafish Cx43alpha1 promoter sequences showed the conservation of several transcription factor motifs, which otherwise shared little overall sequence homology. The conservation of protein sequence and developmental gene regulation would suggest that Cx43alpha1 gap junctions are likely to have conserved roles in vertebrate embryonic development.
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Affiliation(s)
- Bishwanath Chatterjee
- Laboratory of Developmental Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
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22
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Abstract
Notochord, floor plate, and in anamniotes hypochord, are vertebrate embryonic midline structures that are the sources of molecules that pattern the nervous system, somites, and dorsal aorta. Midline precursor cells arise from the dorsal organizer during gastrulation, and Notch signaling is an important regulator of midline cell fate specification. To understand fully how Notch signaling regulates midline development, we investigated the role of potential Notch target genes. We show here that midline precursors express her9, a member of the hairy/Enhancer of split gene family. Although her9 inhibits notochord development and promotes floor plate specification, her9 expression in floor plate cells appears not to require Notch signaling. We show that, instead, her9 is a downstream effector of Nodal signaling for floor plate specification.
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Affiliation(s)
- Andrew J Latimer
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235-1634, USA
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23
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Abstract
One of the key organizers in the CNS is the floor plate - a group of cells that is responsible for instructing neural cells to acquire distinctive fates, and that has an important role in establishing the elaborate neuronal networks that underlie the function of the brain and spinal cord. In recent years, considerable controversy has arisen over the mechanism by which floor plate cells form. Here, we describe recent evidence that indicates that discrete populations of floor plate cells, with characteristic molecular properties, form in different regions of the neuraxis, and we discuss data that imply that the mode of floor plate induction varies along the anteroposterior axis.
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Affiliation(s)
- Marysia Placzek
- Centre for Developmental and Biomedical Genetics, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK.
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24
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Norton WH, Mangoli M, Lele Z, Pogoda HM, Diamond B, Mercurio S, Russell C, Teraoka H, Stickney HL, Rauch GJ, Heisenberg CP, Houart C, Schilling TF, Frohnhoefer HG, Rastegar S, Neumann CJ, Gardiner RM, Strähle U, Geisler R, Rees M, Talbot WS, Wilson SW. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphé neurones and cranial motoneurones. Development 2005; 132:645-58. [PMID: 15677724 PMCID: PMC2790417 DOI: 10.1242/dev.01611] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this study, we elucidate the roles of the winged-helix transcription factor Foxa2 in ventral CNS development in zebrafish. Through cloning of monorail (mol), which we find encodes the transcription factor Foxa2, and phenotypic analysis of mol-/- embryos, we show that floorplate is induced in the absence of Foxa2 function but fails to further differentiate. In mol-/- mutants, expression of Foxa and Hh family genes is not maintained in floorplate cells and lateral expansion of the floorplate fails to occur. Our results suggest that this is due to defects both in the regulation of Hh activity in medial floorplate cells as well as cell-autonomous requirements for Foxa2 in the prospective laterally positioned floorplate cells themselves. Foxa2 is also required for induction and/or patterning of several distinct cell types in the ventral CNS. Serotonergic neurones of the raphenucleus and the trochlear motor nucleus are absent in mol-/- embryos, and oculomotor and facial motoneurones ectopically occupy ventral CNS midline positions in the midbrain and hindbrain. There is also a severe reduction of prospective oligodendrocytes in the midbrain and hindbrain. Finally, in the absence of Foxa2, at least two likely Hh pathway target genes are ectopically expressed in more dorsal regions of the midbrain and hindbrain ventricular neuroepithelium, raising the possibility that Foxa2 activity may normally be required to limit the range of action of secreted Hh proteins.
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Affiliation(s)
- Will H. Norton
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Maryam Mangoli
- Department of Paediatrics and Child Health, Royal Free and University College Medical School, University College London, 5 University Street, London WC1E 6JJ, UK
| | - Zsolt Lele
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Hans-Martin Pogoda
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center B315, 279 Campus Drive, Stanford, CA 94305-5329, USA
| | - Brianne Diamond
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center B315, 279 Campus Drive, Stanford, CA 94305-5329, USA
| | - Sara Mercurio
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Claire Russell
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Hiroki Teraoka
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Heather L. Stickney
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center B315, 279 Campus Drive, Stanford, CA 94305-5329, USA
| | - Gerd-Jörg Rauch
- Department 3 – Genetics, Max-Planck-Institut für Entwicklungsbiologie, Spemannstrasse 35/III, D-72076 Tübingen, Germany
| | | | - Corinne Houart
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Thomas F. Schilling
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
| | - Hans-Georg Frohnhoefer
- Department 3 – Genetics, Max-Planck-Institut für Entwicklungsbiologie, Spemannstrasse 35/III, D-72076 Tübingen, Germany
| | - Sepand Rastegar
- IGBMC, CNRS/INSERM/ULP, Parc d’Innovation, BP 10142, 67404 Illkirch Cedex, C.U. de Strasbourg, France
| | | | - R. Mark Gardiner
- Department of Paediatrics and Child Health, Royal Free and University College Medical School, University College London, 5 University Street, London WC1E 6JJ, UK
| | - Uwe Strähle
- Universität Heidelberg und Institut für Toxikologie und Genetik, Forschungszentrum Karlsruhe, Postfach 3640, Germany
| | - Robert Geisler
- Department 3 – Genetics, Max-Planck-Institut für Entwicklungsbiologie, Spemannstrasse 35/III, D-72076 Tübingen, Germany
| | - Michelle Rees
- Department of Paediatrics and Child Health, Royal Free and University College Medical School, University College London, 5 University Street, London WC1E 6JJ, UK
| | - William S. Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center B315, 279 Campus Drive, Stanford, CA 94305-5329, USA
| | - Stephen W. Wilson
- Department of Anatomy and Developmental Biology, UCL, Gower Street, London WC1E 6BT, UK
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25
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Pohl BS, Knöchel W. Of Fox and Frogs: Fox (fork head/winged helix) transcription factors in Xenopus development. Gene 2005; 344:21-32. [PMID: 15656969 DOI: 10.1016/j.gene.2004.09.037] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Revised: 09/09/2004] [Accepted: 09/28/2004] [Indexed: 01/03/2023]
Abstract
Transcription factors of the Fox (fork head box) family have been found in all metazoan organisms. They are characterised by an evolutionary conserved DNA-binding domain of winged helix structure. In the South African clawed frog, Xenopus laevis, more than 30 Fox genes have been found so far. This review summarises our present knowledge regarding the general structure and common features of the fork head box and will then characterise Fox genes that have been described in Xenopus. Special attention was paid to the temporal and spatial expression patterns during early embryonic development. For some of these genes, the molecular mechanisms leading to their regulation after the onset of zygotic transcription are known. We also report on functional aspects including target gene regulation, cell or tissue specification and interference with the cell cycle. Finally, Fox proteins serve as mediators of signalling pathways and they might function as checkpoint molecules for the cross-regulatory interactions of different intracellular signal transduction chains.
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Affiliation(s)
- Barbara S Pohl
- Abteilung Biochemie, Universität Ulm, Albert-Einstein-Allee 11, Ulm D-89081, Germany
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26
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Liu Y, Festing M, Thompson JC, Hester M, Rankin S, El-Hodiri HM, Zorn AM, Weinstein M. Smad2 and Smad3 coordinately regulate craniofacial and endodermal development. Dev Biol 2004; 270:411-26. [PMID: 15183723 DOI: 10.1016/j.ydbio.2004.03.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Revised: 02/27/2004] [Accepted: 03/02/2004] [Indexed: 11/30/2022]
Abstract
Ligands of the transforming growth factor-beta (TGF-beta) superfamily are involved in numerous developmental and disease processes. TGF-beta, activins, and nodal ligands operate through the highly homologous Smad2 and Smad3 intracellular mediators. Smad2 mutants exhibit early embryonic lethality, while Smad3 mutants are viable, but show a plethora of postnatal phenotypes, including immune dysfunction and skeletal abnormalities. Previously, we have shown that the Smad2 and Smad3 genes function cooperatively during liver morphogenesis. Here we show that Smad2 and Smad3 are required at a full dosage for normal embryonic development. Animals lacking one allele of each gene exhibit a variably penetrant phenotype in which structures in the anterior and ventral midline are reduced or lost; additionally, we demonstrate that this craniofacial defect and the previously reported hepatic phenotypes are both due to defects in the definitive endoderm. A reduction of endodermal gene expression as well as a failure to displace the visceral endoderm occurs despite the formation of a normal foregut pocket. This precedes any defects in anterior patterning and likely causes the abnormalities observed in craniofacial and midline development, as well as hepatogenesis.
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Affiliation(s)
- Ye Liu
- Program in Molecular, Cellular, and Developmental Biology, Ohio State University, Columbus, OH 43210-1392, USA
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27
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Affiliation(s)
- Jennifer O Liang
- Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21210, USA
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28
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Dickmeis T, Plessy C, Rastegar S, Aanstad P, Herwig R, Chalmel F, Fischer N, Strähle U. Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo. Genome Res 2004; 14:228-38. [PMID: 14718378 PMCID: PMC327098 DOI: 10.1101/gr.1819204] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for the identification of regulatory sequences in genomes. We tested this approach to identify regulatory sequences that control expression in the midline of the zebrafish embryo. We first isolated a set of genes that are coexpressed in the midline of the zebrafish embryo during somitogenesis stages by gene array analysis and subsequent rescreens by in situ hybridization. We subjected 45 of these genes to Compare and DotPlot analysis to detect conserved sequences in noncoding regions of orthologous loci in the zebrafish and Takifugu genomes. The regions of homology that were scored in nonconserved regions were inserted into expression vectors and tested for their regulatory activity by transient transgenesis in the zebrafish embryo. We identified one conserved region from the connective tissue growth factor gene (ctgf), which was able to drive expression in the midline of the embryo. This region shares sequence similarity with other floor plate/notochord-specific regulatory regions. Our results demonstrate that an unbiased comparative approach is a relevant method for the identification of tissue-specific cis-regulatory sequences in the zebrafish embryo.
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Affiliation(s)
- Thomas Dickmeis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 10142, F-67404 Illkirch Cedex, C.U. de Strasbourg, France
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29
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Abstract
Zebrafish embryos represent an ideal vertebrate model organism for noninvasive intravital imaging because of their optical clarity, external embryogenesis, and fast development. Many different labeling techniques have been adopted from other model organisms or newly developed to address a wealth of different developmental questions directly inside the living organism. The parallel advancements in the field of optical imaging let us now observe dynamic processes at the cellular and subcellular resolution. Combined with the repertoire of available surgical and genetic manipulations, zebrafish embryos provide the powerful and almost unique possibility to observe the interplay of molecular signals with cellular, morphological, and behavioral changes directly within a living and developing vertebrate organism. A bright future for zebrafish is yet to come, let there be light.
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Affiliation(s)
- Reinhard W Köster
- GSF-National Research Center for Environment and Health, Institute of Developmental Genetics, 85764 Neuherberg, Germany
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30
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Tian J, Yam C, Balasundaram G, Wang H, Gore A, Sampath K. A temperature-sensitive mutation in the nodal-related gene cyclops reveals that the floor plate is induced during gastrulation in zebrafish. Development 2003; 130:3331-42. [PMID: 12783802 DOI: 10.1242/dev.00544] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The floor plate, a specialized group of cells in the ventral midline of the neural tube of vertebrates, plays crucial roles in patterning the central nervous system. Recent work from zebrafish, chick, chick-quail chimeras and mice to investigate the development of the floor plate have led to several models of floor-plate induction. One model suggests that the floor plate is formed by inductive signalling from the notochord to the overlying neural tube. The induction is thought to be mediated by notochord-derived Sonic hedgehog (Shh), a secreted protein, and requires direct cellular contact between the notochord and the neural tube. Another model proposes a role for the organizer in generating midline precursor cells that produce floor plate cells independent of notochord specification, and proposes that floor plate specification occurs early, during gastrulation. We describe a temperature-sensitive mutation that affects the zebrafish Nodal-related secreted signalling factor, Cyclops, and use it to address the issue of when the floor plate is induced in zebrafish. Zebrafish cyclops regulates the expression of shh in the ventral neural tube. Although null mutations in cyclops result in the lack of the medial floor plate, embryos homozygous for the temperature-sensitive mutation have floor plate cells at the permissive temperature and lack floor plate cells at the restrictive temperature. We use this mutant allele in temperature shift-up and shift-down experiments to answer a central question pertaining to the timing of vertebrate floor plate induction. Abrogation of Cyc/Nodal signalling in the temperature-sensitive mutant embryos at various stages indicates that the floor plate in zebrafish is induced early in development, during gastrulation. In addition, continuous Cyclops signalling is required through gastrulation for a complete ventral neural tube throughout the length of the neuraxis. Finally, by modulation of Nodal signalling levels in mutants and in ectopic overexpression experiments, we show that, similar to the requirements for prechordal plate mesendoderm fates, uninterrupted and high levels of Cyclops signalling are required for induction and specification of a complete ventral neural tube.
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Affiliation(s)
- Jing Tian
- Laboratory of Fish Embryology, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
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31
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Winkler C, Schafer M, Duschl J, Schartl M, Volff JN. Functional divergence of two zebrafish midkine growth factors following fish-specific gene duplication. Genome Res 2003; 13:1067-81. [PMID: 12743018 PMCID: PMC403662 DOI: 10.1101/gr.1097503] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In mammals, the unique midkine (mdk) gene encodes a secreted heparin-binding growth factor with neurotrophic activity. Here, we show the presence of two functional mdk genes named mdka and mdkb in zebrafish and rainbow trout. Both midkine proteins are clearly different from the related pleiotrophin, which was also identified in zebrafish and other fishes. Zebrafish mdka and mdkb genes map to linkage groups LG7 and LG25, respectively, both presenting synteny to human chromosome 11, in which the unique human ortholog mdk is located. At least four other genes unique in mammals are also present as duplicates on LG7 and LG25. Phylogenetic and divergence analyses suggested that LG7/LG25 paralogs including mdka and mdkb have been formed at approximately the same time, early during the evolution of the fish lineage. Hence, zebrafish and rainbow trout mdka and mdkb might have been generated by an ancient block duplication, and might be remnants of the proposed fish-specific whole-genome duplication. In contrast to the ubiquitous expression of their mammalian counterpart, zebrafish mdka and mdkb are expressed in spatially restricted, mostly nonoverlapping patterns during embryonic development and strongly in distinct domains in the adult brain. Ectopic ubiquitous expression of both mdk genes in early zebrafish embryos caused completely distinct effects on neural crest and floorplate development. These data indicate that mdka and mdkb underwent functional divergence after duplication. This provides an outstanding model to analyze the molecular mechanisms that lead to differences in pathways regulating the formation of homologous embryonic structures in different vertebrates.
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Affiliation(s)
- Christoph Winkler
- Department of Physiological Chemistry I, Biocenter, University of Wuerzburg, 97074 Wuerzburg, Germany.
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32
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Abstract
The ability of an animal to carry out its normal behavioral repertoire requires generation of an enormous diversity of neurons and glia. The relative simplicity of the spinal cord makes this an especially attractive part of the nervous system for addressing questions about the development of vertebrate neural specification and function. The last decade has witnessed an explosion in our understanding of spinal cord development and the functional interactions among spinal cord neurons and glia. Cellular, genetic, molecular, physiological and behavioral studies in zebrafish have all been important in providing insights into questions that remained unanswered by studies from other vertebrate model organisms. This is the case because many zebrafish spinal neurons can be individually identified and followed over time in living embryos and larvae. In this review, we discuss what is currently known about the cellular, genetic and molecular mechanisms involved in specifying distinct cell types in the zebrafish spinal cord and how these cells establish the functional circuitry that mediates particular behaviors. We start by describing the early signals and morphogenetic movements that form the nervous system, and in particular, the spinal cord. We then provide an overview of the cell types within the spinal cord and describe how they are specified and patterned. We begin ventrally with floor plate and proceed dorsally, through motoneurons and oligodendrocytes, interneurons, astrocytes and radial glia, spinal sensory neurons and neural crest. We next describe axon pathfinding of spinal neurons. Finally, we discuss the roles of particular spinal cord neurons in specific behaviors.
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Affiliation(s)
- Katharine E Lewis
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97403, USA.
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