DOCSLIB.ORG

Molecular Analysis of GTF2IRD1: a Protein Implicated in the Neurobehavioural Features of Williams-Beuren Syndrome

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Molecular Analysis of GTF2IRD1: a Protein Implicated in the Neurobehavioural Features of Williams-Beuren Syndrome Molecular analysis of GTF2IRD1: a protein implicated in the neurobehavioural features of Williams-Beuren Syndrome Jocelyn Widagdo BSc (Hons Class I) A thesis submitted to the University of New South Wales in fulfillment of the requirements for the degree of Doctor of Philosophy Faculty of Medicine University of New South Wales Sydney, Australia February 2011 COPYRIGHT STATEMENT ‘I hereby grant the University of New South Wales or its agents the right to archive and to make available my thesis or dissertation in whole or part in the University libraries in all forms of media, now or here after known, subject to the provisions of the Copyright Act 1968. I retain all proprietary rights, such as patent rights. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. I also authorise University Microfilms to use the 350 word abstract of my thesis in Dissertation Abstract International (this is applicable to doctoral theses only). I have either used no substantial portions of copyright material in my thesis or I have obtained permission to use copyright material; where permission has not been granted I have applied/will apply for a partial restriction of the digital copy of my thesis or dissertation.' Signed ( 05 j 5- o t \ Date AUTHENTICITY STATEMENT ‘I certify that the Library deposit digital copy is a direct equivalent of the final officially approved version of my thesis. No emendation of content has occurred and if there are any minor variations in formatting, they are the result of the conversion to digital format.’ Signed Date ORIGINALITY STATEMENT ‘I hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom I have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.’ Signed JOCELYN WIDAGDO Date ACKNOWLEDGEMENTS There are so many people who have given me supports in many ways during the past four years of this challenging yet most rewarding experience. Firstly, thank you to Prof Edna Hardeman, who has given me continual supports and encouragement since I was an undergraduate summer scholar, and which I have no doubt, will keep going beyond this day. I am grateful for your mentoring, attentiveness, and critical mind that always push me to find ways to reach for the 'answer. To Dr Stephen Palmer, 1 am greatly thankful for your dedicated supervision, invaluable advice from project direction to lab technical matters, and your support during the intense thesis writing. Yes, it has come to an end! Thank you to Kylie Taylor who is always happy to help with any experiments and lab matters. To all members of the Oncology Research Unit and the bigger Cellular Genetic Medicine Unit, thank you for the friendship and making work so much more enjoyable. Thanks to Prof Peter Gunning for the many enthusiastic discussions, constant support and direction to the project. Thanks to Renee Szokolai for keeping our lab safe and running efficiently. Thanks to Christine Lucas who can always bring laughter and to Josephine Joya for being the mother figure in the lab. I would like to thank the past members of the lab and colleagues at the Children’s Medical Research Institute (CMRI) at Westmead for getting me started in the early years of my research life. Special thanks to Dr Enoch Tay for the supervision and introducing me to the research world and to Kata Popovic for the friendship and assistance. Thanks to Dr Christine Smyth and staffs at the Westmead Millenium Institute for the tireless help with the seemingly impossible FACS project! I would also like to thank all our colleagues who have kindly provided me with the reagents which would otherwise not be available for my research. I would also like to acknowledge the financial support from the University of Sydney (University Postgraduate Award) and the CMRI (supplementary scholarship), which then continued by the Faculty of Medicine, University of New South Wales. To Victor Anggono, my fiancee and mentor, thank you for your faith and dedication and endless support throughout this journey. It wasn't easy, but we were where we were, learning what we have to. Lastly, I am blessed for having supportive and loving big families and I thank God for this. PUBLICATIONS PUBLISHED ARTICLES Palmer SJ, Santucci N, Widagdo J, Bontempo SJ, Taylor KM, Tay ES, Hook J, Lemckert F, Gunning PW, Hardeman EC (2010) Negative autoregulation of GTF2IRD1 in Williams-Beuren Syndrome via a novel DNA binding mechanism. J Biol Chem 285: 4715-4724. MANUSCRIPTS IN PREPARA TION Howard ML, Tay E, Palmer SJ, Widagdo J, Taylor KM, Popovic K, Gunning PW, Spitzer MW, Murphy M, Arrthurson GJ, Pang TYC, Renoir T, Hannan AJ, Hardeman EC (201 1) Mutation of the Williams-Beuren syndrome-associated gene Gtflirdl causes altered GABAergic function and a unique behavioural phenotype including heightened vocalization. Submitted to Human Molecular Genetics (under review). Widagdo J, Taylor KM, Bontempo SJ, Hardeman EC, Palmer SJ (2011) Novel interaction between Williams Syndrome-related protein GTF21RD1 and a chromatin- associated protein, ZMYM5, is modulated by SUMOylation. Palmer SJ, Taylor KM, Santucci N, Widagdo J, Chan A, Yeo JL, Reynaud B, Guven K, Joya J, Adams M, Gunning PW, Hardeman EC (2011) GTF2IRD2 from the Williams-Beuren critical region encodes a nuclear/cytoplasmic protein that antagonizes GTF2IRD1 and TFII-I. CONFERENCE ABSTRA CTS Hardeman EC, Widagdo J, Howard ML, Hannan AJ, Gunning PW and Palmer SJ (2011) GTF2IRD1, implicated in the Williams syndrome cognitive profile, interacts with chromatin-regulating proteins. Talk presented at The Australian Neuroscience Society annual meeting, Auckland, New Zealand. Palmer SJ, Widagdo J, Taylor KM, Bontempo S, Gunning PW and Hardeman EC (2010) Specific interactions of the Williams-Beuren syndrome-associated protein GTF2IRD1 suggest a role in the chromatin reorganization. Poster presented at The American Society of Human Genetics annual meeting, Washington DC, USA. Widagdo J, Palmer SJ, Taylor KM, Bontempo S and Hardeman EC (2010) GTF2IRD1, a Williams Syndrome-related protein, is a novel SUMO substrate. Poster presented at the OzBio2010, Melbourne, VIC. Widagdo J, Tay ESE, Howard ML, Hannan AJ, Gunning PW, Hardeman EC and Palmer SJ (2010) GTF2IRD1, a Williams Syndrome-related protein, interacts with chromatin-regulating proteins: a novel role in epigenetics. Poster presented at the Gordon Research Conference: Molecular and Cellular Neurobiology, Hong Kong. Palmer SJ, Santucci N, Widagdo J, Bontempo S, Taylor KM, Tay ESE, Gunning PW and Hardeman EC (2009) The biochemistry and evolution of the Williams Beuren syndrome-associated gene GTF2IRD1. Talk presented at The American Society of Human Genetics annual meeting, Honolulu, Hawaii. Widagdo J, Tay ESE, Popovic K and Hardeman EC (2009) Molecular function of GTF2IRD1, a transcription factor implicated in Williams-Beuren Syndrome. Poster presented at The Australian Neuroscience Society annual meeting, Canberra, ACT. Widagdo J, Tay ESE and Hardeman EC (2007) A potential role for the serine protease inhibitor Serpina3n in the anxiety-like phenotype of Williams Syndrome. Poster presented at Westmead Association Research Meeting Symposium, Westmead Hospital, We st me ad, NSW. Widagdo J, Tay ESE and Hardeman EC (2007) Towards the molecular mechanism of Gtf'Iirdl in the neurocognitive pathology of Williams syndrome and human cognition/behaviour. Presented at the 7,h IBRO World Congress of Neuroscience, Melbourne, VIC. (Presenting authors are positioned first) ABSTRACT Background: Williams-Beuren syndrome (WBS) is a complex neurodevelopmental disorder that results from a hemizygous deletion involving up to 28 genes within chromosome 7q 11.23. WBS is characterised by a set of physical abnormalities and specific cognitive and behavioural features that are collectively called the Williams syndrome cognitive profile (WSCP). Genotype-phenotype correlations in patients with atypical deletions have implicated two members of the GTF2I protein family, GTF2IRD1 and TFI1-I, in the main aspects of the WSCP. We and others have generated Gtflirdl knockout mouse lines that show developmental and neurological abnormalities, including social and non-social anxiety-related behavioural changes, reminiscent of the WSCP. By analysing gene expression using a Gtf2irdl knockout/LacZ knockin mouse, we identified a major overlap of Gtfiirdl expression in GABAergic cell types, the major inhibitory neurons in the brain. However, the molecular function of GTF2IRD1 is poorly understood. GTF2IRD1 is generally considered to be a DNA-binding transcription factor with a number of proposed target genes that were originally identified in yeast one-hybrid experiments, but none have been confirmed in vivo, except for the GTF2IRD1 gene itself, which has been shown to be directly regulated by its own protein product. Aims: The aims of this thesis were to understand the molecular and cellular mechanisms of GTF2IRD1 function by investigating: i) potential target genes of GTF2IRD1 in the brain through microarray analyses; ii) novel protein partners of GTF2IRD1 via yeast two-hybrid screening and iii) post-translational regulation of the GTF21RD1 protein by SUMOylation. Results: i) A combination of gene expression profiling and bioinformatics analysis was utilised to search for genes that may be directly or indirectly regulated by GTF2IRD1. Firstly, microarray analyses of various brain regions from the Gtf2irdl knockout mice revealed unexpectedly subtle differences in their transcriptional profiles in comparison with wild type controls.
Load more

Recommended publications
  • KPNA1 Antibody Cat
    KPNA1 Antibody Cat. No.: 5981 Western blot analysis of KPNA1 in Hela cell lysate with KPNA1 antibody at 1μg/mL. Immunocytochemistry of KPNA1 in HeLa cells with KPNA1 antibody at 2.5 μg/mL. Immunofluorescence of KPNA1 in K562 cells with KPNA1 antibody at 20 μg/mL. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse, Rat HOMOLOGY: Predicted species reactivity based on immunogen sequence: Bovine: (100%) KPNA1 antibody was raised against a 15 amino acid synthetic peptide near the amino terminus of human KPNA1. IMMUNOGEN: The immunogen is located within amino acids 30 - 80 of KPNA1. TESTED APPLICATIONS: ELISA, ICC, IF, WB September 30, 2021 1 https://www.prosci-inc.com/kpna1-antibody-5981.html KPNA1 antibody can be used for detection of KPNA1 by Western blot at 1 μg/mL. Antibody can also be used for immunocytochemistry starting at 2.5 μg/mL. For immunofluorescence start at 20 μg/mL. APPLICATIONS: Antibody validated: Western Blot in human samples; Immunocytochemistry in human samples and Immunofluorescence in human samples. All other applications and species not yet tested. POSITIVE CONTROL: 1) Cat. No. 1201 - HeLa Cell Lysate 2) Cat. No. 17-001 - HeLa Cell Slide 3) Cat. No. 17-004 - K-562 Cell Slide Properties PURIFICATION: KPNA1 Antibody is affinity chromatography purified via peptide column. CLONALITY: Polyclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: KPNA1 Antibody is supplied in PBS containing 0.02% sodium azide. CONCENTRATION: 1 mg/mL KPNA1 antibody can be stored at 4˚C for three months and -20˚C, stable for up to one STORAGE CONDITIONS: year.
    [Show full text]
  • Toxicogenomics Article
    Toxicogenomics Article Discovery of Novel Biomarkers by Microarray Analysis of Peripheral Blood Mononuclear Cell Gene Expression in Benzene-Exposed Workers Matthew S. Forrest,1 Qing Lan,2 Alan E. Hubbard,1 Luoping Zhang,1 Roel Vermeulen,2 Xin Zhao,1 Guilan Li,3 Yen-Ying Wu,1 Min Shen,2 Songnian Yin,3 Stephen J. Chanock,2 Nathaniel Rothman,2 and Martyn T. Smith1 1School of Public Health, University of California, Berkeley, California, USA; 2Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA; 3National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China were then ranked and selected for further exam- Benzene is an industrial chemical and component of gasoline that is an established cause of ination using several forms of statistical analysis. leukemia. To better understand the risk benzene poses, we examined the effect of benzene expo- We also specifically examined the expression sure on peripheral blood mononuclear cell (PBMC) gene expression in a population of shoe- of all cytokine genes on the array under the factory workers with well-characterized occupational exposures using microarrays and real-time a priori hypothesis that these key genes polymerase chain reaction (PCR). PBMC RNA was stabilized in the field and analyzed using a involved in immune function are likely to be comprehensive human array, the U133A/B Affymetrix GeneChip set. A matched analysis of six altered by benzene exposure (Aoyama 1986). exposed–control pairs was performed. A combination of robust multiarray analysis and ordering We then attempted to confirm the array find- of genes using paired t-statistics, along with bootstrapping to control for a 5% familywise error ings for the leading differentially expressed rate, was used to identify differentially expressed genes in a global analysis.
    [Show full text]
  • Nuclear Import Protein KPNA7 and Its Cargos Acta Universitatis Tamperensis 2346
    ELISA VUORINEN Nuclear Import Protein KPNA7 and its Cargos ELISA Acta Universitatis Tamperensis 2346 ELISA VUORINEN Nuclear Import Protein KPNA7 and its Cargos Diverse roles in the regulation of cancer cell growth, mitosis and nuclear morphology AUT 2346 AUT ELISA VUORINEN Nuclear Import Protein KPNA7 and its Cargos Diverse roles in the regulation of cancer cell growth, mitosis and nuclear morphology ACADEMIC DISSERTATION To be presented, with the permission of the Faculty Council of the Faculty of Medicine and Life Sciences of the University of Tampere, for public discussion in the auditorium F114 of the Arvo building, Arvo Ylpön katu 34, Tampere, on 9 February 2018, at 12 o’clock. UNIVERSITY OF TAMPERE ELISA VUORINEN Nuclear Import Protein KPNA7 and its Cargos Diverse roles in the regulation of cancer cell growth, mitosis and nuclear morphology Acta Universitatis Tamperensis 2346 Tampere University Press Tampere 2018 ACADEMIC DISSERTATION University of Tampere, Faculty of Medicine and Life Sciences Finland Supervised by Reviewed by Professor Anne Kallioniemi Docent Pia Vahteristo University of Tampere University of Helsinki Finland Finland Docent Maria Vartiainen University of Helsinki Finland The originality of this thesis has been checked using the Turnitin OriginalityCheck service in accordance with the quality management system of the University of Tampere. Copyright ©2018 Tampere University Press and the author Cover design by Mikko Reinikka Acta Universitatis Tamperensis 2346 Acta Electronica Universitatis Tamperensis 1851 ISBN 978-952-03-0641-0 (print) ISBN 978-952-03-0642-7 (pdf) ISSN-L 1455-1616 ISSN 1456-954X ISSN 1455-1616 http://tampub.uta.fi Suomen Yliopistopaino Oy – Juvenes Print Tampere 2018 441 729 Painotuote CONTENTS List of original communications ................................................................................................
    [Show full text]
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology 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. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • Supporting Information
    Supporting Information Mulders et al. 10.1073/pnas.0905780106 SI Materials and Methods in Opti-MEM (Invitrogen) to myoblasts, in both cases at a final Animals. Hemizygous DM500 mice, derived from the DM300– oligo concentration of 200 nM. Fresh medium was supplemented 328 line (1), express a transgenic human DM1 locus, which bears after 4 hours. After 24 h, medium was changed. RNA was a repeat segment that has expanded to Ϸ500 CTG triplets, isolated 48 h after transfection. because of intergenerational triplet-repeat instability. For the isolation of immortal DM500 myoblasts, DM500 mice were RNA Isolation. Typically, RNA from cultured cells was isolated crossed with H-2Kb-tsA58 transgenic mice (2). Homozygous using the Aurum Total RNA mini kit (guanidine-HCl/ HSALR20b mice express a (CUG)250 segment in the context of mercaptoethanol-based lysis, silica membrane binding; Bio- a human skeletal actin transcript (3). All animal experiments Rad), according to the manufacturer’s protocol. RNA from were approved by the Institutional Animal Care and Use Com- muscle tissue was isolated using TRIzol reagent (Invitrogen). mittees of the Radboud University Nijmegen and the University Alternative methods to isolate RNA from cultured cells in- of Rochester Medical Center. volved: (i) use of the TRIzol reagent, according to the manu- facturer’s protocol; (ii) an oligo(dT) affinity column (Nucleo- Cell Culture. An immortal mouse myoblast cell culture expressing Trap mRNA mini kit; Macherey-Nagel) for the isolation of hDMPK (CUG)500 transcripts was derived from GPS tissue poly(A) RNA; or (iii) a TRIzol procedure preceded by a isolated from DM500 mice additionally expressing 1 copy of the proteinase K digestion of the whole cell lysate (7): in short, cells H-2Kb-tsA58 allele (4).
    [Show full text]
  • Program Nr: 1 from the 2004 ASHG Annual Meeting Mutations in A
    Program Nr: 1 from the 2004 ASHG Annual Meeting Mutations in a novel member of the chromodomain gene family cause CHARGE syndrome. L.E.L.M. Vissers1, C.M.A. van Ravenswaaij1, R. Admiraal2, J.A. Hurst3, B.B.A. de Vries1, I.M. Janssen1, W.A. van der Vliet1, E.H.L.P.G. Huys1, P.J. de Jong4, B.C.J. Hamel1, E.F.P.M. Schoenmakers1, H.G. Brunner1, A. Geurts van Kessel1, J.A. Veltman1. 1) Dept Human Genetics, UMC Nijmegen, Nijmegen, Netherlands; 2) Dept Otorhinolaryngology, UMC Nijmegen, Nijmegen, Netherlands; 3) Dept Clinical Genetics, The Churchill Hospital, Oxford, United Kingdom; 4) Children's Hospital Oakland Research Institute, BACPAC Resources, Oakland, CA. CHARGE association denotes the non-random occurrence of ocular coloboma, heart defects, choanal atresia, retarded growth and development, genital hypoplasia, ear anomalies and deafness (OMIM #214800). Almost all patients with CHARGE association are sporadic and its cause was unknown. We and others hypothesized that CHARGE association is due to a genomic microdeletion or to a mutation in a gene affecting early embryonic development. In this study array- based comparative genomic hybridization (array CGH) was used to screen patients with CHARGE association for submicroscopic DNA copy number alterations. De novo overlapping microdeletions in 8q12 were identified in two patients on a genome-wide 1 Mb resolution BAC array. A 2.3 Mb region of deletion overlap was defined using a tiling resolution chromosome 8 microarray. Sequence analysis of genes residing within this critical region revealed mutations in the CHD7 gene in 10 of the 17 CHARGE patients without microdeletions, including 7 heterozygous stop-codon mutations.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Gene Expression Is Related to Parental Origin and Regional Coordinate Control
    Journal of Human Genetics (2009) 54, 193–198 & 2009 The Japan Society of Human Genetics All rights reserved 1434-5161/09 $32.00 www.nature.com/jhg ORIGINAL ARTICLE William’s syndrome: gene expression is related to parental origin and regional coordinate control Jeremy C Collette1, Xiao-Ning Chen1, Debra L Mills2, Albert M Galaburda3, Allan L Reiss4, Ursula Bellugi5 and Julie R Korenberg1,6 William’s syndrome (WS) features a spectrum of neurocognitive and behavioral abnormalities due to a rare 1.5 MB deletion that includes about 24–28 genes on chromosome band 7q11.23. Study of the expression of these genes from the single normal copy provides an opportunity to elucidate the genetic and epigenetic controls on these genes as well as their roles in both WS and normal brain development and function. We used quantitative RT-PCR to determine the transcriptional level of 14 WS gene markers in a cohort of 77 persons with WS and 48 normal controls. Results reported here: (1) show that the expression of the genes deleted in WS is decreased in some but not all cases, (2) demonstrate that the parental origin of the deletion contributes to the level of expression of GTF2I independently of age and gender and (3) indicate that the correlation of expression between GTF2I and some other genes in the WS region differs in WS subjects and normal controls, which in turn points toward a regulatory role for this gene. Interspecies comparisons suggest GTF2I may play a key role in normal brain development. Journal of Human Genetics (2009) 54, 193–198; doi:10.1038/jhg.2009.5; published online 13 March 2009 Keywords: William’s syndrome; gene expression; RT-PCR; parental origin; GTF2I INTRODUCTION As an approach toward understanding the role of the deleted genes William’s syndrome (WS) is a neurogenetic disorder affecting human in WS, we have characterized WS subjects according to genetic, social/ development and adult cognition.
    [Show full text]
  • Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
    Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen,
    [Show full text]
  • Downloaded from [266]
    Patterns of DNA methylation on the human X chromosome and use in analyzing X-chromosome inactivation by Allison Marie Cotton B.Sc., The University of Guelph, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate Studies (Medical Genetics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) January 2012 © Allison Marie Cotton, 2012 Abstract The process of X-chromosome inactivation achieves dosage compensation between mammalian males and females. In females one X chromosome is transcriptionally silenced through a variety of epigenetic modifications including DNA methylation. Most X-linked genes are subject to X-chromosome inactivation and only expressed from the active X chromosome. On the inactive X chromosome, the CpG island promoters of genes subject to X-chromosome inactivation are methylated in their promoter regions, while genes which escape from X- chromosome inactivation have unmethylated CpG island promoters on both the active and inactive X chromosomes. The first objective of this thesis was to determine if the DNA methylation of CpG island promoters could be used to accurately predict X chromosome inactivation status. The second objective was to use DNA methylation to predict X-chromosome inactivation status in a variety of tissues. A comparison of blood, muscle, kidney and neural tissues revealed tissue-specific X-chromosome inactivation, in which 12% of genes escaped from X-chromosome inactivation in some, but not all, tissues. X-linked DNA methylation analysis of placental tissues predicted four times higher escape from X-chromosome inactivation than in any other tissue. Despite the hypomethylation of repetitive elements on both the X chromosome and the autosomes, no changes were detected in the frequency or intensity of placental Cot-1 holes.
    [Show full text]
  • Primary Driver Mutations in GTF2I Specific to the Development Of
    cancers Article Primary Driver Mutations in GTF2I Specific to the Development of Thymomas Rumi Higuchi 1, Taichiro Goto 1,* , Yosuke Hirotsu 2 , Yujiro Yokoyama 1, Takahiro Nakagomi 1, Sotaro Otake 1, Kenji Amemiya 2,3, Toshio Oyama 3, Hitoshi Mochizuki 2 and Masao Omata 2,4 1 Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Yamanashi 400-8506, Japan; [email protected] (R.H.); [email protected] (Y.Y.); [email protected] (T.N.); [email protected] (S.O.) 2 Genome Analysis Center, Yamanashi Central Hospital, Yamanashi 400-8506, Japan; [email protected] (Y.H.); [email protected] (K.A.); [email protected] (H.M.); [email protected] (M.O.) 3 Department of Pathology, Yamanashi Central Hospital, Yamanashi 400-8506, Japan; [email protected] 4 Department of Gastroenterology, The University of Tokyo Hospital, Tokyo 113-8655, Japan * Correspondence: [email protected]; Tel.: +81-55-253-7111 Received: 16 June 2020; Accepted: 22 July 2020; Published: 24 July 2020 Abstract: Thymomas are rare mediastinal tumors that are difficult to treat and pose a major public health concern. Identifying mutations in target genes is vital for the development of novel therapeutic strategies. Type A thymomas possess a missense mutation in GTF2I (chromosome 7 c.74146970T>A) with high frequency. However, the molecular pathways underlying the tumorigenesis of other thymomas remain to be elucidated. We aimed to detect this missense mutation in GTF2I in other thymoma subtypes (types B). This study involved 22 patients who underwent surgery for thymomas between January 2014 and August 2019.
    [Show full text]
  • Whole Genome Comparative Genomic Hybridization of Ewing Sarcoma Indicates Cytoskeleton, Migration and Protein Trafficking †
    Proceedings Whole Genome Comparative Genomic Hybridization of Ewing Sarcoma Indicates Cytoskeleton, Migration and Protein Trafficking † Burçin Baran 1, Safiye Aktaş 1,*, Hülya Tosun 1,2, Gülden Diniz 1,2, Yasemin Çakır 1,2, Tekincan Çağrı Aktaş 1, Zekiye Altun 1 and Nur Olgun 1 1 Institute of Oncology, Dokuz Eylul University, Izmir 35340, Turkey; [email protected] (B.B.); [email protected] (H.T.); [email protected] (G.D.); [email protected] (Y.Ç.); [email protected] (T.Ç.A.); [email protected] (Z.A.); [email protected] (N.O.) 2 Dr.Behcet Uz Children’s Research Hospital, Izmir 35210, Turkey * Correspondence: [email protected] † Presented at the 2nd International Cell Death Research Congress, Izmir, Turkey, 1–4 November 2018. Published: 5 December 2018 Abstract: Ewing sarcoma is a bone and soft tissue tumor either neuroectodermal or mesenchymal originated and affecting children and adolescents. In the present study, we aimed to find out prognostic and predictive biomarkers for Ewing sarcoma. Hence, we examined the copy number alterations (and related possible genes) among ten Ewing sarcoma patient samples and possible associations with the clinical outcome. DNA extraction from formalin fixed paraffin embedded archive tissues was performed. Whole genome Comparative Genomic Hybridization (CGH) was performed by NimbleGen and recorded as single Panel Rainbow through chromosomes 1–22, X and Y. Data was interpreted by SignalMap software and genetic regions matching the deletion or amplification loci were recorded. The mean age of the patients was 8.6 years. Three of the cases were male, while seven were female. According to CGH analysis, the most common DNA copy number alterations were found in SLIT-ROBO Rho GTPase activating protein (srGAP2), RANBP2 like GRIP domain (RGPD5), nephrocystin 1 (NPHP1), GTF2I repeat domain containing 2 (GTF2IRD2), pyridoxal dependent decarboxylase domain containing 1 (PXDC1), which were found down- regulated among 7 of 10 patients.
    [Show full text]