Suppression of Interneuron Programs and Maintenance of Selected Spinal Motor Neuron Fates by the Transcription Factor AML1/Runx1
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
SOX11 Interactome Analysis: Implication in Transcriptional Control and Neurogenesis
SOX11 interactome analysis: Implication in transcriptional control and neurogenesis Dissertation der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) vorgelegt von Birgit Heim, geb.Kick aus Augsburg Tübingen 2014 Gedruckt mit Genehmigung der Mathematisch-Naturwissenschaftlichen Fakultät der Eberhard Karls Universität Tübingen. Tag der mündlichen Qualifikation: 12.02.2015 Dekan: Prof. Dr. Wolfgang Rosenstiel 1. Berichterstatter: Prof. Dr. Olaf Rieß 2. Berichterstatter: Prof. Dr. Marius Ueffing Für meine Familie TABLE OF CONTENTS Table of contents Summary ................................................................................................................ 5 Zusammenfassung ............................................................................................... 7 1. Introduction ...................................................................................... 9 1.1. Adult neurogenesis .................................................................................... 9 1.1.1. Adult neural stem cells and neuronal precursor cells ............................ 9 1.1.2. Neurogenic niches .............................................................................. 11 1.1.3. Regulation of adult neurogenesis ........................................................ 12 1.1.3.1. Extrinsic mechanisms .................................................................. 12 1.1.3.2. Intrinsic mechanisms .................................................................. -
Phox2b and Motoneuronal Differentiation
Development 127, 1349-1358 (2000) 1349 Printed in Great Britain © The Company of Biologists Limited 2000 DEV1515 Control of hindbrain motor neuron differentiation by the homeobox gene Phox2b Alexandre Pattyn, Marie-Rose Hirsch, Christo Goridis and Jean-François Brunet* Laboratoire de Génétique et Physiologie du Développement, Developmental Biology Institute of Marseille, CNRS/INSERM/Univ Méditerranée/AP de Marseille, Luminy Case 907, 13288 Marseille Cedex 9, France *Author for correspondence (e-mail: [email protected]) Accepted 11 January; published on WWW 7 March 2000 SUMMARY Motor neurons are a widely studied model of vertebrate both the generic and subtype-specific programs of neurogenesis. They can be subdivided in somatic, branchial motoneuronal differentiation are disrupted at an early and visceral motor neurons. Recent studies on the stage. Most motor neuron precursors die inside the dorsoventral patterning of the rhombencephalon have neuroepithelium while those that emigrate to the mantle implicated the homeobox genes Pax6 and Nkx2.2 in the layer fail to switch on early postmitotic markers and to early divergence of the transcriptional programme of downregulate neuroepithelial markers. Thus, the loss of hindbrain somatic and visceral motor neuronal function of Phox2b in hindbrain motor neurons exemplifies differentiation. We provide genetic evidence that the a novel control point in the generation of CNS neurons. paired-like homeodomain protein Phox2b is required for the formation of all branchial and visceral, but not somatic, Key words: Neurogenesis, Motor neuron, Homeobox gene, motor neurons in the hindbrain. In mice lacking Phox2b, Rhombencephalon, Phox2b, Mouse INTRODUCTION of sm neurons has been studied most extensively and some of the transcriptional cascades controlling their differentiation are The specification of neuronal subtype identity in the beginning to be understood. -
The Evolving Genetic Landscape of Hirschprung Disease: an Update and Review
Review Article Clinics in Surgery Published: 11 Oct, 2017 The Evolving Genetic Landscape of Hirschprung Disease: An Update and Review Amit Kumar Yadav* and Gaurav Chopra Department of Pathology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India Abstract Hirschsprung Disease (HD) is a developmental disorder characterized by the complete absence of ganglion cells in the distal gastrointestinal tract. It is the most common cause of functional intestinal obstruction in neonates and children. The aganglionosis is believed to be either due to failure of neural crest cells to migrate, proliferate, differentiate or survive during gut development in the embryonic stage. The incidence of HD is estimated at 1/5000 live births and shows a male predominance. It is usually sporadic, although it can be familial and may be inherited as autosomal dominant or autosomal recessive. In 70% of cases, HD occurs as an isolated trait and in the other 30% it is associated with other congenital malformation syndromes. HD has a complex multifactorial etiology, and genetic factors play a key role in its pathogenesis. Several gene loci appear to be involved. Many of these have been identified by conducting Genome Wide Association (GWAS) studies and recently by Next Generation Sequencing (NGS). These genes encode for receptors, ligands (especially those participating in the RET, EDNRB and Semaphorin signaling pathways), transcriptional factors (PHOX2B & SOX10). These genes are involved in the neural crest cell development and migration that give rise to ganglion cells. Overall, the RET proto-oncogene is considered the major disease causing gene in HD. A greater understanding of the genetic landscape of this disease might pave way for genetic counseling, prenatal and preimplantation diagnosis in the management of HD. -
Expanding the Phenotypic Spectrum of PAX6 Mutations: from Congenital Cataracts to Nystagmus
G C A T T A C G G C A T genes Article Expanding the Phenotypic Spectrum of PAX6 Mutations: From Congenital Cataracts to Nystagmus Maria Nieves-Moreno 1,* , Susana Noval 1 , Jesus Peralta 1, María Palomares-Bralo 2 , Angela del Pozo 3 , Sixto Garcia-Miñaur 4, Fernando Santos-Simarro 4 and Elena Vallespin 5 1 Department of Ophthalmology, Hospital Universitario La Paz, 28046 Madrid, Spain; [email protected] (S.N.); [email protected] (J.P.) 2 Department of Molecular Developmental Disorders, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain; [email protected] 3 Department of Bioinformatics, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain; [email protected] 4 Department of Clinical Genetics, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain; [email protected] (S.G.-M.); [email protected] (F.S.-S.) 5 Department of Molecular Ophthalmology, Medical and Molecular Genetics Institue (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain; [email protected] * Correspondence: [email protected] Abstract: Background: Congenital aniridia is a complex ocular disorder, usually associated with severe visual impairment, generally caused by mutations on the PAX6 gene. The clinical phenotype of PAX6 mutations is highly variable, making the genotype–phenotype correlations difficult to establish. Methods: we describe the phenotype of eight patients from seven unrelated families Citation: Nieves-Moreno, M.; Noval, with confirmed mutations in PAX6, and very different clinical manifestations. -
Pax6 During Visual System Development
Hedgehog-dependent E3-ligase Midline1 regulates ubiquitin-mediated proteasomal degradation of Pax6 during visual system development Thorsten Pfirrmanna,1, Enrico Jandta,1, Swantje Ranfta,b, Ashwin Lokapallya, Herbert Neuhausa, Muriel Perronc, and Thomas Hollemanna,2 aInstitute for Physiological Chemistry, University of Halle-Wittenberg, 06114 Halle, Germany; bGynecological Hospital, University Medical Center Mannheim, 68167 Mannheim, Germany; and cParis-Saclay Institute of Neuroscience, CNRS, Univ Paris Sud, Université Paris-Saclay, 91405 Orsay, France Edited by Richard M. Harland, University of California, Berkeley, CA, and approved July 19, 2016 (received for review January 16, 2016) Pax6 is a key transcription factor involved in eye, brain, and pancreas remains unclear how Pax6 protein is removed from the eyestalk development. Although pax6 is expressed in the whole prospective territory on time. Some authors report the regulation of Pax6 retinal field, subsequently its expression becomes restricted to the activity by posttranslational modifications (21–23), and most optic cup by reciprocal transcriptional repression of pax6 and pax2. interestingly, Tuoc et al. showed that in cortical progenitor cells, However, it remains unclear how Pax6 protein is removed from the Pax6 protein is degraded by the proteasome mediated by Trim11 eyestalk territory on time. Here, we report that Mid1, a member of (24). However, the existence of similar mechanisms leading to the RBCC/TRIM E3 ligase family, which was first identified in patients the development of the visual system is not known. with the X-chromosome–linked Opitz BBB/G (OS) syndrome, inter- The data of our present study show that Midline1 (Mid1) acts with Pax6. We found that the forming eyestalk is a major do- serves as one of these links. -
Supplementary Materials
Supplementary Materials + - NUMB E2F2 PCBP2 CDKN1B MTOR AKT3 HOXA9 HNRNPA1 HNRNPA2B1 HNRNPA2B1 HNRNPK HNRNPA3 PCBP2 AICDA FLT3 SLAMF1 BIC CD34 TAL1 SPI1 GATA1 CD48 PIK3CG RUNX1 PIK3CD SLAMF1 CDKN2B CDKN2A CD34 RUNX1 E2F3 KMT2A RUNX1 T MIXL1 +++ +++ ++++ ++++ +++ 0 0 0 0 hematopoietic potential H1 H1 PB7 PB6 PB6 PB6.1 PB6.1 PB12.1 PB12.1 Figure S1. Unsupervised hierarchical clustering of hPSC-derived EBs according to the mRNA expression of hematopoietic lineage genes (microarray analysis). Hematopoietic-competent cells (H1, PB6.1, PB7) were separated from hematopoietic-deficient ones (PB6, PB12.1). In this experiment, all hPSCs were tested in duplicate, except PB7. Genes under-expressed or over-expressed in blood-deficient hPSCs are indicated in blue and red respectively (related to Table S1). 1 C) Mesoderm B) Endoderm + - KDR HAND1 GATA6 MEF2C DKK1 MSX1 GATA4 WNT3A GATA4 COL2A1 HNF1B ZFPM2 A) Ectoderm GATA4 GATA4 GSC GATA4 T ISL1 NCAM1 FOXH1 NCAM1 MESP1 CER1 WNT3A MIXL1 GATA4 PAX6 CDX2 T PAX6 SOX17 HBB NES GATA6 WT1 SOX1 FN1 ACTC1 ZIC1 FOXA2 MYF5 ZIC1 CXCR4 TBX5 PAX6 NCAM1 TBX20 PAX6 KRT18 DDX4 TUBB3 EPCAM TBX5 SOX2 KRT18 NKX2-5 NES AFP COL1A1 +++ +++ 0 0 0 0 ++++ +++ ++++ +++ +++ ++++ +++ ++++ 0 0 0 0 +++ +++ ++++ +++ ++++ 0 0 0 0 hematopoietic potential H1 H1 H1 H1 H1 H1 PB6 PB6 PB7 PB7 PB6 PB6 PB7 PB6 PB6 PB6.1 PB6.1 PB6.1 PB6.1 PB6.1 PB6.1 PB12.1 PB12.1 PB12.1 PB12.1 PB12.1 PB12.1 Figure S2. Unsupervised hierarchical clustering of hPSC-derived EBs according to the mRNA expression of germ layer differentiation genes (microarray analysis) Selected ectoderm (A), endoderm (B) and mesoderm (C) related genes differentially expressed between hematopoietic-competent (H1, PB6.1, PB7) and -deficient cells (PB6, PB12.1) are shown (related to Table S1). -
HAND2 Synergistically Enhances Transcription of Dopamine-ß
Available online at www.sciencedirect.com R Developmental Biology 262 (2003) 183–193 www.elsevier.com/locate/ydbio HAND2 synergistically enhances transcription of dopamine-- hydroxylase in the presence of Phox2a Haiming Xu,a Anthony B. Firulli,b Xiaotong Zhang,a and Marthe J. Howarda,* a Department of Anatomy and Neurobiology, Medical College of Ohio, 3000 Arlington Ave., Toledo, OH 43614, USA b Wells Center for Pediatric Research, James Whitcomb Riley Hospital for Children, 702 Barnhill Drive, Room 2666, Indianapolis, IN 46202-5225, USA Received for publication 28 March 2003, revised 5 June 2003, accepted 5 June 2003 Abstract Noradrenergic neuronal identity and differentiation are controlled by cascades of transcription factors acting downstream of BMP4, including the basic helix–loop–helix DNA binding protein HAND2 and the homeodomain factor Phox2a. Dopamine--hydroxylase (DBH) is the penultimate enzyme required for synthesis of norepinephrine and is thus a noradrenergic cell type-specific marker. We have examined the interaction of HAND2 and Phox2a at the DBH promoter. Using transient transfection of P19 or NT-2 cells, HAND2 is shown to synergistically enhance Phox2a-driven transcriptional activity at the DBH promoter, an effect that is enhanced by cAMP. While mutation of the Phox2a homeodomain binding sites HD1, HD2, and HD3 results in the loss of HAND2/Phox2a transactivation of DBH, it is the interaction of HAND2/Phox2a at the CRE/AP1-HD1/2 domains in the DBH enhancer that are required for synergistic activation by HAND2. We find that HAND2 functions as a transcriptional activator without directly binding to E-box sequences in the DBH promoter, suggesting that HAND2-mediated DBH activity occurs by protein–protein interactions with other transcriptional regulators. -
Drosophila Pax6 Promotes Development of the Entire Eye-Antennal Disc, Thereby Ensuring Proper Adult Head Formation
PAPER Drosophila Pax6 promotes development of the entire COLLOQUIUM eye-antennal disc, thereby ensuring proper adult head formation Jinjin Zhua, Sneha Palliyila, Chen Ranb, and Justin P. Kumara,1 aDepartment of Biology, Indiana University, Bloomington, IN 47405; and bDepartment of Biology, Stanford University, Stanford, CA 94305 Edited by Ellen V. Rothenberg, California Institute of Technology, Pasadena, CA, and accepted by Editorial Board Member Neil H. Shubin February 17, 2017 (received for review July 26, 2016) Paired box 6 (Pax6) is considered to be the master control gene for molecular battle among GRNs allows for the subdivision of the eye development in all seeing animals studied so far. In vertebrates, eye-antennal disc to be maintained within a single continuous it is required not only for lens/retina formation but also for the cellular field (13–16). Of the GRNs that are known to operate development of the CNS, olfactory system, and pancreas. Although within the eye-antennal disc, the retinal determination (RD) Pax6 plays important roles in cell differentiation, proliferation, and network, which controls eye development, is the best studied (17). patterning during the development of these systems, the underlying At the core of the RD network lie the Paired box 6 (Pax6) genes mechanism remains poorly understood. In the fruit fly, Drosophila eyeless (ey)andtwin of eyeless (toy), the SIX family member sine melanogaster, Pax6 also functions in a range of tissues, including oculis (so), the transcriptional coactivator eyes absent (eya), and the the eye and brain. In this report, we describe the function of Pax6 in Ski/Sno family member dachshund (dac)(17). -
Defining the Transcriptomic Landscape of the Developing Enteric Nervous System and Its Cellular Environment Sweta Roy-Carson Iowa State University, [email protected]
Genetics, Development and Cell Biology Genetics, Development and Cell Biology Publications 2017 Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment Sweta Roy-Carson Iowa State University, [email protected] Kevin Natukunda Iowa State University, [email protected] Hsien-chao Chou Iowa State University Narinder Pal Iowa State University Caitlin Farris Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/gdcb_las_pubs See next page for additional authors Part of the Cell and Developmental Biology Commons, and the Molecular Genetics Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ gdcb_las_pubs/202. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Genetics, Development and Cell Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Genetics, Development and Cell Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment Abstract Background: Motility and the coordination of moving food through the gastrointestinal tract rely on a complex network of neurons known as the enteric nervous system (ENS). Despite its critical function, many of the molecular mechanisms that direct the development of the ENS and the elaboration of neural network connections remain unknown. The og al of this study was to transcriptionally identify molecular pathways and candidate genes that drive specification, differentiation and the neural circuitry of specific neural progenitors, the phox2b expressing ENS cell lineage, during normal enteric nervous system development. -
Distinct Activities of Gli1 and Gli2 in the Absence of Ift88 and the Primary Cilia
Journal of Developmental Biology Article Distinct Activities of Gli1 and Gli2 in the Absence of Ift88 and the Primary Cilia Yuan Wang 1,2,†, Huiqing Zeng 1,† and Aimin Liu 1,* 1 Department of Biology, Eberly College of Sciences, Center for Cellular Dynamics, Huck Institute of Life Science, The Penn State University, University Park, PA 16802, USA; [email protected] (Y.W.); [email protected] (H.Z.) 2 Department of Occupational Health, School of Public Health, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang 110122, China * Correspondence: [email protected]; Tel.: +1-814-865-7043 † These authors contributed equally to this work. Received: 2 November 2018; Accepted: 16 February 2019; Published: 19 February 2019 Abstract: The primary cilia play essential roles in Hh-dependent Gli2 activation and Gli3 proteolytic processing in mammals. However, the roles of the cilia in Gli1 activation remain unresolved due to the loss of Gli1 transcription in cilia mutant embryos, and the inability to address this question by overexpression in cultured cells. Here, we address the roles of the cilia in Gli1 activation by expressing Gli1 from the Gli2 locus in mouse embryos. We find that the maximal activation of Gli1 depends on the cilia, but partial activation of Gli1 by Smo-mediated Hh signaling exists in the absence of the cilia. Combined with reduced Gli3 repressors, this partial activation of Gli1 leads to dorsal expansion of V3 interneuron and motor neuron domains in the absence of the cilia. Moreover, expressing Gli1 from the Gli2 locus in the presence of reduced Sufu has no recognizable impact on neural tube patterning, suggesting an imbalance between the dosages of Gli and Sufu does not explain the extra Gli1 activity.