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Siniscalco AM, Perera RP, Greenslade JE, Veeravenkatasubramanian H, Masters A, Doll HM, Raj B. Barcoding Notch signaling in the developing brain. Development 2024; 151:dev203102. [PMID: 39575683 DOI: 10.1242/dev.203102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 11/10/2024] [Indexed: 11/27/2024]
Abstract
Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control, while the recorder obtains mutations in ancestral cells where Notch is active. We combine SABER-seq with an expanded juvenile brain atlas to identify cell types derived from Notch-active founders. Our data reveal rare examples where differential Notch activities in ancestral progenitors are detected in terminally differentiated neuronal subtypes. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.
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Affiliation(s)
- Abigail M Siniscalco
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Roshan Priyarangana Perera
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jessie E Greenslade
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Aiden Masters
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hannah M Doll
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bushra Raj
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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2
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Neuromasts and Olfactory Organs of Zebrafish Larvae Represent Possible Sites of SARS-CoV-2 Pseudovirus Host Cell Entry. J Virol 2022; 96:e0141822. [PMID: 36448804 PMCID: PMC9769390 DOI: 10.1128/jvi.01418-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the acute respiratory disease coronavirus disease 2019 (COVID-19), which has resulted in millions of deaths globally. Here, we explored the mechanism of host cell entry of a luciferase-ZsGreen spike (SARS-CoV-2)-pseudotyped lentivirus using zebrafish embryos/larvae as an in vivo model. Successful pseudovirus entry was demonstrated via the expression of the luciferase (luc) gene, which was validated by reverse transcription-PCR (RT-PCR). Treatment of larvae with chloroquine (a broad-spectrum viral inhibitor that blocks membrane fusion) or bafilomycin A1 (a specific inhibitor of vacuolar proton ATPases, which blocks endolysosomal trafficking) significantly reduced luc expression, indicating the possible involvement of the endolysosomal system in the viral entry mechanism. The pharmacological inhibition of two-pore channel (TPC) activity or use of the tpcn2dhkz1a mutant zebrafish line also led to diminished luc expression. The localized expression of ACE2 and TPC2 in the anterior neuromasts and the forming olfactory organs was demonstrated, and the occurrence of endocytosis in both locations was confirmed. Together, our data indicate that zebrafish embryos/larvae are a viable and tractable model to explore the mechanism of SARS-CoV-2 host cell entry, that the peripheral sense organs are a likely site for viral host cell entry, and that TPC2 plays a key role in the translocation of the virus through the endolysosomal system. IMPORTANCE Despite the development of effective vaccines to combat the COVID-19 pandemic, which help prevent the most life-threatening symptoms, full protection cannot be guaranteed, especially with the emergence of new viral variants. Moreover, some resistance to vaccination remains in certain age groups and cultures. As such, there is an urgent need for the development of new strategies and therapies to help combat this deadly disease. Here, we provide compelling evidence that the peripheral sensory organs of zebrafish possess several key components required for SARS-CoV-2 host cell entry. The nearly transparent larvae provide a most amenable complementary platform to investigate the key steps of viral entry into host cells, as well as its spread through the tissues and organs. This will help in the identification of key viral entry steps for therapeutic intervention, provide an inexpensive model for screening novel antiviral compounds, and assist in the development of new and more effective vaccines.
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Carstensen MB, Medvetzky A, Weinberger A, Driever W, Gothilf Y, Rath MF. Genetic ablation of the Bsx homeodomain transcription factor in zebrafish: Impact on mature pineal gland morphology and circadian behavior. J Pineal Res 2022; 72:e12795. [PMID: 35249239 PMCID: PMC9285933 DOI: 10.1111/jpi.12795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
The pineal gland is a neuroendocrine structure in the brain, which produces and secretes the hormone melatonin at nighttime and is considered a key element in the circadian clock system. Early morphogenesis of the gland is controlled by a number of transcription factors, some of which remain active in adult life. One of these is the brain-specific homeobox (Bsx), a highly conserved homeodomain transcription factor with a developmental role in the pineal gland of several species, including zebrafish, and regulatory roles in mature pinealocytes of the rat. To determine the role of Bsx in circadian biology, we here examined the effects of a bsx loss-of-function mutation on the pineal gland in adult zebrafish and on behavioral circadian rhythms in larvae. In pineal cell type-specific Gfp/Egfp reporter zebrafish lines, we did not detect fluorescence signals in the pineal area of homozygous (bsx-/- ) mutants. Interestingly, a nonpigmented area on the dorsal surface of the head above the gland, known as the pineal window, was pigmented in the homozygous mutants. Furthermore, a structure corresponding to the pineal gland was not detectable in the midline of the adult brain in histological sections analyzed by Nissl staining and S-antigen immunohistochemistry. Moreover, the levels of pineal transcripts were greatly reduced in bsx-/- mutants, as revealed by quantitative real-time polymerase chain reaction analysis. Notably, analysis of locomotor activity at the larval stage revealed altered circadian rhythmicity in the bsx mutants with periods and phases similar to wildtype, but severely reduced amplitudes in locomotor activity patterns. Thus, Bsx is essential for full development of the pineal gland, with its absence resulting in a phenotype of morphological pineal gland ablation and disrupted circadian behavior.
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Affiliation(s)
- Mikkel Bloss Carstensen
- Department of Neuroscience, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Adar Medvetzky
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Alon Weinberger
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
| | - Wolfgang Driever
- Developmental Biology, Institute Biology, Faculty of BiologyAlbert Ludwig University of FreiburgFreiburgGermany
| | - Yoav Gothilf
- School of Neurobiology, Biochemistry and Biophysics, Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael
- Sagol School of NeuroscienceTel Aviv UniversityTel AvivIsrael
| | - Martin Fredensborg Rath
- Department of Neuroscience, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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4
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Engerer P, Petridou E, Williams PR, Suzuki SC, Yoshimatsu T, Portugues R, Misgeld T, Godinho L. Notch-mediated re-specification of neuronal identity during central nervous system development. Curr Biol 2021; 31:4870-4878.e5. [PMID: 34534440 DOI: 10.1016/j.cub.2021.08.049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 06/27/2021] [Accepted: 08/18/2021] [Indexed: 11/27/2022]
Abstract
Neuronal identity has long been thought of as immutable, so that once a cell acquires a specific fate, it is maintained for life.1 Studies using the overexpression of potent transcription factors to experimentally reprogram neuronal fate in the mouse neocortex2,3 and retina4,5 have challenged this notion by revealing that post-mitotic neurons can switch their identity. Whether fate reprogramming is part of normal development in the central nervous system (CNS) is unclear. While there are some reports of physiological cell fate reprogramming in invertebrates,6,7 and in the vertebrate peripheral nervous system,8 endogenous fate reprogramming in the vertebrate CNS has not been documented. Here, we demonstrate spontaneous fate re-specification in an interneuron lineage in the zebrafish retina. We show that the visual system homeobox 1 (vsx1)-expressing lineage, which has been associated exclusively with excitatory bipolar cell (BC) interneurons,9-12 also generates inhibitory amacrine cells (ACs). We identify a role for Notch signaling in conferring plasticity to nascent vsx1 BCs, allowing suitable transcription factor programs to re-specify them to an AC fate. Overstimulating Notch signaling enhances this physiological phenotype so that both daughters of a vsx1 progenitor differentiate into ACs and partially differentiated vsx1 BCs can be converted into ACs. Furthermore, this physiological re-specification can be mimicked to allow experimental induction of an entirely distinct fate, that of retinal projection neurons, from the vsx1 lineage. Our observations reveal unanticipated plasticity of cell fate during retinal development.
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Affiliation(s)
- Peter Engerer
- Institute of Neuronal Cell Biology, Technische Universität München, Biedersteiner Strasse 29, 80802 Munich, Germany
| | - Eleni Petridou
- Institute of Neuronal Cell Biology, Technische Universität München, Biedersteiner Strasse 29, 80802 Munich, Germany; Graduate School of Systemic Neurosciences (GSN), Ludwig-Maximilian University of Munich, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Philip R Williams
- Institute of Neuronal Cell Biology, Technische Universität München, Biedersteiner Strasse 29, 80802 Munich, Germany
| | - Sachihiro C Suzuki
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Takeshi Yoshimatsu
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
| | - Ruben Portugues
- Institute of Neuroscience, Technische Universität München, Biedersteiner Strasse 29, 80802 Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
| | - Thomas Misgeld
- Institute of Neuronal Cell Biology, Technische Universität München, Biedersteiner Strasse 29, 80802 Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Strasse 17, 81377 Munich, Germany; Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
| | - Leanne Godinho
- Institute of Neuronal Cell Biology, Technische Universität München, Biedersteiner Strasse 29, 80802 Munich, Germany.
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Sapède D, Chaigne C, Blader P, Cau E. Functional heterogeneity in the pineal projection neurons of zebrafish. Mol Cell Neurosci 2020; 103:103468. [PMID: 32027966 DOI: 10.1016/j.mcn.2020.103468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/31/2020] [Accepted: 02/01/2020] [Indexed: 01/11/2023] Open
Abstract
The zebrafish pineal organ is a photoreceptive structure containing two main neuronal populations (photoreceptors and projections neurons). Here we describe a subpopulation of projection neurons that expresses the melanopsin gene, opn4xa. This new pineal cell type, that displays characteristics of both projection neurons and photoreceptors, share a similar dependency for BMP and Notch signalling pathways with classical non-photosensitive projection neurons (PN). Functionally, however, whereas classical, opn4xa-negative PNs display an achromatic LIGHT OFF response, the novel cell type we describe exhibit a LIGHT ON character that is elicited by green and blue light. Taken together, our data suggest a previously unanticipated heterogeneity in the projection neuron population in the zebrafish pineal organ raising the question of the importance of these differences in pineal function.
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Affiliation(s)
- Dora Sapède
- Centre de Biologie du Développement (CBD, UMR5547), Centre de Biologie Intégrative (CBI, FR 3743), Université de Toulouse, CNRS, UPS, France; IRMB, Université de Montpellier, INSERM, Montpellier, France
| | - Clair Chaigne
- Centre de Biologie du Développement (CBD, UMR5547), Centre de Biologie Intégrative (CBI, FR 3743), Université de Toulouse, CNRS, UPS, France
| | - Patrick Blader
- Centre de Biologie du Développement (CBD, UMR5547), Centre de Biologie Intégrative (CBI, FR 3743), Université de Toulouse, CNRS, UPS, France
| | - Elise Cau
- Centre de Biologie du Développement (CBD, UMR5547), Centre de Biologie Intégrative (CBI, FR 3743), Université de Toulouse, CNRS, UPS, France.
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6
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A Notch-mediated, temporal asymmetry in BMP pathway activation promotes photoreceptor subtype diversification. PLoS Biol 2019; 17:e2006250. [PMID: 30703098 PMCID: PMC6372210 DOI: 10.1371/journal.pbio.2006250] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 02/12/2019] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
Neural progenitors produce neurons whose identities can vary as a function of the time that specification occurs. Here, we describe the heterochronic specification of two photoreceptor (PhR) subtypes in the zebrafish pineal gland. We find that accelerating PhR specification by impairing Notch signaling favors the early fate at the expense of the later fate. Using in vivo lineage tracing, we show that most pineal PhRs are born from a fate-restricted progenitor. Furthermore, sister cells derived from the division of PhR-restricted progenitors activate the bone morphogenetic protein (BMP) signaling pathway at different times after division, and this heterochrony requires Notch activity. Finally, we demonstrate that PhR identity is established as a function of when the BMP pathway is activated. We propose a novel model in which division of a progenitor with restricted potential generates sister cells with distinct identities via a temporal asymmetry in the activation of a signaling pathway. A major goal in the field of developmental neurobiology is to identify the mechanisms that underly the diversification of the subtypes of neurons that are needed for the function of the nervous system. When investigating these mechanisms, time is an often-overlooked variable. Here, we show that in the zebrafish pineal gland—a neuroendocrine organ containing mostly photoreceptors (PhRs) and projection neurons—different classes of PhRs appear in a temporal sequence. In this simple system, the decision to adopt a PhR fate is driven by the activation of the bone morphogenetic protein (BMP) signaling pathway. Following the final cell division of a PhR progenitor, the sister cells normally activate the BMP pathway at different times. When Notch signaling activity is abrogated, activation of the BMP pathway occurs earlier and synchronously, which in turn favors the development of early PhR fates at the expense of later fates. We propose a model in which preventing sister cells from activating a signaling pathway in a synchronous fashion after their final division allows diversification of cell fates.
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7
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Halluin C, Madelaine R, Naye F, Peers B, Roussigné M, Blader P. Habenular Neurogenesis in Zebrafish Is Regulated by a Hedgehog, Pax6 Proneural Gene Cascade. PLoS One 2016; 11:e0158210. [PMID: 27387288 PMCID: PMC4936704 DOI: 10.1371/journal.pone.0158210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 06/13/2016] [Indexed: 11/19/2022] Open
Abstract
The habenulae are highly conserved nuclei in the dorsal diencephalon that connect the forebrain to the midbrain and hindbrain. These nuclei have been implicated in a broad variety of behaviours in humans, primates, rodents and zebrafish. Despite this, the molecular mechanisms that control the genesis and differentiation of neural progenitors in the habenulae remain relatively unknown. We have previously shown that, in zebrafish, the timing of habenular neurogenesis is left-right asymmetric and that in the absence of Nodal signalling this asymmetry is lost. Here, we show that habenular neurogenesis requires the homeobox transcription factor Pax6a and the redundant action of two proneural bHLH factors, Neurog1 and Neurod4. We present evidence that Hedgehog signalling is required for the expression of pax6a, which is in turn necessary for the expression of neurog1 and neurod4. Finally, we demonstrate by pharmacological inhibition that Hedgehog signalling is required continuously during habenular neurogenesis and by cell transplantation experiments that pathway activation is required cell autonomously. Our data sheds light on the mechanism underlying habenular development that may provide insights into how Nodal signalling imposes asymmetry on the timing of habenular neurogenesis.
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Affiliation(s)
- Caroline Halluin
- Université de Toulouse III, UPS, Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), 118 route de Narbonne, F-31062 Toulouse, France
- CNRS, CBD UMR 5547, F-31062 Toulouse, France
- Stanford University, School of Medicine, 269–279 Campus Drive, Stanford, CA 94305, United States of America
| | - Romain Madelaine
- Université de Toulouse III, UPS, Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), 118 route de Narbonne, F-31062 Toulouse, France
- CNRS, CBD UMR 5547, F-31062 Toulouse, France
- Stanford University, School of Medicine, 269–279 Campus Drive, Stanford, CA 94305, United States of America
| | - François Naye
- Unit of Molecular Biology and Genetic Engineering, University of Liège, GIGA-R, B34, Avenue de l'Hôpital 1, B-4000 Liège, Belgium
| | - Bernard Peers
- Unit of Molecular Biology and Genetic Engineering, University of Liège, GIGA-R, B34, Avenue de l'Hôpital 1, B-4000 Liège, Belgium
| | - Myriam Roussigné
- Université de Toulouse III, UPS, Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), 118 route de Narbonne, F-31062 Toulouse, France
- CNRS, CBD UMR 5547, F-31062 Toulouse, France
- * E-mail: (MR); (PB)
| | - Patrick Blader
- Université de Toulouse III, UPS, Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), 118 route de Narbonne, F-31062 Toulouse, France
- CNRS, CBD UMR 5547, F-31062 Toulouse, France
- * E-mail: (MR); (PB)
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8
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Khuansuwan S, Clanton JA, Dean BJ, Patton JG, Gamse JT. A transcription factor network controls cell migration and fate decisions in the developing zebrafish pineal complex. Development 2016; 143:2641-50. [PMID: 27317804 PMCID: PMC4958332 DOI: 10.1242/dev.131680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 06/02/2016] [Indexed: 11/20/2022]
Abstract
The zebrafish pineal complex consists of four cell types (rod and cone photoreceptors, projection neurons and parapineal neurons) that are derived from a single pineal complex anlage. After specification, parapineal neurons migrate unilaterally away from the rest of the pineal complex whereas rods, cones and projection neurons are non-migratory. The transcription factor Tbx2b is important for both the correct number and migration of parapineal neurons. We find that two additional transcription factors, Flh and Nr2e3, negatively regulate parapineal formation. Flh induces non-migratory neuron fates and limits the extent of parapineal specification, in part by activation of Nr2e3 expression. Tbx2b is positively regulated by Flh, but opposes Flh action during specification of parapineal neurons. Loss of parapineal neuron specification in Tbx2b-deficient embryos can be partially rescued by loss of Nr2e3 or Flh function; however, parapineal migration absolutely requires Tbx2b activity. We conclude that cell specification and migration in the pineal complex are regulated by a network of at least three transcription factors. Summary: Cell fate specification and migration in the zebrafish pineal complex are regulated by a network of at least three transcription factors: Tbx2b, Flh and Nr2e3.
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Affiliation(s)
- Sataree Khuansuwan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Joshua A Clanton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Benjamin J Dean
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Joshua T Gamse
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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9
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Dyer C, Linker C, Graham A, Knight R. Specification of sensory neurons occurs through diverse developmental programs functioning in the brain and spinal cord. Dev Dyn 2014; 243:1429-39. [PMID: 25179866 DOI: 10.1002/dvdy.24184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/11/2014] [Accepted: 08/18/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Vertebrates possess two populations of sensory neurons located within the central nervous system: Rohon-Beard (RB) and mesencephalic trigeminal nucleus (MTN) neurons. RB neurons are transient spinal cord neurons whilst MTN neurons are the proprioceptive cells that innervate the jaw muscles. It has been suggested that MTN and RB neurons share similarities and may have a common developmental program, but it is unclear how similar or different their development is. RESULTS We have dissected RB and MTN neuronal specification in zebrafish. We find that RB and MTN neurons express a core set of genes indicative of sensory neurons, but find these are also expressed by adjacent diencephalic neurons. Unlike RB neurons, our evidence argues against a role for the neural crest during MTN development. We additionally find that neurogenin1 function is dispensable for MTN differentiation, unlike RB cells and all other sensory neurons. Finally, we demonstrate that, although Notch signalling is involved in RB development, it is not involved in the generation of MTN cells. CONCLUSIONS Our work reveals fundamental differences between the development of MTN and RB neurons and suggests that these populations are non-homologous and thus have distinct developmental and, probably, evolutionary origins.
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Affiliation(s)
- Carlene Dyer
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London, United Kingdom
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10
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Khuansuwan S, Gamse JT. Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing. Dev Biol 2014; 395:144-53. [PMID: 25173875 DOI: 10.1016/j.ydbio.2014.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/17/2014] [Accepted: 08/17/2014] [Indexed: 02/03/2023]
Abstract
We describe a method for isolating RNA suitable for high-throughput RNA sequencing (RNA-seq) from small numbers of fluorescently labeled cells isolated from live zebrafish (Danio rerio) embryos without using costly, commercially available columns. This method ensures high cell viability after dissociation and suspension of cells and gives a very high yield of intact RNA. We demonstrate the utility of our new protocol by isolating RNA from fluorescence activated cell sorted (FAC sorted) pineal complex neurons in wild-type and tbx2b knockdown embryos at 24 hours post-fertilization. Tbx2b is a transcription factor required for pineal complex formation. We describe a bioinformatics pipeline used to analyze differential expression following high-throughput sequencing and demonstrate the validity of our results using in situ hybridization of differentially expressed transcripts. This protocol brings modern transcriptome analysis to the study of small cell populations in zebrafish.
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Affiliation(s)
- Sataree Khuansuwan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Joshua T Gamse
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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11
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Pavlou S, Astell K, Kasioulis I, Gakovic M, Baldock R, van Heyningen V, Coutinho P. Pleiotropic effects of Sox2 during the development of the zebrafish epithalamus. PLoS One 2014; 9:e87546. [PMID: 24498133 PMCID: PMC3909122 DOI: 10.1371/journal.pone.0087546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/26/2013] [Indexed: 12/01/2022] Open
Abstract
The zebrafish epithalamus is part of the diencephalon and encompasses three major components: the pineal, the parapineal and the habenular nuclei. Using sox2 knockdown, we show here that this key transcriptional regulator has pleiotropic effects during the development of these structures. Sox2 negatively regulates pineal neurogenesis. Also, Sox2 is identified as the unknown factor responsible for pineal photoreceptor prepatterning and performs this function independently of the BMP signaling. The correct levels of sox2 are critical for the functionally important asymmetrical positioning of the parapineal organ and for the migration of parapineal cells as a coherent structure. Deviations from this strict control result in defects associated with abnormal habenular laterality, which we have documented and quantified in sox2 morphants.
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Affiliation(s)
- Sofia Pavlou
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Katy Astell
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Ioannis Kasioulis
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Milica Gakovic
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Richard Baldock
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Veronica van Heyningen
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Pedro Coutinho
- Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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12
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Wu SY, de Borsetti NH, Bain EJ, Bulow CR, Gamse JT. Mediator subunit 12 coordinates intrinsic and extrinsic control of epithalamic development. Dev Biol 2014; 385:13-22. [DOI: 10.1016/j.ydbio.2013.10.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/01/2013] [Accepted: 10/23/2013] [Indexed: 12/22/2022]
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13
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Clanton JA, Hope KD, Gamse JT. Fgf signaling governs cell fate in the zebrafish pineal complex. Development 2013; 140:323-32. [PMID: 23250206 DOI: 10.1242/dev.083709] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Left-right (L-R) asymmetries in neuroanatomy exist throughout the animal kingdom, with implications for function and behavior. The molecular mechanisms that control formation of such asymmetries are beginning to be understood. Significant progress has been made by studying the zebrafish parapineal organ, a group of neurons on the left side of the epithalamus. Parapineal cells arise from the medially located pineal complex anlage and migrate to the left side of the brain. We have found that Fgf8a regulates a fate decision among anterior pineal complex progenitors that occurs just prior to the initiation of leftward migration. Cell fate analysis shows that in the absence of Fgf8a a subset of cells in the anterior pineal complex anlage differentiate as cone photoreceptors rather than parapineal neurons. Fgf8a acts permissively to promote parapineal fate in conjunction with the transcription factor Tbx2b, but might also block cone photoreceptor fate. We conclude that this subset of anterior pineal complex precursors, which normally become parapineal cells, are bipotential and require Fgf8a to maintain parapineal identity and/or prevent cone identity.
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Affiliation(s)
- Joshua A Clanton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37205, USA
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Roussigne M, Blader P, Wilson SW. Breaking symmetry: the zebrafish as a model for understanding left-right asymmetry in the developing brain. Dev Neurobiol 2012; 72:269-81. [PMID: 22553774 DOI: 10.1002/dneu.20885] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
How does left-right asymmetry develop in the brain and how does the resultant asymmetric circuitry impact on brain function and lateralized behaviors? By enabling scientists to address these questions at the levels of genes, neurons, circuitry and behavior,the zebrafish model system provides a route to resolve the complexity of brain lateralization. In this review, we present the progress made towards characterizing the nature of the gene networks and the sequence of morphogenetic events involved in the asymmetric development of zebrafish epithalamus. In an attempt to integrate the recent extensive knowledge into a working model and to identify the future challenges,we discuss how insights gained at a cellular/developmental level can be linked to the data obtained at a molecular/genetic level. Finally, we present some evolutionary thoughts and discuss how significant discoveries made in zebrafish should provide entry points to better understand the evolutionary origins of brain lateralization.
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Affiliation(s)
- Myriam Roussigne
- Universite Paul Sabatier, Centre de Biologie du Developpement,Toulouse, France.
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Quillien A, Blanco-Sanchez B, Halluin C, Moore JC, Lawson ND, Blader P, Cau E. BMP signaling orchestrates photoreceptor specification in the zebrafish pineal gland in collaboration with Notch. Development 2011; 138:2293-302. [PMID: 21558377 DOI: 10.1242/dev.060988] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A variety of signaling pathways have been shown to regulate specification of neuronal subtype identity. However, the mechanisms by which future neurons simultaneously process information from multiple pathways to establish their identity remain poorly understood. The zebrafish pineal gland offers a simple system with which to address questions concerning the integration of signaling pathways during neural specification as it contains only two types of neurons - photoreceptors and projection neurons. We have previously shown that Notch signaling inhibits the projection neuron fate. Here, we show that BMP signaling is both necessary and sufficient to promote the photoreceptor fate. We also demonstrate that crosstalk between BMP and Notch signaling is required for the inhibition of a projection neuron fate in future photoreceptors. In this case, BMP signaling is required as a competence factor for the efficient activation of Notch targets. Our results indicate that both the induction of a photoreceptor fate and the interaction with Notch relies on a canonical BMP/Smad5 pathway. However, the activation of Notch-dependent transcription does not require a canonical Smad5-DNA interaction. Our results provide new insights into how multiple signaling influences are integrated during cell fate specification in the vertebrate CNS.
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Affiliation(s)
- Aurélie Quillien
- Université de Toulouse, UPS, Centre de Biologie du Développement (CBD), CNRS, Toulouse, France
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DeltaA/DeltaD regulate multiple and temporally distinct phases of notch signaling during dopaminergic neurogenesis in zebrafish. J Neurosci 2011; 30:16621-35. [PMID: 21148001 DOI: 10.1523/jneurosci.4769-10.2010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Dopaminergic neurons develop at distinct anatomical sites to form some of the major neuromodulatory systems in the vertebrate brain. Despite their relevance in neurodegenerative diseases and the interests in reconstitutive therapies from stem cells, mechanisms of the neurogenic switch from precursor populations to dopaminergic neurons are not well understood. Here, we investigated neurogenesis of different dopaminergic and noradrenergic neuron populations in the zebrafish embryo. Birth-dating analysis by EdU (5-ethynyl-2'-deoxyuridine) incorporation revealed temporal dynamics of catecholaminergic neurogenesis. Analysis of Notch signaling mutants and stage-specific pharmacological inhibition of Notch processing revealed that dopaminergic neurons form by temporally distinct mechanisms: dopaminergic neurons of the posterior tuberculum derive directly from neural plate cells during primary neurogenesis, whereas other dopaminergic groups form in continuous or wavelike neurogenesis phases from proliferating precursor pools. Systematic analysis of Notch ligands revealed that the two zebrafish co-orthologs of mammalian Delta1, DeltaA and DeltaD, control the neurogenic switch of all early developing dopaminergic neurons in a partially redundant manner. DeltaA/D may also be involved in maintenance of dopaminergic precursor pools, as olig2 expression in ventral diencephalic dopaminergic precursors is affected in dla/dld mutants. DeltaA/D act upstream of sim1a and otpa during dopaminergic specification. However, despite the fact that both dopaminergic and corticotropin-releasing hormone neurons derive from sim1a- and otpa-expressing precursors, DeltaA/D does not act as a lineage switch between these two neuronal types. Rather, DeltaA/D limits the size of the sim1a- and otpa-expressing precursor pool from which dopaminergic neurons differentiate.
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Zanazzi G, Matthews G. Enrichment and differential targeting of complexins 3 and 4 in ribbon-containing sensory neurons during zebrafish development. Neural Dev 2010; 5:24. [PMID: 20809954 PMCID: PMC2941751 DOI: 10.1186/1749-8104-5-24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/01/2010] [Indexed: 12/01/2022] Open
Abstract
Background In sensory systems with broad bandwidths, polarized receptor cells utilize highly specialized organelles in their apical and basolateral compartments to transduce and ultimately transmit signals to the rest of the nervous system. While progress has been made in elucidating the assembly of the transduction apparatus, the development of synaptic ribbon-containing terminals remains poorly understood. To begin to delineate the targeting of the exocytotic machinery specifically in ribbon-containing neurons, we have examined the expression of complexins 3 and 4 in the zebrafish visual and acousticolateral systems during the first week of development. Results We have identified five members of the complexin 3/4 subfamily in zebrafish that show 50 to 75% amino acid identity with mammalian complexins 3 and 4. Utilizing a polyclonal antibody that recognizes all five orthologs, we demonstrate that these proteins are enriched in ribbon-containing sensory neurons. Complexin 3/4 is rapidly targeted to presynaptic terminals in the pineal organ and retina concomitantly with RIBEYE b, a component of ribbons. In hair cells of the inner ear and lateral line, however, complexin 3/4 immunoreactivity clusters on the apical surfaces of hair cells, among their stereocilia, rather than along the basolateral plasma membrane with RIBEYE b. A complexin 4a-specific antibody selectively labels the presynaptic terminals of visual system ribbon-containing neurons. Conclusions These results provide evidence for the concurrent transport and/or assembly of multiple components of the active zone in developing ribbon terminals. Members of the complexin 3/4 subfamily are enriched in these terminals in the visual system and in hair bundles of the acousticolateral system, suggesting that these proteins are differentially targeted and may have multiple roles in ribbon-containing sensory neurons.
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Affiliation(s)
- George Zanazzi
- Graduate Program in Neuroscience, State University of New York, Stony Brook, NY 11794, USA
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Notch activity levels control the balance between quiescence and recruitment of adult neural stem cells. J Neurosci 2010; 30:7961-74. [PMID: 20534844 DOI: 10.1523/jneurosci.6170-09.2010] [Citation(s) in RCA: 189] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The limited generation of neurons during adulthood is controlled by a balance between quiescence and recruitment of neural stem cells (NSCs). We use here the germinal zone of the zebrafish adult telencephalon to examine how the frequency of NSC divisions is regulated. We show, using several in vivo techniques, that progenitors transit back and forth between the quiescent and dividing state, according to varying levels of Notch activity: Notch induction drives progenitors into quiescence, whereas blocking Notch massively reinitiates NSC division and subsequent commitment toward becoming neurons. Notch activation appears predominantly triggered by newly recruited progenitors onto their neighbors, suggesting an involvement of Notch in a self-limiting mechanism, once neurogenesis is started. These results identify for the first time a lateral inhibition-like mechanism in the context of adult neurogenesis and suggest that the equilibrium between quiescence and neurogenesis in the adult brain is controlled by fluctuations of Notch activity, thereby regulating the amount of adult-born neurons.
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Xenopus Bsx links daily cell cycle rhythms and pineal photoreceptor fate. Proc Natl Acad Sci U S A 2010; 107:6352-7. [PMID: 20308548 DOI: 10.1073/pnas.1000854107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the developing central nervous system, the cell cycle clock plays a crucial role in determining cell fate specification. A second clock, the circadian oscillator, generates daily rhythms of cell cycle progression. Although these two clocks interact, the mechanisms linking circadian cell cycle progression and cell fate determination are still poorly understood. A convenient system to address this issue is the pineal organ of lower vertebrates, which contains only two neuronal types, photoreceptors and projection neurons. In particular, photoreceptors constitute the core of the pineal circadian system, being able to transduce daily light inputs into the rhythmical production of melatonin. However, the genetic program leading to photoreceptor fate largely remains to be deciphered. Here, we report a previously undescribed function for the homeobox gene Bsx in controlling pineal proliferation and photoreceptor fate in Xenopus. We show that Xenopus Bsx (Xbsx) is expressed rhythmically in postmitotic photoreceptor precursors, reaching a peak during the night, with a cycle that is complementary to the daily rhythms of S-phase entry displayed by pineal cells. Xbsx knockdown results in increased night levels of pineal proliferation, whereas activation of a GR-Xbsx protein flattens the daily rhythms of S-phase entry to the lowest level. Furthermore, evidence is presented that Xbsx is necessary and sufficient to promote a photoreceptor fate. Altogether, these data indicate that Xbsx plays a dual role in contributing to shape the profile of the circadian cell cycle progression and in the specification of pineal photoreceptors, thus acting as a unique link between these two events.
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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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Cau E, Blader P. Notch activity in the nervous system: to switch or not switch? Neural Dev 2009; 4:36. [PMID: 19799767 PMCID: PMC2761386 DOI: 10.1186/1749-8104-4-36] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 10/02/2009] [Indexed: 12/23/2022] Open
Abstract
The Notch pathway is instrumental for cell fate diversification during development. Pioneer studies conducted in Drosophila and more recent work performed in vertebrates have shown that in the nervous system, Notch is reiteratively employed when cells choose between two alternative fates, a process referred to as a binary fate decision. While the early (neural versus epidermal) fate decisions mainly involve an inhibitory effect of Notch on the neural fate, late fate decisions (choice between different subtypes of neural cells) have been proposed to involve a binary switch activity whereby Notch would be instructive for one fate and inhibitory for the other. We re-examine this binary switch model in light of two recent findings made in the vertebrate nervous system. First, in the zebrafish epiphysis, Notch is required to resolve a mixed identity through the inhibition of one specific fate. Second, in the murine telencephalon, Notch regulates the competence of neural progenitors to respond to the JAK/STAT pathway, thereby allowing for the induction of an astrocyte fate. In neither case is Notch instructive for the alternative fate, but rather cooperates with another signalling pathway to coordinate binary fate choices. We also review current knowledge on the molecular cascades acting downstream of Notch in the context of neural subtype diversification, a crucial issue if one is to determine Notch function as an instructive, permissive or inhibitory signal in the various cellular contexts where it is implicated. Finally, we speculate as to how such a 'non-switch' activity could contribute to the expansion of neuronal subtype diversity.
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Affiliation(s)
- Elise Cau
- Université de Toulouse, UPS, Centre de Biologie du Développement (CBD), 118 route de Narbonne, F-31062 Toulouse, France.
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Rocha SF, Lopes SS, Gossler A, Henrique D. Dll1 and Dll4 function sequentially in the retina and pV2 domain of the spinal cord to regulate neurogenesis and create cell diversity. Dev Biol 2009; 328:54-65. [PMID: 19389377 DOI: 10.1016/j.ydbio.2009.01.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 12/26/2008] [Accepted: 01/05/2009] [Indexed: 12/11/2022]
Abstract
Signalling mediated by Notch receptors is known to have multiple functions during vertebrate neural development, regulating processes like progenitor differentiation and cell type diversification. Various Notch ligands are expressed in the developing nervous system and their activities might contribute to this multiplicity of functions. Here, we show that two Delta-like genes, Dll1 and Dll4, are sequentially expressed in differentiating neurons of the embryonic mouse retina and spinal cord's pV2 domain, with Dll1 starting to be expressed before Dll4. Analysis of Dll1 mutants reveals this gene is necessary and sufficient to maintain a pool of progenitors in the embryonic neuroepithelium. Accordingly, in the spinal cord domains where Dll1 is the only expressed Notch ligand, its inactivation leads to an increased rate of neurogenesis and premature differentiation of neural progenitors. In contrast, in the pV2 domain and retina where Dll1 is co-expressed with Dll4, progenitors are not exhausted and cell diversity is maintained. Together, our results support a model where Dll1 and Dll4 are part of a unique genetic circuitry that regulates subsequent steps of neurogenesis in the retina and pV2 domain: while Dll1 serves to prevent the untimely differentiation of neural progenitors, Dll4 might function to generate diversity within the population of differentiating neurons.
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Affiliation(s)
- Susana Ferreira Rocha
- Instituto de Medicina Molecular, Faculdade de Medicina de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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Recent Papers on Zebrafish and Other Aquarium Fish Models. Zebrafish 2008. [DOI: 10.1089/zeb.2008.9987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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