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Olig2 and Ngn2 Function in Opposition to Modulate Gene Expression in Motor Neuron Progenitor Cells
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Olig2 and Ngn2 function in opposition to modulate gene expression in motor neuron progenitor cells Soo-Kyung Lee,1 Bora Lee,1 Esmeralda C. Ruiz, and Samuel L. Pfaff2 Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA Spinal motor neurons and oligodendrocytes are generated sequentially from a common pool of progenitors termed pMN cells. Olig2 is a bHLH-class transcription factor in pMN cells, but it has remained unclear how its transcriptional activity is modulated to first produce motor neurons and then oligodendrocytes. Previous studies have shown that Olig2 primes pMN cells to become motor neurons by triggering the expression of Ngn2 and Lhx3. Here we show that Olig2 also antagonizes the premature expression of post-mitotic motor neuron genes in pMN cells. This blockade is counteracted by Ngn2, which accumulates heterogeneously in pMN cells, thereby releasing a subset of the progenitors to differentiate and activate expression of post-mitotic motor neuron genes. The antagonistic relationship between Ngn2 and Olig2 is mediated by protein interactions that squelch activity as well as competition for shared DNA-binding sites. Our data support a model in which the Olig2/Ngn2 ratio in progenitor cells serves as a gate for timing proper gene expression during the development of pMN cells: Olig2high maintains the pMN state, thereby holding cells in reserve for oligodendrocyte generation, whereas Ngn2high favors the conversion of pMN cells into post-mitotic motor neurons. [Keywords: Motor neuron; oligodendrocyte; development; basic helix–loop–helix (bHLH); neurogenin (Ngn); Olig] Supplemental material is available at http://www.genesdev.org. -
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
International Journal of Molecular Sciences Article Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins M. Quadir Siddiqui 1,† , Maulik D. Badmalia 1,† and Trushar R. Patel 1,2,3,* 1 Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada; [email protected] (M.Q.S.); [email protected] (M.D.B.) 2 Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive, Calgary, AB T2N 4N1, Canada 3 Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Members of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and func- tions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share Citation: Siddiqui, M.Q.; Badmalia, similarities with transcriptional regulators and have positively charged electrostatic patches, which M.D.; Patel, T.R. -
The NOTCH4-HEY1 Pathway Induces Epithelial Mesenchymal Transition in Head and Neck Squamous Cell Carcinoma
Author Manuscript Published OnlineFirst on November 16, 2017; DOI: 10.1158/1078-0432.CCR-17-1366 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. The NOTCH4-HEY1 pathway induces epithelial mesenchymal transition in head and neck squamous cell carcinoma Authors: Takahito Fukusumi1, Theresa W Guo2, Akihiro Sakai1, Mizuo Ando1, Shuling Ren1, Sunny Haft1, Chao Liu1, Panomwat Amornphimoltham1, J. Silvio Gutkind1, Joseph A Califano1 1 Moores Cancer Center, University of California San Diego, 3855 Health Science Drive, MC 0803 La Jolla, California 92093, U.S.A. 2 Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, 1550 Orleans Street, Baltimore, Maryland 21231, U.S.A. Running Title: NOTCH4-HEY1 induces EMT in HNSCC Key Words: Head and neck squamous cell carcinoma, TCGA, NOTCH4, HEY1, EMT Financial Support This study was supported by National Institute of Dental and Craniofacial Research (NIDCR, number: R01DE023347). J.A.Califano received this grant. Correspondence: Joseph A. Califano, MD, Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, 3855 Health Science Drive, MC 0803 La Jolla, California 92093, U.S.A. Phone: 619-543-7895; E-mail; [email protected] Disclosure of Potential Conflict of Interest The authors declare no potential conflicts of interest. 1 Downloaded from clincancerres.aacrjournals.org on October 1, 2021. © 2017 American Association for Cancer Research. Author Manuscript Published OnlineFirst on November 16, 2017; DOI: 10.1158/1078-0432.CCR-17-1366 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. ABSTRACT Background: Recently, several comprehensive genomic analyses demonstrated NOTCH1 and NOTCH3 mutations in head and neck squamous cell carcinoma (HNSCC) in approximately 20% of cases. -
The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid
The Capacity of Long-Term in Vitro Proliferation of Acute Myeloid Leukemia Cells Supported Only by Exogenous Cytokines Is Associated with a Patient Subset with Adverse Outcome Annette K. Brenner, Elise Aasebø, Maria Hernandez-Valladares, Frode Selheim, Frode Berven, Ida-Sofie Grønningsæter, Sushma Bartaula-Brevik and Øystein Bruserud Supplementary Material S2 of S31 Table S1. Detailed information about the 68 AML patients included in the study. # of blasts Viability Proliferation Cytokine Viable cells Change in ID Gender Age Etiology FAB Cytogenetics Mutations CD34 Colonies (109/L) (%) 48 h (cpm) secretion (106) 5 weeks phenotype 1 M 42 de novo 241 M2 normal Flt3 pos 31.0 3848 low 0.24 7 yes 2 M 82 MF 12.4 M2 t(9;22) wt pos 81.6 74,686 low 1.43 969 yes 3 F 49 CML/relapse 149 M2 complex n.d. pos 26.2 3472 low 0.08 n.d. no 4 M 33 de novo 62.0 M2 normal wt pos 67.5 6206 low 0.08 6.5 no 5 M 71 relapse 91.0 M4 normal NPM1 pos 63.5 21,331 low 0.17 n.d. yes 6 M 83 de novo 109 M1 n.d. wt pos 19.1 8764 low 1.65 693 no 7 F 77 MDS 26.4 M1 normal wt pos 89.4 53,799 high 3.43 2746 no 8 M 46 de novo 26.9 M1 normal NPM1 n.d. n.d. 3472 low 1.56 n.d. no 9 M 68 MF 50.8 M4 normal D835 pos 69.4 1640 low 0.08 n.d. -
Essential Role of Retinoblastoma Protein in Mammalian Hair Cell Development and Hearing
Essential role of retinoblastoma protein in mammalian hair cell development and hearing Cyrille Sage*, Mingqian Huang*, Melissa A. Vollrath†, M. Christian Brown‡, Philip W. Hinds§, David P. Corey†, Douglas E. Vetter¶, and Zheng-Yi Chen*ʈ *Neurology Service, Center for Nervous System Repair, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; †Howard Hughes Medical Institute and Department of Neurobiology, Harvard Medical School, Boston, MA 02115; ‡Department of Otology and Laryngology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, MA 02114; §Department of Radiation Oncology, Molecular Oncology Research Institute, Tufts–New England Medical Center, Boston, MA 02111; and ¶Departments of Neuroscience and Biomedical Engineering, Tufts University School of Medicine, Boston, MA 02111 Edited by Kathryn V. Anderson, Sloan–Kettering Institute, New York, NY, and approved March 27, 2006 (received for review December 9, 2005) The retinoblastoma protein pRb is required for cell-cycle exit of 10 (E10) causes an overproduction of sensory progenitor cells, embryonic mammalian hair cells but not for their early differenti- which subsequently differentiate into hair cells and supporting cells. ation. However, its role in postnatal hair cells is unknown. To study Remarkably, pRbϪ/Ϫ hair cells and supporting cells also continue the function of pRb in mature animals, we created a new condi- to differentiate and express cellular markers appropriate for their tional mouse model, with the Rb gene deleted primarily in the embryonic stages. Furthermore, pRbϪ/Ϫ hair cells are able to inner ear. Progeny survive up to 6 months. During early postnatal transduce mechanical stimuli and appear capable of forming syn- development, pRb؊/؊ hair cells continue to divide and can trans- apses with ganglion neurons. -
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Review Xatzipsalti Maria et al. Congenital Hypopituitarism: Various Genes, … Horm Metab Res 2018; 00: 00–00 Congenital Hypopituitarism: Various Genes, Various Phenotypes Authors Maria Xatzipsalti1, 2, Antonis Voutetakis1, Lela Stamoyannou2, George P. Chrousos1, Christina Kanaka-Gantenbein1 Affiliations ABSTRacT 1 Division of Endocrinology, Diabetes and Metabolism, The ontogenesis and development of the pituitary gland is a First Department of Pediatrics, Medical School, National highly complex process that depends on a cascade of transcrip- and Kapodistrian University of Athens, “Aghia Sofia” tion factors and signaling molecules. Spontaneous mutations Children's Hospital, Athens, Greece and transgenic murine models have demonstrated a role for 2 First Department of Pediatrics, “Aglaia Kyriakou” many of these factors, including HESX1, PROP1, PIT1, LHX3, Children's Hospital, Athens, Greece LHX4, SOX2, SOX3, OTX2, PAX6, FGFR1, SHH, GLI2, and FGF8 in the etiology of congenital hypopituitarism. Genetic muta- Key words tions in any of these factors can lead to congenital hypopitui- pituitary, combined pituitary hormone deficiency, congenital tarism, which is characterized by the deficiency in one or more hypopituitarism, transcription factors, syndromic hypopitui- pituitary hormones. The phenotype can be highly variable, tarism, non-syndromic hypopituitarism consisting of isolated hypopituitarism or more complex disor- ders. The same phenotype can be attributed to different gene received 27.03.2018 mutations; while a given gene mutation can -
Drosophila and Human Transcriptomic Data Mining Provides Evidence for Therapeutic
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome Author Abhay Sharma Institute of Genomics and Integrative Biology Council of Scientific and Industrial Research Delhi University Campus, Mall Road Delhi 110007, India Tel: +91-11-27666156, Fax: +91-11-27662407 Email: [email protected] Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 Running head: Pentylenetetrazole mechanism in Down syndrome 1 Abstract Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ Nature Precedings : hdl:10101/npre.2010.4330.1 Posted 5 Apr 2010 downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation. -
Motoneurons Derived from Embryonic Stem Cells Express Transcription Factors and Develop Phenotypes Characteristic of Medial Motor Column Neurons
3256 • The Journal of Neuroscience, March 22, 2006 • 26(12):3256–3268 Development/Plasticity/Repair Motoneurons Derived from Embryonic Stem Cells Express Transcription Factors and Develop Phenotypes Characteristic of Medial Motor Column Neurons Prabakaran Soundararajan,1 Gareth B. Miles,1 Lee L. Rubin,3 Robert M. Brownstone,1,2 and Victor F. Rafuse1 Departments of 1Anatomy and Neurobiology and 2Surgery, Dalhousie University, Halifax, Nova Scotia, Canada, B3H 1X5, and 3Curis, Inc., Cambridge, Massachusetts 02138 Embryonic stem (ES) cells differentiate into functional motoneurons when treated with a sonic hedgehog (Shh) agonist and retinoic acid (RA). Whether ES cells can be directed to differentiate into specific subtypes of motoneurons is unknown. We treated embryoid bodies generated from HBG3 ES cells with a Shh agonist and RA for 5 d in culture to induce motoneuron differentiation. Enhanced green fluorescentprotein(eGFP)expressionwasusedtoidentifyputativemotoneurons,becauseeGFPisexpressedunderthecontroloftheHb9 promoter in HBG3 cells. We found that 96 Ϯ 0.7% of the differentiated eGFP ϩ motoneurons expressed Lhx3, a homeobox gene expressed by postmitotic motoneurons in the medial motor column (MMCm ), when the treated cells were plated on a neurite-promoting substrate for 5 d. When the treated embryoid bodies were transplanted into stage 17 chick neural tubes, the eGFP ϩ motoneurons migrated to the MMCm ,expressedLhx3,projectedaxonstotheappropriatetargetforMMCm motoneurons(i.e.,epaxialmuscles),andcontainedsynaptic vesicles within intramuscular -
Homotypic Clusters of Transcription Factor Binding Sites Are a Key Component of Human Promoters and Enhancers
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers Valer Gotea,1 Axel Visel,2,3 John M. Westlund,4 Marcelo A. Nobrega,4 Len A. Pennacchio,2,3 and Ivan Ovcharenko1,5 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA; 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 3United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 4Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA Clustering of multiple transcription factor binding sites (TFBSs) for the same transcription factor (TF) is a common feature of cis-regulatory modules in invertebrate animals, but the occurrence of such homotypic clusters of TFBSs (HCTs) in the human genome has remained largely unknown. To explore whether HCTs are also common in human and other verte- brates, we used known binding motifs for vertebrate TFs and a hidden Markov model–based approach to detect HCTs in the human, mouse, chicken, and fugu genomes, and examined their association with cis-regulatory modules. We found that evolutionarily conserved HCTs occupy nearly 2% of the human genome, with experimental evidence for individual TFs supporting their binding to predicted HCTs. More than half of the promoters of human genes contain HCTs, with a dis- tribution around the transcription start site in agreement with the experimental data from the ENCODE project. In addition, almost half of the 487 experimentally validated developmental enhancers contain them as well—a number more than 25-fold larger than expected by chance. -
Genomics 93 (2009) 449–460
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 93 (2009) 449–460 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches Michelle L. Brinkmeier a, Shannon W. Davis a, Piero Carninci b, James W. MacDonald c, Jun Kawai b, Debashis Ghosh e,1, Yoshihide Hayashizaki b, Robert H. Lyons d, Sally A. Camper a,⁎ a Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA b Omics Science Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan c Affymetrix and cDNA Microarray Core Facility, University of Michigan Cancer Center, Ann Arbor, MI 48109-0946, USA d Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109-5638, USA e Department of Biostatistics, School of Public Health, University of Michigan, 48109-2029, USA article info abstract Article history: We report a catalog of the mouse embryonic pituitary gland transcriptome consisting of five cDNA libraries Received 13 December 2007 including wild type tissue from E12.5 and E14.5, Prop1df/df mutant at E14.5, and two cDNA subtractions: E14.5 Accepted 24 November 2008 WT–E14.5 Prop1df/df and E14.5 WT–E12.5 WT. DNA sequence information is assembled into a searchable Available online 11 February 2009 database with gene ontology terms representing 12,009 expressed genes. We validated coverage of the libraries by detecting most known homeobox gene transcription factor cDNAs. -
The Transcriptome of Utricle Hair Cell Regeneration in the Avian Inner Ear
The Journal of Neuroscience, March 5, 2014 • 34(10):3523–3535 • 3523 Development/Plasticity/Repair The Transcriptome of Utricle Hair Cell Regeneration in the Avian Inner Ear Yuan-Chieh Ku,1 Nicole A. Renaud,1 Rose A. Veile,1 Cynthia Helms,1 Courtney C.J. Voelker,2 Mark E. Warchol,2 and Michael Lovett1 1Department of Genetics and 2Department of Otolaryngology, Washington University School of Medicine, St Louis, Missouri 63110 Sensory hair cell loss is the major cause of hearing and balance disorders. Mammals are incapable of sustained hair cell regeneration, but lower vertebrates can regenerate these mechano-electrical transducers. We present the first comprehensive transcriptome (by mRNA- Seq) of hair cell regeneration in the chick utricle. We provide pathway and pattern annotations and correlate these with the phenotypic events that occur during regeneration. These patterns are surprisingly synchronous and highly punctuated. We show how these patterns are a new resource for identifying components of the hair cell transcriptome and identify 494 new putative hair-cell-specific genes and validate three of these (of three tested) by immunohistochemical staining. We describe many surprising new components and dynamic expression patterns, particularly within NOTCH signaling. For example, we show that HES7 is specifically expressed during utricle hair cell regeneration and closely parallels the expression of HES5. Likewise, the expression of ATOH1 is closely correlated with HEYL and the HLH inhibitory transcription factors ID1, ID2, and ID4. -
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Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility This information is current as Ramesh Ram, Munish Mehta, Quang T. Nguyen, Irma of September 23, 2021. Larma, Bernhard O. Boehm, Flemming Pociot, Patrick Concannon and Grant Morahan J Immunol 2016; 196:3043-3053; Prepublished online 24 February 2016; doi: 10.4049/jimmunol.1502056 Downloaded from http://www.jimmunol.org/content/196/7/3043 Supplementary http://www.jimmunol.org/content/suppl/2016/02/19/jimmunol.150205 Material 6.DCSupplemental http://www.jimmunol.org/ References This article cites 44 articles, 5 of which you can access for free at: http://www.jimmunol.org/content/196/7/3043.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 23, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility Ramesh Ram,*,† Munish Mehta,*,† Quang T.