Download Thesis

Total Page:16

File Type:pdf, Size:1020Kb

Download Thesis This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ The Development and Function of Cerebellar Nucleo-Olivary Neurons Prekop, Hong-Ting Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 10. Oct. 2021 Hong-Ting Prekop Centre for Developmental Neurobiology King’s College London Thesis submitted for the degree of Doctor of Philosophy (PhD) September 2017 Abstract The neuronal circuitry between the cerebellum and inferior olive is of crucial importance in motor function. While the climbing fibres that send olivary signals to the cerebellum have been shown to play a significant role in modulating cerebellar output, little is known of the origins or function of the nucleo-olivary neurons of the cerebellar nuclei that send reciprocal feedback to the inferior olive. In this thesis, the Sox14 gene is identified as a novel genetic developmental marker for nucleo-olivary neurons of the lateral and interposed, but not medial, cerebellar nuclei. Using Sox14-GFP and Sox14-Cre knock-in and Sox14 knock-out mouse lines, in combination with birth dating, marker analysis and tract tracing techniques, I characterised the projections and development of nucleo-olivary neurons. These experiments established that Sox14 is expressed in early born GABAergic nuclear projection neurons that exclusively target the inferior olive. A separate population of Sox14+ cells in Nucleus Y target the oculomotor nucleus. Sox14 expression is observed from E12.5 directly ventral to the nuclear transitory zone, where glutamatergic nuclear cells are known to reside during development. Injection of Cre-dependent AAV-mCherry-flex-dtA was used to drive expression of diphtheria toxin A subunit in Sox14 expressing cells. Ablation of Sox14+ nucleo- olivary neurons leads to some deficits in motor performance and motor learning. However, no deficits in associative motor learning were observed, suggesting that models of associative learning that invoke a key role for the nucleo-olivary feedback may be incorrect or incomplete. 2 This work establishes that nucleo-olivary neurons of the lateral and interposed cerebellar nuclei comprise a homogeneous and genetically distinct population and sheds light on the function of this projection in cerebellar function. Furthermore, this thesis establishes Sox14 transgenic mice as a unique tool in cerebellar research that will provide an important window on the function of the cerebellum in future studies. 3 Acknowledgments / funding With gratitude, this thesis represents independent research funded by the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London. The views expressed are my own and not necessarily those of the NHS, the NIHR, or the Department of Health. I would like to thank Prof. Thomas Jessell and Dr. Laskaro Zagoraiou for the generation of the Sox14-Gfp and Sox14-Cre mouse lines. The mice are central to the research, so thank you for the generosity in making the mice available. Thank you to Stephanie and Reinko at Noldus, who arranged the trial period for use of the Erasmus ladder. They were so kind in arranging to come to help me set up and provided technical assistance in the analysis of the data. I owe much of this work to the dedicated supervision from Alessio Delogu and Richard Wingate. Alessio, I can’t think of a more competent and knowledgeable mentor that I could have had. The range of skills that you have acquired throughout your career and was able to impart onto me (as best as you could!) is inspiring. I have learnt a lot of technical skills and even though not all of them worked out, you encouraged me to troubleshoot and supported new ideas. Richard, our discussions helped me enormously to think through the data and put them into context. Your enthusiasm for the subject and positivity in general is infectious and was crucial in keeping me on track, particularly over the writing up period. I also have many to thank and acknowledge in both the labs that I was a part of. Thanks to Polona and Olivier for the collaborative efforts in the production of AAVs and for general lab assistance. Without you both, my weekends would have been filled with long journeys for short tasks in the lab! Thanks to Marcela, Tristan, Micha, Margarita, Flo and Leigh for all the help provided for my work at the CDN, the pub trips, coffee breaks, constant snacks and for increased happiness in general! I would like to acknowledge assistance with some of the data presented in this thesis. I had the opportunity to supervise Niyoti for her master’s research project and Daniel for his Erasmus project, who both helped with the production of the Cre-expressing 4 HEK293 cell line presented in Chapter 3. I am very grateful to Anna, an Erasmus student, who I only knew for a short while before I left the lab. She helped with the Gad1 ISH for the ablation analysis presented in Chapter 5 and repeating some of the BrdU data presented in Chapter 4. Special thanks to the other labs at the Wohl and IoP, especially to Cathy Fernandes for lending me equipment for mouse behavioural tests and helping me to perform the pilot testing in Appendix D. Thank you to all those in Deepak Srivastava’s lab for help in primary cell culture work and the antibodies “borrowed”. Thank you to all in the Wohl for the lunch times and the socials. You all made it such a pleasant and friendly work environment to be part of. During the relentless hours spent in the animal facility, I would like to thank Ted, John and Louis for their dedication and assistance in caring for the mice and for me in times of panic. This research project has been a steadfast pursuit during four years in which my life has radically changed. I must thank all those outside my “science world” for their support and affection throughout. To my various housemates, especially Esme and Hannah, thank you for bearing with my crazy use of the fridge. Christchurch Kensington is the sole reason I chose to complete a PhD in London. Thank you to all in this adopted family for your love, prayers and friendship over the years. Thank you to my real family for loving me regardless of what path I choose in life. Mum and dad, you are my role models, with your hard work ethic and inexhaustible love for others. You have shown me what it looks like to prioritise people and give time generously. Chris, thank you for dating, proposing to and marrying a PhD student! Your support has been unconditional and constant. Thank you for the emotional support, the endless cups of tea and the proof-reading. You have made all the transitions over the past years effortless with your loving compromises. Lastly, I would like to thank God for his work in my life. Soli Deo gloria. 5 The highest reward for a person's toil is not what they get for it, but what they become by it. -John Ruskin 6 Table of Contents Abstract 2 Acknowledgments / funding 4 Table of Contents 7 Table of Figures 15 Table of Tables 17 1 Introduction 18 1.1 What are Cerebellar nuclei? 18 1.2 Structure of the cerebellum 20 1.3 Nuclear cells as components of models of cerebellar function 24 1.3.1 Circuitry is linked to function 24 1.3.2 Convergent Networks within the cerebellar nuclei 26 1.3.3 Cerebellar role in Motor Learning 29 1.3.4 Cerebellar role in Motor timing 31 1.3.5 Non-motor functions of the cerebellum 32 1.4 Nucleus anatomy and Cellular diversity 33 1.4.1 Glutamatergic Projection Neurons 34 1.4.2 Nucleo-Olivary Projection Neurons 35 1.4.3 Glycinergic Projection Neurons 35 1.4.4 Interneurons 36 1.5 Development of the Cerebellum 38 1.6 Development of Cerebellar nuclei 40 1.6.1 Origin of glutamatergic neurons 41 1.6.2 Origin of GABAergic projection neurons 43 1.6.3 Origin of Other nuclear neurons 44 1.6.4 Nucleogenesis and cell migration 45 1.6.5 Evolution and the diversification of cerebellar nuclei 47 7 1.7 Cerebellar nuclei and disease 48 1.8 Sox14 and the Cerebellar nuclei 53 2 Characterisation 54 2.1 Introduction 54 2.1.1 The Sox14 gene 54 2.1.2 Identifying the cells of the cerebellar nuclei 56 2.1.2.1 GABA and GAD 58 2.1.2.2 Calcium binding proteins 59 2.1.3 Aims of the Chapter 60 2.2 Results 61 2.2.1 Sox14+ cells are non-uniformly distributed across the cerebellar nuclei 61 2.2.2 Identification of Sox14+ cells by immunohistochemistry 69 2.2.2.1
Recommended publications
  • Uncovering the Signaling Landscape Controlling Breast Cancer Cell Migration Identifies Novel Metastasis Driver Genes
    ARTICLE https://doi.org/10.1038/s41467-019-11020-3 OPEN Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes Esmee Koedoot1,4, Michiel Fokkelman 1,4, Vasiliki-Maria Rogkoti1,4, Marcel Smid2, Iris van de Sandt1, Hans de Bont1, Chantal Pont1, Janna E. Klip1, Steven Wink 1, Mieke A. Timmermans2, Erik A.C. Wiemer2, Peter Stoilov3, John A. Foekens2, Sylvia E. Le Dévédec 1, John W.M. Martens 2 & Bob van de Water1 1234567890():,; Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential for cancer cell migration, amplified in human primary breast tumors and associated with metastasis-free survival. Depletion of PRPF4B, BUD31 and BPTF causes primarily down regulation of genes involved in focal adhesion and ECM-interaction pathways. PRPF4B is essential for TNBC metastasis formation in vivo, making PRPF4B a candidate for further drug development. 1 Division of Drug Discovery and Safety, LACDR, Leiden University, Einsteinweg 55, Leiden 2333 CC, Netherlands. 2 Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3008 AE, Netherlands.
    [Show full text]
  • Drosophila Valosin-Containing Protein Is Required for Dendrite Pruning Through a Regulatory Role in Mrna Metabolism
    Drosophila Valosin-Containing Protein is required for dendrite pruning through a regulatory role in mRNA metabolism Sebastian Rumpfa,b,c,1,2, Joshua A. Bagleya,b,c, Katherine L. Thompson-Peera,b,c, Sijun Zhua,b,c,3, David Gorczycaa,b,c, Robert B. Becksteadd, Lily Yeh Jana,b,c, and Yuh Nung Jana,b,c,2 aHoward Hughes Medical Institute and Departments of bPhysiology and cBiochemistry, University of California, San Francisco, CA 94158; and dPoultry Science Department, University of Georgia, Athens, GA 30602 Contributed by Yuh Nung Jan, April 16, 2014 (sent for review December 20, 2013) The dendritic arbors of the larval Drosophila peripheral class IV for pruning (2, 7, 8), as well as the ATPase associated with di- dendritic arborization neurons degenerate during metamorphosis verse cellular activities (AAA) ATPase Valosin-Containing in an ecdysone-dependent manner. This process—also known as Protein (VCP) (CDC48 in yeast, p97 in vertebrates, also known dendrite pruning—depends on the ubiquitin–proteasome system as TER94 in Drosophila) (11), which acts as a chaperone for (UPS), but the specific processes regulated by the UPS during prun- ubiquitylated proteins (12). Interestingly, autosomal dominant ing have been largely elusive. Here, we show that mutation or mutations in the human VCP gene cause hereditary forms of inhibition of Valosin-Containing Protein (VCP), a ubiquitin-depen- ubiquitin-positive frontotemporal dementia (FTLD-U) (13) and dent ATPase whose human homolog is linked to neurodegenera- amyotrophic lateral sclerosis (ALS) (14). A hallmark of these tive disease, leads to specific defects in mRNA metabolism and that diseases is the occurrence of both cytosolic and nuclear ubiq- this role of VCP is linked to dendrite pruning.
    [Show full text]
  • SOX2 and SOX12 Are Predictive of Prognosis in Patients with Clear Cell Renal Cell Carcinoma
    4564 ONCOLOGY LETTERS 15: 4564-4570, 2018 SOX2 and SOX12 are predictive of prognosis in patients with clear cell renal cell carcinoma WEIJIE GU1,2*, BEIHE WANG1,2*, FANGNING WAN1,2*, JUNLONG WU1,2, XIAOLIN LU1,2, HONGKAI WANG1,2, YAO ZHU1,2, HAILIANG ZHANG1,2, GUOHAI SHI1,2, BO DAI1,2 and DINGWEI YE1,2 1Department of Urology, Fudan University Shanghai Cancer Center; 2Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China Received October 21, 2016; Accepted September 28, 2017 DOI: 10.3892/ol.2018.7828 Abstract. Sex-determining region Y-box protein (SOX) genes were associated with poor prognosis for OS (log-rank test, all serve an important role in cancer growth and metastasis. P<0.05). SOX2 and SOX12 were identified as independent The present study aimed to determine the predictive ability prognostic factors of OS in clear cell RCC. of SOX and associated genes identified through molecular network in clear cell renal cell carcinoma (RCC). A total of Introduction 505 patients with clear cell RCC from The Cancer Genome Atlas (TCGA) cohorts were collected in this study. The Renal cell carcinoma (RCC) accounts for ~2-3% of all malig- expression profile of SOX and associated genes were obtained nancies worldwide (1). Despite an increasing proportion of from the TCGA RNAseq database. Clinicopathological patients with early stage tumors at diagnosis and the develop- characteristics, including age, gender, tumor grade, stage, ment of novel treatment strategies, a quarter still present with laterality disease-free-survival and overall survival (OS) were locally advanced or metastatic disease, and eventually, one collected.
    [Show full text]
  • Loss of the Neural-Specific BAF Subunit ACTL6B Relieves Repression of Early Response Genes and Causes Recessive Autism
    Loss of the neural-specific BAF subunit ACTL6B relieves repression of early response genes and causes recessive autism Wendy Wenderskia,b,c,d, Lu Wange,f,g,1, Andrey Krokhotina,b,c,d,1, Jessica J. Walshh, Hongjie Lid,i, Hirotaka Shojij, Shereen Ghoshe,f,g, Renee D. Georgee,f,g, Erik L. Millera,b,c,d, Laura Eliasa,b,c,d, Mark A. Gillespiek, Esther Y. Sona,b,c,d, Brett T. Staahla,b,c,d, Seung Tae Baeke,f,g, Valentina Stanleye,f,g, Cynthia Moncadaa,b,c,d, Zohar Shiponya,b,c,d, Sara B. Linkerl, Maria C. N. Marchettol, Fred H. Gagel, Dillon Chene,f,g, Tipu Sultanm, Maha S. Zakin, Jeffrey A. Ranishk, Tsuyoshi Miyakawaj, Liqun Luod,i, Robert C. Malenkah, Gerald R. Crabtreea,b,c,d,2, and Joseph G. Gleesone,f,g,2 aDepartment of Pathology, Stanford Medical School, Palo Alto, CA 94305; bDepartment of Genetics, Stanford Medical School, Palo Alto, CA 94305; cDepartment of Developmental Biology, Stanford Medical School, Palo Alto, CA 94305; dHoward Hughes Medical Institute, Stanford University, Palo Alto, CA 94305; eDepartment of Neuroscience, University of California San Diego, La Jolla, CA 92037; fHoward Hughes Medical Institute, University of California San Diego, La Jolla, CA 92037; gRady Children’s Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92037; hNancy Pritztker Laboratory, Department of Psychiatry and Behavioral Sciences, Stanford Medical School, Palo Alto, CA 94305; iDepartment of Biology, Stanford University, Palo Alto, CA 94305; jDivision of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, 470-1192 Toyoake, Aichi, Japan; kInstitute for Systems Biology, Seattle, WA 98109; lLaboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037; mDepartment of Pediatric Neurology, Institute of Child Health, Children Hospital Lahore, 54000 Lahore, Pakistan; and nClinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, 12311 Cairo, Egypt Edited by Arthur L.
    [Show full text]
  • GATA Transcription Factors and Their Co-Regulators Guide the Development Of
    GATA transcription factors and their co-regulators guide the development of GABAergic and serotonergic neurons in the anterior brainstem Laura Tikker Molecular and Integrative Biosciences Research Programme Faculty of Biological and Environmental Sciences Doctoral Programme Integrative Life Science University of Helsinki ACADEMIC DISSERTATION Doctoral thesis, to be presented for public examination, with the permission of the Faculty of Biological and Environmental Sciences of the University of Helsinki, in Raisio Hall (LS B2) in Forest Sciences building, Latokartanonkaari 7, Helsinki, on the 3rd of April, 2020 at 12 noon. Supervisor Professor Juha Partanen University of Helsinki (Finland) Thesis Committee members Docent Mikko Airavaara University of Helsinki (Finland) Professor Timo Otonkoski University of Helsinki (Finland) Pre-examinators Docent Satu Kuure University of Helsinki (Finland) Research Scientist Siew-Lan Ang, PhD The Francis Crick Institute (United Kingdom) Opponent Research Scientist Johan Holmberg, PhD Karolinska Institutet (Sweden) Custos Professor Juha Partanen University of Helsinki (Finland) The Faculty of Biological and Environmental Sciences, University of Helsinki, uses the Urkund system for plagiarism recognition to examine all doctoral dissertations. ISBN: 978-951-51-5930-4 (paperback) ISBN: 978-951-51-5931-1 (PDF) ISSN: 2342-3161 (paperback) ISSN: 2342-317X (PDF) Printing house: Painosalama Oy Printing location: Turku, Finland Printed on: 03.2020 Cover artwork: Serotonergic neurons in adult dorsal raphe (mouse).
    [Show full text]
  • Mechanisms Regulating Gabaergic Neurogenesis in the Developing Mouse Midbrain
    WISSENSCHAFTSZENTRUM WEIHENSTEPHAN FÜR ERNÄHRUNG, LANDNUTZUNG UND UMWELT LEHRSTUHL FÜR ENTWICKLUNGSGENETIK Mechanisms regulating GABAergic neurogenesis in the developing mouse midbrain Clara Elisabeth Teresa Agathe Tabea Zoe Wende Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ. Prof. Dr. S. Scherer Prüfer der Dissertation: 1. Univ. Prof. Dr. W. Wurst 2. Univ. Prof. Dr. H. Lickert Die Dissertation wurde am 28.07.2015 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 12.11.2015 angenommen. Für meinen Großvater 2 1 CONTENT 2 SUMMARY ......................................................................................................................................................... 7 3 ZUSAMMENFASSUNG .................................................................................................................................... 9 4 REVIEW OF LITERATURE ......................................................................................................................... 11 4.1 THE NEUROTRANSMITTER Γ-AMINOBUTYRIC ACID ..................................................................................... 11 4.1.1 TWO ENZYMES FOR THE SYNTHESIS OF GABA ........................................................................................................
    [Show full text]
  • Grimme, Acadia.Pdf
    MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Bachelors of Science in Biological Sciences with Distinction Spring 2018 © 2018 Acadia Grimme All Rights Reserved MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme Approved: __________________________________________________________ Matthew E. R. Butchbach, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Deni S. Galileo, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Carlton R. Cooper, Ph.D. Committee member from the Department of Biological Sciences Approved: __________________________________________________________ Gary H. Laverty, Ph.D. Committee member from the Board of Senior Thesis Readers Approved: __________________________________________________________ Michael Chajes, Ph.D. Chair of the University Committee on Student and Faculty Honors ACKNOWLEDGMENTS I would like to acknowledge my thesis director Dr. Butchbach for his wonderful guidance and patience as I worked through my project. He has been an excellent research mentor over the last two years and I am forever thankful that he welcomed me into his lab. His dedication to his work inspires me as an aspiring research scientist. His lessons will carry on with me as I pursue future research in graduate school and beyond. I would like to thank both current and former members of the Motor Neuron Disease Laboratory: Sambee Kanda, Kyle Hinkle, and Andrew Connell. Sambee and Andrew patiently taught me many of the techniques I utilized in my project, and without them it would not be what it is today.
    [Show full text]
  • The Ciliopathy Gene Ftm/Rpgrip1l Controls Mouse Forebrain Patterning Via Region-Specific Modulation of Hedgehog/Gli Signaling
    2398 • The Journal of Neuroscience, March 27, 2019 • 39(13):2398–2415 Development/Plasticity/Repair The Ciliopathy Gene Ftm/Rpgrip1l Controls Mouse Forebrain Patterning via Region-Specific Modulation of Hedgehog/Gli Signaling Abraham Andreu-Cervera, Isabelle Anselme, Alice Karam, Christine Laclef, Martin Catala, and X Sylvie Schneider-Maunoury Sorbonne Universite´, Centre National de la Recherche Scientifique (CNRS) UMR7622, Institut national pour la Sante´ et la Recherche Me´dicale U1156, Institut de Biologie Paris Seine-Laboratoire de Biologie du De´veloppement (IBPS-LBD), 75005 Paris, France Primary cilia are essential for CNS development. In the mouse, they play a critical role in patterning the spinal cord and telencephalon via the regulation of Hedgehog/Gli signaling. However, despite the frequent disruption of this signaling pathway in human forebrain mal- formations, the role of primary cilia in forebrain morphogenesis has been little investigated outside the telencephalon. Here we studied development of the diencephalon, hypothalamus and eyes in mutant mice in which the Ftm/Rpgrip1l ciliopathy gene is disrupted. At the end of gestation, Ftm Ϫ/Ϫ fetuses displayed anophthalmia, a reduction of the ventral hypothalamus and a disorganization of diencephalic nuclei and axonal tracts. In Ftm Ϫ/Ϫ embryos, we found that the ventral forebrain structures and the rostral thalamus were missing. Optic vesicles formed but lacked the optic cups. In Ftm Ϫ/Ϫ embryos, Sonic hedgehog (Shh) expression was virtually lost in the ventral forebrain but maintained in the zona limitans intrathalamica (ZLI), the mid-diencephalic organizer. Gli activity was severely downregulated but not lost in the ventral forebrain and in regions adjacent to the Shh-expressing ZLI.
    [Show full text]
  • Function of Sox2 As a Transcriptional Repressor
    Function of Sox2 as a transcriptional repressor By Yu-Ru Liu, M. Sc Thesis submitted to the University of Nottingham for the degree of Doctor of Philosophy September 2011 1 Abstract Sox2 is one of the earliest known transcription factors to be expressed during development of the nervous system (Rex et al., 1997; Silvia Brunelli, 2003; Wang et al., 2006b; Dee et al., 2008). Ectodermal cells expressing Sox2 have the potential to differentiate into nerve cells. Cells expressing Sox2 are specified to a neural fate during neural induction. Sox2 belongs to the SoxB1 family, comprising Sox1, Sox2 and Sox3, which are generally considered to activate specific target genes, whereas, the SoxB2 group, Sox14 and Sox21, act as transcriptional repressors (Uchikawa, Kamachi, & Kondoh, 1999). However, Sox2 has also been demonstrated to act as a repressor (Kopp et al., 2008) which implies that Sox2 could have a dual-function in vivo . Previous studies indicated that the HMG box-containing protein, Tcf/Lef, interacts with the transcriptional co-repressor, Groucho (Helen Brantjes, 2001). We therefore set out to determine if interaction with the Groucho co-repressor could also explain the repressor ability of Sox2. In this study, we have examined the interaction between Sox2 and Groucho using nuclear translocation, yeast-two-hybrid and co-immunoprecipitation assays. The data suggest that Sox2 interacts with Groucho through a C-terminal, engrailed-like motif. The effect of Groucho on Sox2 function was measured using a luciferase reporter assay. The transcriptional activation activity of Sox2 was repressed after co-expressing with Groucho. To address the biological function of Sox2-Groucho interaction, a loss-of-repressor-function mutant of Sox2 was created by point mutating the essential engrailed-like motif.
    [Show full text]
  • Table 1. Known Neural Tube Transcription Factors
    Table 1. Known neural tube transcription factors Gene Green White Probe Max. Fold ∆b Avg ∆c Review ref.d Functional Expression sets sig.a ref.e ref. f Mantle Zone Lhx2 None dI1 1 815 +3.4 na (1) nk (2) Lhx9 None dI1 3 269 +12.8 6.3 (1) nk (2) BarHl1 None dI1 2 100 +3.7 2.9† (1) nk (3) Brn3a dI5, dI4LB dI1,dI2,dI3 2 5556 -2.1 -2.3 (1) (4) (5) Foxd3 None dI2, V1 1 115 +7.5 na (1, 6) (7) (8, 9) Lhx1 dI4.dI6 dI2, M 2 5763 -7.3 -7.6 (1) nk (10, 11) Lhx5 dI4.dI6 dI2. 1 1589 -3.2 na (1) nk (10, 11) Isl1 None dI3, M 2 1215 +5.2 +5.0 (1, 6, 12) (13, 14) (15) Tlx3 dI5 dI3 1 729 -3.2 na (1, 6) (16) (17) Lbx1 dI4-dI6, dI4LA,dI4LB None 2 3374 -13.2 -11.8 (1, 6) (9, 18) (19) Pax2 dI4,dI6, dI4LA V0, V1 0 na na na (1, 6) nk (20) Drg11 dI4LB None 1 1467 -8.2 na (6) (21) (22) Ebf1 dI4L nk 4 1804 -1.9 -1.9* nk (23, 24) Ebf3 dI4L nk 2 2394 -1.9 -1.8* nk (23, 24) Phox2a dI5 None 1 23 -1.4*† na nk (25, 26) Lmx1b dI5, dI4LB None 2 601 -7.7* -4.5*† (1, 6) (26, 27) (10) Tlx1 dI5 None 1 214 -4.3* na (1, 6) (16, 28) (17, 29) Evx1 None V0 1 202 +5.1 na (6, 30) (31) (32) Evx2 None nk 1 3 no ∆† na (6) nk (33) En1 None V1 1 31 +3.5† na (6) (10, 34) (20) Gata2 None V2 2 160 +3.9 2.7* (35) (36) Gata3 None V2 1 189 +6.7 na (6) nk (36, 37) Sox14 None V1 1 17 +1.9*† na nk (38) Chx10 None V2 1 130 +5.9 na (6, 12) nk (39) Lhx3 None V2, MN 2 173 +6.6 +4.1* (12) (40, 41) (40) Lhx4 None MN 1 135 +3.7 +2.5† (12) (40, 41) (40) Isl2 None MN 1 27 1.2*† na (12) (42) (40) Hlxb9 None MN 1 7 no∆† na (12) (43, 44) (13) Etv1 None MN 3 197 +6.7 +4.4*† (6, 12) (45) (46) Etv4 None MN 2 7
    [Show full text]
  • Robles JTO Supplemental Digital Content 1
    Supplementary Materials An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma based on mRNA, microRNA and DNA Methylation Biomarkers Ana I. Robles1, Eri Arai2, Ewy A. Mathé1, Hirokazu Okayama1, Aaron Schetter1, Derek Brown1, David Petersen3, Elise D. Bowman1, Rintaro Noro1, Judith A. Welsh1, Daniel C. Edelman3, Holly S. Stevenson3, Yonghong Wang3, Naoto Tsuchiya4, Takashi Kohno4, Vidar Skaug5, Steen Mollerup5, Aage Haugen5, Paul S. Meltzer3, Jun Yokota6, Yae Kanai2 and Curtis C. Harris1 Affiliations: 1Laboratory of Human Carcinogenesis, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 2Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 3Genetics Branch, NCI-CCR, National Institutes of Health, Bethesda, MD 20892, USA. 4Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan. 5Department of Chemical and Biological Working Environment, National Institute of Occupational Health, NO-0033 Oslo, Norway. 6Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), 08916 Badalona (Barcelona), Spain. List of Supplementary Materials Supplementary Materials and Methods Fig. S1. Hierarchical clustering of based on CpG sites differentially-methylated in Stage I ADC compared to non-tumor adjacent tissues. Fig. S2. Confirmatory pyrosequencing analysis of DNA methylation at the HOXA9 locus in Stage I ADC from a subset of the NCI microarray cohort. 1 Fig. S3. Methylation Beta-values for HOXA9 probe cg26521404 in Stage I ADC samples from Japan. Fig. S4. Kaplan-Meier analysis of HOXA9 promoter methylation in a published cohort of Stage I lung ADC (J Clin Oncol 2013;31(32):4140-7). Fig. S5. Kaplan-Meier analysis of a combined prognostic biomarker in Stage I lung ADC.
    [Show full text]
  • A Genomic and Functional Analysis Ancient Duplicated Conserved
    Downloaded from www.genome.org on May 1, 2007 Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis Gayle K. McEwen, Adam Woolfe, Debbie Goode, Tanya Vavouri, Heather Callaway and Greg Elgar Genome Res. 2006 16: 451-465; originally published online Mar 13, 2006; Access the most recent version at doi:10.1101/gr.4143406 Supplementary "Supplemental Research Data" data http://www.genome.org/cgi/content/full/gr.4143406/DC1 References This article cites 87 articles, 39 of which can be accessed free at: http://www.genome.org/cgi/content/full/16/4/451#References Article cited in: http://www.genome.org/cgi/content/full/16/4/451#otherarticles Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here Notes To subscribe to Genome Research go to: http://www.genome.org/subscriptions/ © 2006 Cold Spring Harbor Laboratory Press Downloaded from www.genome.org on May 1, 2007 Article Ancient duplicated conserved noncoding elements in vertebrates: A genomic and functional analysis Gayle K. McEwen,1,2,3,4 Adam Woolfe,1,2,4 Debbie Goode,1,4 Tanya Vavouri,1,2 Heather Callaway,1 and Greg Elgar1,5 1School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom; 2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, United Kingdom; 3MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, United Kingdom Fish–mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development.
    [Show full text]