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Gupta S, Polit LD, Fitzgerald M, Rowland HA, Murali D, Buckley NJ, Subramaniam S. Temporal transcriptional control of neural induction in human induced pluripotent stem cells. Front Mol Neurosci 2023; 16:1139287. [PMID: 37213689 PMCID: PMC10195998 DOI: 10.3389/fnmol.2023.1139287] [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] [Received: 01/06/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Neural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of the temporal and causal relationships that are required for this state transition. Methods Here, we have carried out a longitudinal analysis of the transcriptome of human iPSCs undergoing neural induction. Using the temporal relationships between the changing profile of key transcription factors and subsequent changes in their target gene expression profiles, we have identified distinct functional modules operative throughout neural induction. Results In addition to modules that govern loss of pluripotency and gain of neural ectoderm identity, we discover other modules governing cell cycle and metabolism. Strikingly, some of these functional modules are retained throughout neural induction, even though the gene membership of the module changes. Systems analysis identifies other modules associated with cell fate commitment, genome integrity, stress response and lineage specification. We then focussed on OTX2, one of the most precociously activated transcription factors during neural induction. Our temporal analysis of OTX2 target gene expression identified several OTX2 regulated gene modules representing protein remodelling, RNA splicing and RNA processing. Further CRISPRi inhibition of OTX2 prior to neural induction promotes an accelerated loss of pluripotency and a precocious and aberrant neural induction disrupting some of the previously identified modules. Discussion We infer that OTX2 has a diverse role during neural induction and regulates many of the biological processes that are required for loss of pluripotency and gain of neural identity. This dynamical analysis of transcriptional changes provides a unique perspective of the widespread remodelling of the cell machinery that occurs during neural induction of human iPSCs.
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Affiliation(s)
- Shakti Gupta
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Lucia Dutan Polit
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Michael Fitzgerald
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Helen A. Rowland
- Department of Psychiatry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Divya Murali
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Noel J. Buckley
- Department of Psychiatry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
- *Correspondence: Noel J. Buckley, ; Shankar Subramaniam,
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
- Departments of Computer Science and Engineering, and Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- *Correspondence: Noel J. Buckley, ; Shankar Subramaniam,
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Miyake T, Kuge M, Matsumoto Y, Shimada M. α-glucosyl-rutin activates immediate early genes in human induced pluripotent stem cells. Stem Cell Res 2021; 56:102511. [PMID: 34455240 DOI: 10.1016/j.scr.2021.102511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022] Open
Abstract
Rutin is a natural flavonoid glycoside found in several vegetables and fruits such as buckwheat and onion. Rutin has a range of pharmacological effects that include anti-oxidant, anti-inflammation, anti-bacterial, and anti-cancer activities. α-glucosyl-rutin (AGR) is a derivative of rutin with increased water solubility that is used in cosmetics and foods. However, the effects of AGR on cellular responses have not been clarified, especially in stem cells. Induced pluripotent stem cells (iPSCs) show high proliferative activity and pluripotency; however, regulation of molecular machinery such as cell cycle, metabolism, and DNA repair differs between iPSCs and somatic cells. Here, we compared the effects of AGR on iPSCs and differentiated cells (fibroblasts and skin keratinocytes). AGR-treated iPSCs exhibited increased cell viability. RNA sequencing and reverse transcriptase PCR analysis revealed that AGR induced expression of immediate early genes (IEGs) and differentiation-related genes in iPSCs. Our results suggest that AGR may activate differentiation signals mediated by IEG responses in iPSCs, resulting in altered metabolic activity and increased cell viability.
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Affiliation(s)
- Tomoko Miyake
- Cosmetic R&D Department, Takara Belmont Corp, 7-1-19 Akasaka, Minato-ku, Tokyo 107-0052, Japan.
| | - Munekazu Kuge
- Cosmetic R&D Department, Takara Belmont Corp, 7-1-19 Akasaka, Minato-ku, Tokyo 107-0052, Japan
| | - Yoshihisa Matsumoto
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Mikio Shimada
- Laboratory for Zero-Carbon Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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3
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Pelletier L, Moreau M. Ca v1 channels is also a story of non excitable cells: Application to calcium signalling in two different non related models. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118996. [PMID: 33675852 DOI: 10.1016/j.bbamcr.2021.118996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Calcium is a second messenger essential, in all cells, for most cell functions. The spatio-temporal control of changes in intracellular calcium concentration is partly due to the activation of calcium channels. Voltage-operated calcium channels are present in excitable and non-excitable cells. If the mechanism of voltage-operated calcium channels is well known in excitable cells the Ca2+ toolkit used in non-excitable cells to activate the calcium channels is less described. Herein we discuss about very similar pathways involving voltage activated Cav1 channels in two unrelated non-excitable cells; ectoderm cells undergoing neural development and effector Th2 lymphocytes responsible for parasite elimination and also allergic diseases. We will examine the way by which these channels operate and are regulated, as well as the consequences in terms of gene transcription. Finally, we will consider the questions that remain unsolved and how they might be a challenge for the future.
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Affiliation(s)
- Lucette Pelletier
- Infinity - Toulouse Institute For Infectious and Inflammatory Diseases INSERM UMR1291, CNRS UMR5051, University Toulouse III CHU Purpan, BP 3028, 31024 Toulouse CEDEX 3, France
| | - Marc Moreau
- Université Toulouse3, Centre de biologie du développement, CNRS UMR5547, 118 route de Narbonne, F31062 Toulouse Cedex 04, France.
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4
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Kim JY, Kim JY, Kim JH, Jung H, Lee WT, Lee JE. Restorative Mechanism of Neural Progenitor Cells Overexpressing Arginine Decarboxylase Genes Following Ischemic Injury. Exp Neurobiol 2019; 28:85-103. [PMID: 30853827 PMCID: PMC6401554 DOI: 10.5607/en.2019.28.1.85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/13/2022] Open
Abstract
Cell replacement therapy using neural progenitor cells (NPCs) following ischemic stroke is a promising potential therapeutic strategy, but lacks efficacy for human central nervous system (CNS) therapeutics. In a previous in vitro study, we reported that the overexpression of human arginine decarboxylase (ADC) genes by a retroviral plasmid vector promoted the neuronal differentiation of mouse NPCs. In the present study, we focused on the cellular mechanism underlying cell proliferation and differentiation following ischemic injury, and the therapeutic feasibility of NPCs overexpressing ADC genes (ADC-NPCs) following ischemic stroke. To mimic cerebral ischemia in vitro , we subjected the NPCs to oxygen-glucose deprivation (OGD). The overexpressing ADC-NPCs were differentiated by neural lineage, which was related to excessive intracellular calcium-mediated cell cycle arrest and phosphorylation in the ERK1/2, CREB, and STAT1 signaling cascade following ischemic injury. Moreover, the ADC-NPCs were able to resist mitochondrial membrane potential collapse in the increasingly excessive intracellular calcium environment. Subsequently, transplanted ADC-NPCs suppressed infarct volume, and promoted neural differentiation, synapse formation, and motor behavior performance in an in vivo tMCAO rat model. The results suggest that ADC-NPCs are potentially useful for cell replacement therapy following ischemic stroke.
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Affiliation(s)
- Jae Young Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jong Youl Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jae Hwan Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science, Sungkyunkwan University, Suwon 16419, Korea
| | - Hosung Jung
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
- BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Won Taek Lee
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jong Eun Lee
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
- BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Brain Research Institute, Yonsei University College of Medicine, Seoul 03722, Korea
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Abstract
Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene. The Gli-Glis-Nkl-Zic superfamily and some other eukaryotic zinc finger proteins share a tandem CWCH2 (tCWCH2) motif, a hallmark for inter-zinc finger interaction between two adjacent C2H2 zinc fingers. In Zic family proteins, there exist additional evolutionally conserved domains known as ZOC and ZFNC, both of which may have appeared before cnidarian-bilaterian divergence. Comparison of the exon-intron boundaries in the Zic zinc finger domains revealed an intron (A-intron) that was absolutely conserved in bilaterians (metazoans with bilateral symmetry) and a placozoan (a simple nonparasitic metazoan). In vertebrates, there are five to seven Zic paralogs among which Zic1, Zic2, and Zic3 are generated through a tandem gene duplication and carboxy-terminal truncation in a vertebrate common ancestor, sharing a conserved carboxy-terminal sequence. Several hypotheses have been proposed to explain the Zic family phylogeny, including their origin, unique features in the first and second zinc finger motif, evolution of the nuclear localization signal, significance of the animal taxa-selective degeneration, gene multiplication in the vertebrate lineage, and involvement in the evolutionary alteration of the animal body plan.
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6
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Kjolby RAS, Harland RM. Genome-wide identification of Wnt/β-catenin transcriptional targets during Xenopus gastrulation. Dev Biol 2017; 426:165-175. [PMID: 27091726 PMCID: PMC6288011 DOI: 10.1016/j.ydbio.2016.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/16/2016] [Accepted: 03/16/2016] [Indexed: 10/21/2022]
Abstract
The canonical Wnt/β-catenin signaling pathway plays multiple roles during Xenopus gastrulation, including posteriorization of the neural plate, patterning of the mesoderm, and induction of the neural crest. Wnt signaling stabilizes β-catenin, which then activates target genes. However, few targets of this signaling pathway that mediate early developmental processes are known. Here we sought to identify transcriptional targets of the Wnt/β-catenin signaling pathway using a genome-wide approach. We selected putative targets using the criteria of reduced expression upon zygotic Wnt knockdown, β-catenin binding within 50kb of the gene, and expression in tissues that receive Wnt signaling. Using these criteria, we found 21 novel direct transcriptional targets of Wnt/β-catenin signaling during gastrulation and in addition have identified putative regulatory elements for further characterization in future studies.
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Affiliation(s)
- Rachel A S Kjolby
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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7
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Nettersheim D, Jostes S, Sharma R, Schneider S, Hofmann A, Ferreira HJ, Hoffmann P, Kristiansen G, Esteller MB, Schorle H. BMP Inhibition in Seminomas Initiates Acquisition of Pluripotency via NODAL Signaling Resulting in Reprogramming to an Embryonal Carcinoma. PLoS Genet 2015; 11:e1005415. [PMID: 26226633 PMCID: PMC4520454 DOI: 10.1371/journal.pgen.1005415] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/02/2015] [Indexed: 12/18/2022] Open
Abstract
Type II germ cell cancers (GCC) can be subdivided into seminomas and non-seminomas. Seminomas are similar to carcinoma in situ (CIS) cells, the common precursor of type II GCCs, with regard to epigenetics and expression, while embryonal carcinomas (EC) are totipotent and differentiate into teratomas, yolk-sac tumors and choriocarcinomas. GCCs can present as seminomas with a non-seminoma component, raising the question if a CIS gives rise to seminomas and ECs at the same time or whether seminomas can be reprogrammed to ECs. In this study, we utilized the seminoma cell line TCam-2 that acquires an EC-like status after xenografting into the murine flank as a model for a seminoma to EC transition and screened for factors initiating and driving this process. Analysis of expression and DNA methylation dynamics during transition of TCam-2 revealed that many pluripotency- and reprogramming-associated genes were upregulated while seminoma-markers were downregulated. Changes in expression level of 53 genes inversely correlated to changes in DNA methylation. Interestingly, after xenotransplantation 6 genes (GDF3, NODAL, DNMT3B, DPPA3, GAL, AK3L1) were rapidly induced, followed by demethylation of their genomic loci, suggesting that these 6 genes are poised for expression driving the reprogramming. We demonstrate that inhibition of BMP signaling is the initial event in reprogramming, resulting in activation of the pluripotency-associated genes and NODAL signaling. We propose that reprogramming of seminomas to ECs is a multi-step process. Initially, the microenvironment causes inhibition of BMP signaling, leading to induction of NODAL signaling. During a maturation phase, a fast acting NODAL loop stimulates its own activity and temporarily inhibits BMP signaling. During the stabilization phase, a slow acting NODAL loop, involving WNTs re-establishes BMP signaling and the pluripotency circuitry. In parallel, DNMT3B-driven de novo methylation silences seminoma-associated genes and epigenetically fixes the EC state.
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Affiliation(s)
- Daniel Nettersheim
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Sina Jostes
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Rakesh Sharma
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Simon Schneider
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University Medical School, Bonn, Germany
| | - Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain
| | - Per Hoffmann
- Institute of Human Genetics, University Medical School, Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Medical School, Bonn, Germany
| | - Manel B Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Hubert Schorle
- Institute of Pathology, Department of Developmental Pathology, University Medical School, Bonn, Germany
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Winata CL, Kondrychyn I, Korzh V. Changing Faces of Transcriptional Regulation Reflected by Zic3. Curr Genomics 2015; 16:117-27. [PMID: 26085810 PMCID: PMC4467302 DOI: 10.2174/1389202916666150205124519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023] Open
Abstract
The advent of genomics in the study of developmental mechanisms has brought a trove of information
on gene datasets and regulation during development, where the Zic family of zinc-finger proteins
plays an important role. Genomic analysis of the modes of action of Zic3 in pluripotent cells demonstrated its
requirement for maintenance of stem cells pluripotency upon binding to the proximal regulatory regions
(promoters) of genes associated with cell pluripotency (Nanog, Sox2, Oct4, etc.) as well as cell cycle, proliferation, oncogenesis
and early embryogenesis. In contrast, during gastrulation and neurulation Zic3 acts by binding the distal regulatory
regions (enhancers, etc) associated with control of gene transcription in the Nodal and Wnt signaling pathways, including
genes that act to break body symmetry. This illustrates a general role of Zic3 as a transcriptional regulator that
acts not only alone, but in many instances in conjunction with other transcription factors. The latter is done by binding to
adjacent sites in the context of multi-transcription factor complexes associated with regulatory elements.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
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9
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Janesick A, Wu SC, Blumberg B. Retinoic acid signaling and neuronal differentiation. Cell Mol Life Sci 2015; 72:1559-76. [PMID: 25558812 PMCID: PMC11113123 DOI: 10.1007/s00018-014-1815-9] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 01/13/2023]
Abstract
The identification of neurological symptoms caused by vitamin A deficiency pointed to a critical, early developmental role of vitamin A and its metabolite, retinoic acid (RA). The ability of RA to induce post-mitotic, neural phenotypes in various stem cells, in vitro, served as early evidence that RA is involved in the switch between proliferation and differentiation. In vivo studies have expanded this "opposing signal" model, and the number of primary neurons an embryo develops is now known to depend critically on the levels and spatial distribution of RA. The proneural and neurogenic transcription factors that control the exit of neural progenitors from the cell cycle and allow primary neurons to develop are partly elucidated, but the downstream effectors of RA receptor (RAR) signaling (many of which are putative cell cycle regulators) remain largely unidentified. The molecular mechanisms underlying RA-induced primary neurogenesis in anamniote embryos are starting to be revealed; however, these data have been not been extended to amniote embryos. There is growing evidence that bona fide RARs are found in some mollusks and other invertebrates, but little is known about their necessity or functions in neurogenesis. One normal function of RA is to regulate the cell cycle to halt proliferation, and loss of RA signaling is associated with dedifferentiation and the development of cancer. Identifying the genes and pathways that mediate cell cycle exit downstream of RA will be critical for our understanding of how to target tumor differentiation. Overall, elucidating the molecular details of RAR-regulated neurogenesis will be decisive for developing and understanding neural proliferation-differentiation switches throughout development.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300 USA
| | - Stephanie Cherie Wu
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300 USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, 92697-2300 USA
- Department of Pharmaceutical Sciences, University of California, Irvine, USA
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10
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Pai VP, Lemire JM, Paré JF, Lin G, Chen Y, Levin M. Endogenous gradients of resting potential instructively pattern embryonic neural tissue via Notch signaling and regulation of proliferation. J Neurosci 2015; 35:4366-85. [PMID: 25762681 PMCID: PMC4355204 DOI: 10.1523/jneurosci.1877-14.2015] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 12/21/2014] [Accepted: 01/14/2015] [Indexed: 12/26/2022] Open
Abstract
Biophysical forces play important roles throughout embryogenesis, but the roles of spatial differences in cellular resting potentials during large-scale brain morphogenesis remain unknown. Here, we implicate endogenous bioelectricity as an instructive factor during brain patterning in Xenopus laevis. Early frog embryos exhibit a characteristic hyperpolarization of cells lining the neural tube; disruption of this spatial gradient of the transmembrane potential (Vmem) diminishes or eliminates the expression of early brain markers, and causes anatomical mispatterning of the brain, including absent or malformed regions. This effect is mediated by voltage-gated calcium signaling and gap-junctional communication. In addition to cell-autonomous effects, we show that hyperpolarization of transmembrane potential (Vmem) in ventral cells outside the brain induces upregulation of neural cell proliferation at long range. Misexpression of the constitutively active form of Notch, a suppressor of neural induction, impairs the normal hyperpolarization pattern and neural patterning; forced hyperpolarization by misexpression of specific ion channels rescues brain defects induced by activated Notch signaling. Strikingly, hyperpolarizing posterior or ventral cells induces the production of ectopic neural tissue considerably outside the neural field. The hyperpolarization signal also synergizes with canonical reprogramming factors (POU and HB4), directing undifferentiated cells toward neural fate in vivo. These data identify a new functional role for bioelectric signaling in brain patterning, reveal interactions between Vmem and key biochemical pathways (Notch and Ca(2+) signaling) as the molecular mechanism by which spatial differences of Vmem regulate organogenesis of the vertebrate brain, and suggest voltage modulation as a tractable strategy for intervention in certain classes of birth defects.
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Affiliation(s)
- Vaibhav P Pai
- Biology Department, Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts 02155-4243 and
| | - Joan M Lemire
- Biology Department, Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts 02155-4243 and
| | - Jean-François Paré
- Biology Department, Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts 02155-4243 and
| | - Gufa Lin
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ying Chen
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota 55455
| | - Michael Levin
- Biology Department, Center for Regenerative and Developmental Biology, Tufts University, Medford, Massachusetts 02155-4243 and
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Jin X, Chen Z, Xiang L, Luo Q, Guo Z, Ding X, Jin X. Colorectal polyp model established by transplacental BMP4 RNAi. Mol Med Rep 2014; 10:33-8. [PMID: 24806485 PMCID: PMC4068724 DOI: 10.3892/mmr.2014.2216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 03/26/2014] [Indexed: 12/28/2022] Open
Abstract
Previous studies have shown that disruption of the bone morphogenetic protein (BMP) signaling pathway is an important cause of intestinal cancer in human and animal models. Thus, the purpose of this study was to construct a Balb/C model of colorectal polyps. Pregnant mice at 9.5 days gestation were injected via the tail vein with the pSES-Si BMP4 plasmid bearing a fluorochrome (DsRed) reporter, in order to silence the BMP4 gene in the first generation (F1); this group of mice was named the pSES-BMP4 group Intestinal fluorescence was detected at 1-, 4- and 8-week-old F1 mice, and reverse transcription-polymerase chain reaction (RT-PCR) and western-blotting assays were used to determine changes in the expression of BMP4. A dissecting microscope and hematoxylin and eosin (H&E) staining were used to observe the cell morphology and appearance of the polyps. DsRed fluorescence was observed in the intestines of 1-week-old F1 mice of the pSES-BMP4 group. BMP4 expression at the mRNA and protein level was reduced in 1-, 4- and 8-week-old F1 mice (P<0.05). However, the level of Smad4 mRNA was only reduced in 8-week-old F1 mice (P<0.05). Multiple hyperplasic polyps emerged in the colon and rectum of the intestines of 4-week-old F1 mice in the pSES-BMP4 group. The size of colorectal polyps increased at 8 weeks, when vessels and polyp pedicles became apparent. In conclusion, silencing of the BMP4 gene using transplacental RNAi injection can induce formation of colorectal polyps in mice.
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Affiliation(s)
- Xin Jin
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Zhongmei Chen
- General Hospital of Chongqing Iron and Steel Group, Chongqing 400081, P.R. China
| | - Li Xiang
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Qing Luo
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Zhenghua Guo
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Xionghui Ding
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
| | - Xianqing Jin
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing 400014, P.R. China
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12
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Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genet 2013; 9:e1003852. [PMID: 24204288 PMCID: PMC3814314 DOI: 10.1371/journal.pgen.1003852] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 08/19/2013] [Indexed: 02/06/2023] Open
Abstract
Zic3 regulates early embryonic patterning in vertebrates. Loss of Zic3 function is known to disrupt gastrulation, left-right patterning, and neurogenesis. However, molecular events downstream of this transcription factor are poorly characterized. Here we use the zebrafish as a model to study the developmental role of Zic3 in vivo, by applying a combination of two powerful genomics approaches – ChIP-seq and microarray. Besides confirming direct regulation of previously implicated Zic3 targets of the Nodal and canonical Wnt pathways, analysis of gastrula stage embryos uncovered a number of novel candidate target genes, among which were members of the non-canonical Wnt pathway and the neural pre-pattern genes. A similar analysis in zic3-expressing cells obtained by FACS at segmentation stage revealed a dramatic shift in Zic3 binding site locations and identified an entirely distinct set of target genes associated with later developmental functions such as neural development. We demonstrate cis-regulation of several of these target genes by Zic3 using in vivo enhancer assay. Analysis of Zic3 binding sites revealed a distribution biased towards distal intergenic regions, indicative of a long distance regulatory mechanism; some of these binding sites are highly conserved during evolution and act as functional enhancers. This demonstrated that Zic3 regulation of developmental genes is achieved predominantly through long distance regulatory mechanism and revealed that developmental transitions could be accompanied by dramatic changes in regulatory landscape. The Zic3 transcription factor regulates early embryonic patterning, and the loss of its function leads to defects in left-right body asymmetry. Previous studies have only identified a small number of Zic3 targets, which renders the molecular mechanism underlying its activity insufficiently understood. Utilizing two genomics technologies, next generation sequencing and microarray, we profile the genome-wide binding sites of Zic3 and identified its target genes in the developing zebrafish embryo. Our results show that Zic3 regulates its target genes predominantly through regulatory elements located far from promoters. Among the targets of Zic3 are the Nodal and Wnt pathways known to regulate gastrulation and left-right body asymmetry, as well as neural pre-pattern genes regulating proliferation of neural progenitors. Using enhancer activity assay, we further show that genomic regions bound by Zic3 function as enhancers. Our study provides a genome-wide view of the regulatory landscape of Zic3 and its changes during vertebrate development.
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Houtmeyers R, Souopgui J, Tejpar S, Arkell R. The ZIC gene family encodes multi-functional proteins essential for patterning and morphogenesis. Cell Mol Life Sci 2013; 70:3791-811. [PMID: 23443491 PMCID: PMC11113920 DOI: 10.1007/s00018-013-1285-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 01/16/2013] [Accepted: 01/28/2013] [Indexed: 12/18/2022]
Abstract
The zinc finger of the cerebellum gene (ZIC) discovered in Drosophila melanogaster (odd-paired) has five homologs in Xenopus, chicken, mice, and humans, and seven in zebrafish. This pattern of gene copy expansion is accompanied by a divergence in gene and protein structure, suggesting that Zic family members share some, but not all, functions. ZIC genes are implicated in neuroectodermal development and neural crest cell induction. All share conserved regions encoding zinc finger domains, however their heterogeneity and specification remain unexplained. In this review, the evolution, structure, and expression patterns of the ZIC homologs are described; specific functions attributable to individual family members are supported. A review of data from functional studies in Xenopus and murine models suggest that ZIC genes encode multifunctional proteins operating in a context-specific manner to drive critical events during embryogenesis. The identification of ZIC mutations in congenital syndromes highlights the relevance of these genes in human development.
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Affiliation(s)
- Rob Houtmeyers
- Department of Oncology, Katholieke Universiteit Leuven, O&N1, 3000, Leuven, Belgium,
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Janesick A, Abbey R, Chung C, Liu S, Taketani M, Blumberg B. ERF and ETV3L are retinoic acid-inducible repressors required for primary neurogenesis. Development 2013; 140:3095-106. [PMID: 23824578 DOI: 10.1242/dev.093716] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cells in the developing neural tissue demonstrate an exquisite balance between proliferation and differentiation. Retinoic acid (RA) is required for neuronal differentiation by promoting expression of proneural and neurogenic genes. We show that RA acts early in the neurogenic pathway by inhibiting expression of neural progenitor markers Geminin and Foxd4l1, thereby promoting differentiation. Our screen for RA target genes in early Xenopus development identified Ets2 Repressor Factor (Erf) and the closely related ETS repressors Etv3 and Etv3-like (Etv3l). Erf and Etv3l are RA responsive and inhibit the action of ETS genes downstream of FGF signaling, placing them at the intersection of RA and growth factor signaling. We hypothesized that RA regulates primary neurogenesis by inducing Erf and Etv3l to antagonize proliferative signals. Loss-of-function analysis showed that Erf and Etv3l are required to inhibit proliferation of neural progenitors to allow differentiation, whereas overexpression of Erf led to an increase in the number of primary neurons. Therefore, these RA-induced ETS repressors are key components of the proliferation-differentiation switch during primary neurogenesis in vivo.
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Affiliation(s)
- Amanda Janesick
- Department of Developmental and Cell Biology, 2011 Biological Sciences 3, University of California, Irvine, CA 92697-2300, USA
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Sánchez-Alvarez R, Gayen S, Vadigepalli R, Anni H. Ethanol diverts early neuronal differentiation trajectory of embryonic stem cells by disrupting the balance of lineage specifiers. PLoS One 2013; 8:e63794. [PMID: 23724002 PMCID: PMC3665827 DOI: 10.1371/journal.pone.0063794] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/04/2013] [Indexed: 02/07/2023] Open
Abstract
Background Ethanol is a toxin responsible for the neurodevelopmental deficits of Fetal Alcohol Spectrum Disorders (FASD). Recent evidence suggests that ethanol modulates the protein expression of lineage specifier transcription factors Oct4 (Pou5f1) and Sox2 in early stages of mouse embryonic stem (ES) cell differentiation. We hypothesized that ethanol induced an imbalance in the expression of Oct4 and Sox2 in early differentiation, that dysregulated the expression of associated and target genes and signaling molecules and diverted cells from neuroectodermal (NE) formation. Methodology/Principal Findings We showed modulation by ethanol of 33 genes during ES cell differentiation, using high throughput microfluidic dynamic array chips measuring 2,304 real time quantitative PCR assays. Based on the overall gene expression dynamics, ethanol drove cells along a differentiation trajectory away from NE fate. These ethanol-induced gene expression changes were observed as early as within 2 days of differentiation, and were independent of cell proliferation or apoptosis. Gene expression changes were correlated with fewer βIII-tubulin positive cells of an immature neural progenitor phenotype, as well as a disrupted actin cytoskeleton were observed. Moreover, Tuba1a and Gapdh housekeeping genes were modulated by ethanol during differentiation and were replaced by a set of ribosomal genes with stable expression. Conclusions/Significance These findings provided an ethanol-response gene signature and pointed to the transcriptional dynamics underlying lineage imbalance that may be relevant to FASD phenotype.
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Affiliation(s)
- Rosa Sánchez-Alvarez
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Saurabh Gayen
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Rajanikanth Vadigepalli
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RV); (HA)
| | - Helen Anni
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (RV); (HA)
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Ishii M, Arias AC, Liu L, Chen YB, Bronner ME, Maxson RE. A stable cranial neural crest cell line from mouse. Stem Cells Dev 2012; 21:3069-80. [PMID: 22889333 DOI: 10.1089/scd.2012.0155] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cranial neural crest cells give rise to ectomesenchymal derivatives such as cranial bones, cartilage, smooth muscle, dentin, as well as melanocytes, corneal endothelial cells, and neurons and glial cells of the peripheral nervous system. Previous studies have suggested that although multipotent stem-like cells may exist during the course of cranial neural crest development, they are transient, undergoing lineage restriction early in embryonic development. We have developed culture conditions that allow cranial neural crest cells to be grown as multipotent stem-like cells. With these methods, we obtained 2 independent cell lines, O9-1 and i10-1, which were derived from mass cultures of Wnt1-Cre; R26R-GFP-expressing cells. These cell lines can be propagated and passaged indefinitely, and can differentiate into osteoblasts, chondrocytes, smooth muscle cells, and glial cells. Whole-genome expression profiling of O9-1 cells revealed that this line stably expresses stem cell markers (CD44, Sca-1, and Bmi1) and neural crest markers (AP-2α, Twist1, Sox9, Myc, Ets1, Dlx1, Dlx2, Crabp1, Epha2, and Itgb1). O9-1 cells are capable of contributing to cranial mesenchymal (osteoblast and smooth muscle) neural crest fates when injected into E13.5 mouse cranial tissue explants and chicken embryos. These results suggest that O9-1 cells represent multipotent mesenchymal cranial neural crest cells. The O9-1 cell line should serve as a useful tool for investigating the molecular properties of differentiating cranial neural crest cells.
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Affiliation(s)
- Mamoru Ishii
- Department of Biochemistry and Molecular Biology, USC/Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Leclerc C, Néant I, Moreau M. The calcium: an early signal that initiates the formation of the nervous system during embryogenesis. Front Mol Neurosci 2012; 5:3. [PMID: 22593733 PMCID: PMC3351002 DOI: 10.3389/fnmol.2012.00064] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/25/2012] [Indexed: 01/19/2023] Open
Abstract
The calcium (Ca(2+)) signaling pathways have crucial roles in development from fertilization through differentiation to organogenesis. In the nervous system, Ca(2+) signals are important regulators for various neuronal functions, including formation and maturation of neuronal circuits and long-term memory. However, Ca(2+) signals are also involved in the earliest steps of neurogenesis including neural induction, differentiation of neural progenitors into neurons, and the neuro-glial switch. This review examines when and how Ca(2+) signals are generated during each of these steps with examples taken from in vivo studies in vertebrate embryos and from in vitro assays using embryonic and neural stem cells (NSCs). During the early phases of neurogenesis few investigations have been performed to study the downstream targets of Ca(2+) which posses EF-hand in their structure. This opens an entire field of research. We also discuss the highly specific nature of the Ca(2+) signaling pathway and its interaction with the other signaling pathways involved in early neural development.
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Affiliation(s)
- Catherine Leclerc
- Centre de Biologie du Développement, Université Toulouse III, CNRS UMR 5547Toulouse, France and GDRE n731, “Ca toolkit coded proteins as drug targets in animal and plant cells”
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Xenopus Zic3 controls notochord and organizer development through suppression of the Wnt/β-catenin signaling pathway. Dev Biol 2012; 361:220-31. [DOI: 10.1016/j.ydbio.2011.10.026] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 09/30/2011] [Accepted: 10/08/2011] [Indexed: 11/21/2022]
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The role of Zic family zinc finger transcription factors in the proliferation and differentiation of retinal progenitor cells. Biochem Biophys Res Commun 2011; 415:42-7. [PMID: 22024047 DOI: 10.1016/j.bbrc.2011.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 02/07/2023]
Abstract
Members of the Zic family of zinc finger transcription factors play critical roles in a variety of developmental processes. Using DNA microarray analysis, we found that Zics are strongly expressed in SSEA-1-positive early retinal progenitors in the peripheral region of the mouse retina. Reverse-transcription polymerase chain reaction using mRNA from the retina at various developmental stages showed that Zic1 and Zic2 are expressed in the embryonic retina and then gradually disappear during retinal development. Zic3 is also expressed in the embryonic retina; its expression level slightly decreases but it is expressed until adulthood. We overexpressed Zic1, Zic2, or Zic3 in retinal progenitors at embryonic day 17.5 and cultured the retina as explants for 2 weeks. The number of rod photoreceptors was fewer than in the control, but no other cell types showed significant differences between control and Zic overexpressing cells. The proliferation activity of normal retinal progenitors decreased after 5 days in culture, as observed in normal in vivo developmental processes. However, Zic expressing retinal cells continued to proliferate at days 5 and 7, suggesting that Zics sustain the proliferation activities of retinal progenitor cells. Since the effects of Zic1, 2, and 3 are indistinguishable in terms of differentiation and proliferation of retinal progenitors, the redundant function of Zics in retinal development is suggested.
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Pourebrahim R, Houtmeyers R, Ghogomu S, Janssens S, Thelie A, Tran HT, Langenberg T, Vleminckx K, Bellefroid E, Cassiman JJ, Tejpar S. Transcription factor Zic2 inhibits Wnt/β-catenin protein signaling. J Biol Chem 2011; 286:37732-40. [PMID: 21908606 DOI: 10.1074/jbc.m111.242826] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Zic transcription factors play critical roles during embryonic development. Mutations in the ZIC2 gene are associated with human holoprosencephaly, but the etiology is still unclear. Here, we report a novel function for ZIC2 as a regulator of β-catenin·TCF4-mediated transcription. We show that ZIC2 can bind directly to the DNA-binding high mobility group box of TCF4 via its zinc finger domain and inhibit the transcriptional activity of the β-catenin·TCF4 complex. However, the binding of TCF4 to DNA was not affected by ZIC2. Zic2 RNA injection completely inhibited β-catenin-induced axis duplication in Xenopus embryos and strongly blocked the ability of β-catenin to induce expression of known Wnt targets in animal caps. Moreover, Zic2 knockdown in transgenic Xenopus Wnt reporter embryos led to ectopic Wnt signaling activity mainly at the midbrain-hindbrain boundary. Together, our results demonstrate a previously unknown role for ZIC2 as a transcriptional regulator of the β-catenin·TCF4 complex.
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Affiliation(s)
- Rasoul Pourebrahim
- Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
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Leclerc C, Néant I, Moreau M. Early neural development in vertebrates is also a matter of calcium. Biochimie 2011; 93:2102-11. [PMID: 21742011 DOI: 10.1016/j.biochi.2011.06.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/24/2011] [Indexed: 12/19/2022]
Abstract
The calcium (Ca(2+)) signaling pathways have crucial roles in development from fertilization through differentiation to organogenesis. In the nervous system, Ca(2+) signals are important regulators for various neuronal functions, including formation and maturation of neuronal circuits and long-term memory. However, Ca(2+) signals are mainly involved in the earliest steps of nervous system development including neural induction, differentiation of neural progenitors into neurons, and the neuro-glial switch. This review examines when and how Ca(2+) signals are generated during each of these steps with examples taken from in vivo studies in vertebrate embryos and from in vitro assays using embryonic and neural stem cells. Also discussed is the highly specific nature of the Ca(2+) signaling pathway and its interaction with the other signaling pathways involved in early neural development.
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Affiliation(s)
- Catherine Leclerc
- Centre de Biologie du Développement, UMR CNRS 5547 and GDR 2688, Université de Toulouse, 118 route de Narbonne, Toulouse, France.
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