DOCSLIB.ORG

Ubc 2004-0561.Pdf

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Ubc 2004-0561.Pdf C/S-FEATURES MEDIATING CAG/CTG REPEAT INSTABILITY, THE SATELLOG DATABASE, AND CANDIDATE REPEAT PRIORITIZATION IN SCHIZOPHRENIA by PERSEUS IOANNIS MISSIRLIS B.Sc.H., Queen's University, 2002 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE STUDIES GENETICS GRADUATE PROGRAM We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA August 2004 © Perseus loannis Missirlis, 2004 UBC W THE UNIVERSITY OF BRITISH COLUMBIA FACULTY OF GRADUATE STUDIES 3 Library Authorization In presenting this thesis in partial fulfillment of the requirements for an advanced degree at the University of British Columbia, I agree that the Library shall make it freely available for reference and study. I further agree that permission for extensive copying of this thesis for scholarly purposes may be granted by the head of my department or by his or her representatives. It is understood that copying or publication of this thesis for financial gain shall not be allowed without my written permission. Perseus loannis Missirlis 18/08/2004 Name of Author (please print) Date (dd/mm/yyyy) Title of Thesis: C/S-FEATURES MEDIATING CAG/CTG REPEAT INSTABILITY, THE SATELLOG DATABASE, AND CANDIDATE REPEAT PRIORITIZATION IN SCHIZOPHRENIA Degree: Master of Science Year: 2004 Department of Genetics Graduate Program The University of British Columbia Vancouver, BC Canada grad.ubc.ca/forms/?formlD=THS page 1 of 1 last updated: 18-Aug-04 ABSTRACT Polyglutamine repeat expansions in the coding regions of unrelated genes have been implicated in the neurodegenerative phenotype of nine separate diseases. However, little is known about the role of flanking c/'s-sequences in mediating this repeat instability. Brock et al. identified an association between flanking GC content and CAG/CTG repeat instability at many of these disease loci by using a relative measure of repeat instability called 'expandability'. Using this measure, we have extended the analysis of Brock and colleagues and utilized the expandability metric to associate other features theorized to contribute to CAG/CTG repeat instability such as repeat length and purity, proximity to CCCTC-binding factor (CTCF) binding sites, and the nucleosome formation potential of the surrounding DNA. Our results confirmed earlier relationships regarding flanking GC content and CAG/CTG repeat instability and also suggest a novel one involving flanking CTCF binding sites. Conversely, no relationships between expandability and repeat length, purity, and nucleosome formation were detected. Anticipation refers to the progressive worsening of a disease phenotype and earlier age of onset in successive generations. Anticipation has been reported in a number of diseases in which repeat expansion may have a role in etiology. We developed Satellog, a database that catalogs all pure 1-16 repeat unit repeats in the human genome along with supplementary data of use for the ii prioritization of repeats in disease association studies. For each pure repeat we calculate the percentile rank of its length relative to other repeats of the same class in the genome, its polymorphism within UniGene clusters, its location either within or adjacent to EnsEMBL-defined genes, and its expression profile in normal tissues according to the GeneNote database. By examining the global repeat polymorphism profile, we found that highly polymorphic coding repeats were mostly restricted to trinucleotide repeats, whereas a wider range of repeat unit lengths were tolerated in untranslated sequence. We also found that 3'-UTR sequence tolerates more repeat polymorphisms than 5'-UTR or exonic sequence. Lastly, we use Satellog to prioritize repeats for disease-association studies in schizophrenia. Satellog is available as a freely downloadable MySQL and web-based database. iii TABLE OF CONTENTS ABSTRACT ii TABLE OF CONTENTS iv LIST OF TABLES viii LIST OF FIGURES x LIST OF ABBREVIATIONS xii ACKNOWLEDGEMENTS xv DEDICATION xvi PREFACE xvii CHAPTER 1 INTRODUCTION 2 1.1 c/'s-Features of unstable CAG/CTG repeats 2 1.1.1 Unstable repeats and disease 2 1.1.2 The argument for cis mediators of instability 4 1.1.2.1 Flanking %GC and CpG islands 4 1.1.2.2 Repeat length and purity 5 1.1.2.3 The role of the CTCF insulator protein 7 1.1.2.4 The role of nucleosomes 8 1.1.3 Objectives 9 1.1.4 Specific aims and rationale 10 1.2 The unstable repeat perspective of schizophrenia 10 1.2.1 Biology of schizophrenia 10 1.2.2 Genetics of schizophrenia 12 1.2.3 Anticipation in neuropsychiatric diseases 14 1.2.4 CAG/CTG repeats in schizophrenia 15 1.2.5 Published satellite repeat analyses and databases 18 1.2.6 Objectives. 20 1.2.7 Specific aims and rationale 21 CHAPTER 2 MATERIALS AND METHODS 23 2.1 c/s-Features of unstable CAG/CTG repeats 23 2.1.1 Collection of candidate CAG/CTG repeats for cis sequence analysis 23 2.1.2 Software Dependencies 1 23 2.1.3 Implementing the gems_cis database 25 iv 2.1.4 Overview of the flanker.pl script 27 2.1.4.1 Collection of flanking %GC, CpG islands, length and purity and other repetitive elements 29 2.1.4.2 Detection of flanking CTCF insulator protein binding sites 29 2.1.5 Detection of nucleosome formation potential with NucleoMeter 30 2.1.6 Statistics and plots with R 32 2.2 The satellog database 32 2.2.1 Software Dependencies II 33 2.2.2 Implementing the satellog database 33 2.2.3 Preliminary set-up 37 2.2.3.1 Detecting pure repeats with Tandem Repeats Finder (TRF) 37 2.2.3.2 Identifying unique repeat classes 38 2.2.3.3 Preparing expression data from the GeneNote database 39 2.2.3.4 Detecting repeat polymorphisms within UniGene clusters 40 2.2.4 Overview of the repeatalyzer.pl script 41 2.2.5 Generating a measure of repeat length significance 42 2.2.6 Detection and input of disease-associated repeats 42 2.3 Prioritizing candidate repeats for disease-association studies in schizophrenia 43 2.3.1 Input of neuropsychiatric linkage regions into Satellog 43 2.3.2 Prioritizing candidate repeats with Satellog 43 CHAPTER 3 RESULTS 47 3.1 c/s-Features of unstable CAG/CTG repeats 47 3.1.1 Correlation of flanking CAG/CTG repeat features to Brock etal. expandability data 47 3.1.1.1 Correlation of CpG islands with expandability 47 3.1.1.2 Correlation of flanking %GC with expandability 48 3.1.1.3 Correlation of repeat length and purity with expandability 52 3.1.1.4 Correlation of CTCF binding sites with expandability 52 3.1.1.5 Correlation of nucleosome formation potential with expandability 58 3.2 Genomic repeat analysis with the Satellog database 61 3.2.1 Summary statistics 61 3.2.2 Characteristics of disease-associated repeats 62 3.2.3 Characteristics of repeats polymorphic within UniGene clusters 66 3.2.4 Disease-associated repeats detected in UniGene clusters 68 3.3 Candidate repeats for typing in schizophrenia and bipolar disorder 75 3.3.1 Top 20 polymorphic schizophrenia candidate repeats 76 3.3.2 Top 20 globally prioritized schizophrenia candidate repeats 77 3.3.3 Top 20 polymorphic bipolar disorder candidate repeats 78 3.3.4 Top 20 globally prioritized bipolar candidate repeats 79 3.3.5 Top 20 polymorphic schizophrenia candidate repeats from disease- associated classes 80 3.3.6 Top 20 globally prioritized schizophrenia candidate repeats from disease-associated classes 81 3.3.7 Top 20 polymorphic bipolar disorder candidate repeats from disease- associated classes 82 3.3.8 Top 20 globally prioritized bipolar candidate repeats from disease- associated classes 83 CHAPTER 4 DISCUSSION 86 4.1 c/'s-Features of unstable CAG/CTG repeats 86 4.1.1 Identifying c/s-mediators of instability 86 4.1.1.1 Association between flanking %GC and instability 87 4.1.1.2 Association between flanking repeat length, purity and instability 88 4.1.1.3 Association between flanking CTCF binding sites and instability. 88 4.1.1.4 Association between flanking nucleosome formation and instability 90 4.1.2 Prioritizing candidate CAG/CTG repeats 91 4.2 Genomic repeat analysis with the Satellog database 93 4.3 Repeat prioritization in schizophrenia with Satellog 94 4.3.1 Top 20 polymorphic schizophrenia candidate repeats 95 4.3.2 Top 20 globally prioritized schizophrenia candidate repeats 96 4.3.3 Top 20 polymorphic schizophrenia candidate repeats from disease- associated classes 96 4.3.4 Top 20 globally prioritized schizophrenia candidate repeats from disease-associated classes 97 4.4 Conclusions 97 4.5 Problems encountered and limitations 99 4.5.1 Brock et al.'s expandability metric 99 4.5.2 Limitations of the GeneNote dataset 100 4.5.3 Mapping repeats to UniGene clusters 100 4.5.4 Prioritizing with p-values 101 4.5.5 Multiple repeats detected for known diseases 101 4.6 Future studies 102 4.6.1 Identifying c/'s-mediators of instability 102 4.6.2 Improvements to Satellog 103 4.6.3 Disease association studies in schizophrenia 104 4.6.3.1 Specimens for analysis 104 4.7 Significance 106 BIBLIOGRAPHY 108 APPENDIX A 120 APPENDIX B 124 APPENDIX C 126 APPENDIX D 153 APPENDIX E 157 APPENDIX F 159 APPENDIX G 160 APPENDIX H 170 APPENDIX 1 175 APPENDIX J 177 APPENDIX K 180 APPENDIX L 182 APPENDIX M 184 APPENDIX N 188 APPENDIX O 190 APPENDIX P - 192 APPENDIX Q 195 APPENDIX R 205 vii LIST OF TABLES Table 1: Genetic anticipation in schizophrenia; summary of linkage studies from 1996-1999 (adapted from Vincent et al., 2000) 15 Table 2: All unstable and candidate CAG/CTG repeat-containing genes located within a CpG island.
Load more

Recommended publications
  • Genetic Analysis of Indel Markers in Three Loci Associated with Parkinson’S Disease
    RESEARCH ARTICLE Genetic analysis of indel markers in three loci associated with Parkinson's disease Zhixin Huo1, Xiaoguang Luo2, Xiaoni Zhan1, Qiaohong Chu1, Qin Xu1, Jun Yao1, Hao Pang1* 1 Department of Forensic Genetics and Biology, China Medical University, Shenyang North New Area, Shenyang, P.R., China, 2 Department of Neurology, 1st Affiliated Hospital of China Medical University, Shenyang, P.R., China * [email protected] Abstract a1111111111 a1111111111 The causal mutations and genetic polymorphisms associated with susceptibility to Parkin- a1111111111 son's disease (PD) have been extensively described. To explore the potential contribution a1111111111 a1111111111 of insertion (I)/deletion (D) polymorphisms (indels) to the risk of PD in a Chinese population, we performed genetic analyses of indel loci in ACE, DJ-1, and GIGYF2 genes. Genomic DNA was extracted from venous blood of 348 PD patients and 325 age- and sex-matched controls without neurodegenerative disease. Genotyping of the indel loci was performed by fragment length analysis after PCR and DNA sequencing. Our results showed a statistically OPEN ACCESS significant association for both allele X (alleles without 5) vs. 5 (odds ratio = 1.378, 95% con- Citation: Huo Z, Luo X, Zhan X, Chu Q, Xu Q, Yao fidence interval = 1.112±1.708, P = 0.003) and genotype 5/X+X/X vs. 5/5 (odds ratio = J, et al. (2017) Genetic analysis of indel markers in three loci associated with Parkinson's disease. 1.681, 95% confidence interval = 1.174±2.407, P = 0.004) in the GIGYF2 locus; however, PLoS ONE 12(9): e0184269. https://doi.org/ no significant differences were detected for the ACE and DJ-1 indels.
    [Show full text]
  • "The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
    The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses.
    [Show full text]
  • Supplementary Table 3 Gene Microarray Analysis: PRL+E2 Vs
    Supplementary Table 3 Gene microarray analysis: PRL+E2 vs. control ID1 Field1 ID Symbol Name M Fold P Value 69 15562 206115_at EGR3 early growth response 3 2,36 5,13 4,51E-06 56 41486 232231_at RUNX2 runt-related transcription factor 2 2,01 4,02 6,78E-07 41 36660 227404_s_at EGR1 early growth response 1 1,99 3,97 2,20E-04 396 54249 36711_at MAFF v-maf musculoaponeurotic fibrosarcoma oncogene homolog F 1,92 3,79 7,54E-04 (avian) 42 13670 204222_s_at GLIPR1 GLI pathogenesis-related 1 (glioma) 1,91 3,76 2,20E-04 65 11080 201631_s_at IER3 immediate early response 3 1,81 3,50 3,50E-06 101 36952 227697_at SOCS3 suppressor of cytokine signaling 3 1,76 3,38 4,71E-05 16 15514 206067_s_at WT1 Wilms tumor 1 1,74 3,34 1,87E-04 171 47873 238623_at NA NA 1,72 3,30 1,10E-04 600 14687 205239_at AREG amphiregulin (schwannoma-derived growth factor) 1,71 3,26 1,51E-03 256 36997 227742_at CLIC6 chloride intracellular channel 6 1,69 3,23 3,52E-04 14 15038 205590_at RASGRP1 RAS guanyl releasing protein 1 (calcium and DAG-regulated) 1,68 3,20 1,87E-04 55 33237 223961_s_at CISH cytokine inducible SH2-containing protein 1,67 3,19 6,49E-07 78 32152 222872_x_at OBFC2A oligonucleotide/oligosaccharide-binding fold containing 2A 1,66 3,15 1,23E-05 1969 32201 222921_s_at HEY2 hairy/enhancer-of-split related with YRPW motif 2 1,64 3,12 1,78E-02 122 13463 204015_s_at DUSP4 dual specificity phosphatase 4 1,61 3,06 5,97E-05 173 36466 227210_at NA NA 1,60 3,04 1,10E-04 117 40525 231270_at CA13 carbonic anhydrase XIII 1,59 3,02 5,62E-05 81 42339 233085_s_at OBFC2A oligonucleotide/oligosaccharide-binding
    [Show full text]
  • Ep 2327798 A1
    (19) & (11) EP 2 327 798 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 01.06.2011 Bulletin 2011/22 C12Q 1/68 (2006.01) (21) Application number: 10181185.9 (22) Date of filing: 14.05.2005 (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • Bentwich, Itzhak HU IE IS IT LI LT LU MC NL PL PT RO SE SI SK TR Rosh Haayin (IL) • Avniel, Amir (30) Priority: 14.05.2004 US 709572 76706 Rehovot (IL) 14.05.2004 US 709577 • Karov, Yael 03.10.2004 US 522452 P 76706 Rehovot (IL) 03.10.2004 US 522449 P • Aharonov, Ranit 04.10.2004 US 522457 P 76706 Rehovot (IL) 15.11.2004 US 522860 P 08.12.2004 US 593081 P (74) Representative: King, Hilary Mary et al 06.01.2005 US 593329 P Mewburn Ellis LLP 17.03.2005 US 662742 P 33 Gutter Lane 25.03.2005 US 665094 P London EC2V 8AS (GB) 30.03.2005 US 666340 P Remarks: (62) Document number(s) of the earlier application(s) in This application was filed on 28-09-2010 as a accordance with Art. 76 EPC: divisional application to the application mentioned 05766834.5 / 1 784 501 under INID code 62. (71) Applicant: Rosetta Genomics Ltd 76706 Rehovot (IL) (54) MicroRNAs and uses thereof (57) Described herein are novel polynucleotides as- are disclosed. Also described herein are methods that sociated with prostate and lung cancer. The polynucle- can be used to identify modulators of prostate and lung otides are miRNAs and miRNA precursors.
    [Show full text]
  • UC San Francisco Previously Published Works
    UCSF UC San Francisco Previously Published Works Title Complex landscapes of somatic rearrangement in human breast cancer genomes. Permalink https://escholarship.org/uc/item/51c8s0fm Journal Nature, 462(7276) ISSN 0028-0836 Authors Stephens, Philip J McBride, David J Lin, Meng-Lay et al. Publication Date 2009-12-01 DOI 10.1038/nature08645 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Europe PMC Funders Group Author Manuscript Nature. Author manuscript; available in PMC 2012 July 17. Published in final edited form as: Nature. 2009 December 24; 462(7276): 1005–1010. doi:10.1038/nature08645. Europe PMC Funders Author Manuscripts COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES Philip J Stephens1, David J McBride1, Meng-Lay Lin1, Ignacio Varela1, Erin D Pleasance1, Jared T Simpson1, Lucy A Stebbings1, Catherine Leroy1, Sarah Edkins1, Laura J Mudie1, Chris D Greenman1, Mingming Jia1, Calli Latimer1, Jon W Teague1, King Wai Lau1, John Burton1, Michael A Quail1, Harold Swerdlow1, Carol Churcher1, Rachael Natrajan2, Anieta M Sieuwerts3, John WM Martens3, Daniel P Silver4, Anita Langerod5, Hege EG Russnes5, John A Foekens3, Jorge S Reis-Filho2, Laura van ’t Veer6, Andrea L Richardson4,7, Anne- Lise Børreson-Dale5,8, Peter J Campbell1, P Andrew Futreal1, and Michael R Stratton1,9 1)Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK 2)Molecular Pathology Laboratory, The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, 237 Fulham Road,
    [Show full text]
  • Supplementary Data
    SUPPLEMENTARY METHODS 1) Characterisation of OCCC cell line gene expression profiles using Prediction Analysis for Microarrays (PAM) The ovarian cancer dataset from Hendrix et al (25) was used to predict the phenotypes of the cell lines used in this study. Hendrix et al (25) analysed a series of 103 ovarian samples using the Affymetrix U133A array platform (GEO: GSE6008). This dataset comprises clear cell (n=8), endometrioid (n=37), mucinous (n=13) and serous epithelial (n=41) primary ovarian carcinomas and samples from 4 normal ovaries. To build the predictor, the Prediction Analysis of Microarrays (PAM) package in R environment was employed (http://rss.acs.unt.edu/Rdoc/library/pamr/html/00Index.html). When more than one probe described the expression of a given gene, we used the probe with the highest median absolute deviation across the samples. The dataset from Hendrix et al. (25) and the dataset of OCCC cell lines described in this manuscript were then overlaid on the basis of 11536 common unique HGNC gene symbols. Only the 99 primary ovarian cancers samples and the four normal ovary samples were used to build the predictor. Following leave one out cross-validation, a predictor based upon 126 genes was able to identify correctly the four distinct phenotypes of primary ovarian tumour samples with a misclassification rate of 18.3%. This predictor was subsequently applied to the expression data from the 12 OCCC cell lines to determine the likeliest phenotype of the OCCC cell lines compared to primary ovarian cancers. Posterior probabilities were estimated for each cell line in comparison to the following phenotypes: clear cell, endometrioid, mucinous and serous epithelial.
    [Show full text]
  • 1 Novel Expression Signatures Identified by Transcriptional Analysis
    ARD Online First, published on October 8, 2009 as 10.1136/ard.2009.108043 Ann Rheum Dis: first published as 10.1136/ard.2009.108043 on 7 October 2009. Downloaded from Novel expression signatures identified by transcriptional analysis of separated leukocyte subsets in SLE and vasculitis 1Paul A Lyons, 1Eoin F McKinney, 1Tim F Rayner, 1Alexander Hatton, 1Hayley B Woffendin, 1Maria Koukoulaki, 2Thomas C Freeman, 1David RW Jayne, 1Afzal N Chaudhry, and 1Kenneth GC Smith. 1Cambridge Institute for Medical Research and Department of Medicine, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK 2Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK Correspondence should be addressed to Dr Paul Lyons or Prof Kenneth Smith, Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK. Telephone: +44 1223 762642, Fax: +44 1223 762640, E-mail: [email protected] or [email protected] Key words: Gene expression, autoimmune disease, SLE, vasculitis Word count: 2,906 The Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non-exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd and its Licensees to permit this article (if accepted) to be published in Annals of the Rheumatic Diseases and any other BMJPGL products to exploit all subsidiary rights, as set out in their licence (http://ard.bmj.com/ifora/licence.pdf). http://ard.bmj.com/ on October 2, 2021 by guest. Protected copyright. 1 Copyright Article author (or their employer) 2009.
    [Show full text]
  • 120409 Thesis
    Mechanisms of Specificity in Neuronal Activity-regulated Gene Transcription by Michelle Renée Lyons Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Anne West, Supervisor ___________________________ Dona Chikaraishi, Chair ___________________________ James O. McNamara ___________________________ Geoffrey Pitt ___________________________ Scott Soderling Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2012 i v ABSTRACT Mechanisms of Specificity in Neuronal Activity-regulated Gene Transcription by Michelle Renée Lyons Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Anne West, Supervisor ___________________________ Dona Chikaraishi, Chair ___________________________ James O. McNamara ___________________________ Geoffrey Pitt ___________________________ Scott Soderling An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2012 Copyright by Michelle Renée Lyons 2012 Abstract In the nervous system, activity-regulated gene transcription is one of the fundamental processes responsible for orchestrating proper brain development – a process that in humans takes over 20 years. Moreover, activity-dependent regulation of gene expression continues to be important
    [Show full text]
  • The Roles of Alternative Cap-Binding Proteins of Arabidopsis Thaliana
    Copyright by Ryan Michael Patrick 2015 The Dissertation Committee for Ryan Michael Patrick Certifies that this is the approved version of the following dissertation: The Roles of Alternative Cap-Binding Proteins of Arabidopsis thaliana Committee: Karen S. Browning, Supervisor David W. Hoffman Enamul Huq Alan M. Lloyd Rick Russell The Roles of Alternative Cap-Binding Proteins of Arabidopsis thaliana by Ryan Michael Patrick, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin December 2015 Dedication To my family for their support. Acknowledgements I would like to thank Dr. Karen Browning and the members of the Browning lab and for their collaboration and support over the years. This work would not have been possible without the extraordinary mentorship of Dr. Browning, for which I am very grateful. This research was made possible by support from the National Science Foundation. v The Roles of Alternative Cap-binding Proteins of Arabidopsis thaliana Ryan Michael Patrick, Ph.D. The University of Texas at Austin, 2015 Supervisor: Karen Browning The mRNA cap-binding complexes eIF4F (made up of the cap-binding protein eIF4E and the large scaffold eIF4G) and eIFiso4F (made up of the plant-specific isoforms eIFiso4E and eIFiso4G) have established roles in translation initiation. However, other cap- binding proteins are known to be encoded in the Arabidopsis thaliana genome. We have chosen to investigate the biochemical properties and potential functions of these proteins. We have identified the eIF4E-like proteins, eIF4E1b and eIF4E1c, as Brassicaceae-specific eIF4E isoforms with the ability to form cap-binding complexes.
    [Show full text]
  • Copy Number Variation in Han Chinese Individuals with Autism
    Gazzellone et al. Journal of Neurodevelopmental Disorders 2014, 6:34 http://www.jneurodevdisorders.com/content/6/1/34 RESEARCH Open Access Copy number variation in Han Chinese individuals with autism spectrum disorder Matthew J Gazzellone1,2†, Xue Zhou1,3,4†, Anath C Lionel1,2, Mohammed Uddin1, Bhooma Thiruvahindrapuram1, Shuang Liang3, Caihong Sun3, Jia Wang3, Mingyang Zou3, Kristiina Tammimies1,5, Susan Walker1, Thanuja Selvanayagam1, John Wei1, Zhuozhi Wang1, Lijie Wu3 and Stephen W Scherer1,2* Abstract Background: Autism spectrum disorders (ASDs) are a group of neurodevelopmental conditions with a demonstrated genetic etiology. Rare (<1% frequency) copy number variations (CNVs) account for a proportion of the genetic events involved, but the contribution of these events in non-European ASD populations has not been well studied. Here, we report on rare CNVs detected in a cohort of individuals with ASD of Han Chinese background. Methods: DNA samples were obtained from 104 ASD probands and their parents who were recruited from Harbin, China. Samples were genotyped on the Affymetrix CytoScan HD platform. Rare CNVs were identified by comparing data with 873 technology-matched controls from Ontario and 1,235 additional population controls of Han Chinese ethnicity. Results: Of the probands, 8.6% had at least 1 de novo CNV (overlapping the GIGYF2, SPRY1, 16p13.3, 16p11.2, 17p13.3- 17p13.2, DMD,andNAP1L6 genes/loci). Rare inherited CNVs affected other plausible neurodevelopmental candidate genes including GRID2, LINGO2,andSLC39A12. A 24-kb duplication was also identified at YWHAE, a gene previously implicated in ASD and other developmental disorders. This duplication is observed at a similar frequency in cases and in population controls and is likely a benign Asian-specific copy number polymorphism.
    [Show full text]
  • Chicken Sperm Transcriptome Profiling by Microarray Analysis
    Genome Chicken sperm transcriptome profiling by microarray analysis Journal: Genome Manuscript ID gen-2015-0106.R2 Manuscript Type: Article Date Submitted by the Author: 29-Nov-2015 Complete List of Authors: Singh, R. P.; Salim Ali Centre for Ornithology and natural History, Avian Physiology and genetics Shafeeque, C M; Salim Ali Centre for Ornithology and Natural History, ; rajiv gandhiDraft centre for biotechnology, HMG Sharma, S; Central Avian Research Institute, Physiology and Reproduction Singh, Renu; Indian Veterinary Research Institute, Mohan, J; Central Avian Research Institute, Physiology and Reproduction Sastry, K; Central Avian Research Institute, Physiology and Reproduction Saxena, V; Central Avian Research Institute, Azeez, P; Salim Ali Centre for Ornithology and natural History, Avian Physiology and genetics Keyword: fertility biomarker, sperm RNA, embryonic development, egg, fertilization https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 158 Genome Chicken sperm transcriptome profiling by microarray analysis R.P. Singh 1,*, C.M. Shafeeque 1, S.K. Sharma 2, R. Singh 3, J. Mohan 2, K.V.H.Sastry 2, V. K. Saxena 2, P. A. Azeez 1 1Avian Physiology and Genetics Division, Sálim Ali Centre for Ornithology and Natural History, Anaikatty-641108, Coimbatore, India 2Central Avian Research Institute, Izatnagar, 243122, India. 3Indian Veterinary Research Institute, Izatnagar, 243122, India. Draft Running title: RNA in chicken sperm *Corresponding author current address Smithsonian Conservation Biology Institute, Front Royal, VA 22630 E-mail address: [email protected] Phone- +1-540-305-5911 https://mc06.manuscriptcentral.com/genome-pubs Genome Page 2 of 158 Abstract It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development.
    [Show full text]
  • Membranes of Human Neutrophils Secretory Vesicle Membranes And
    Downloaded from http://www.jimmunol.org/ by guest on September 30, 2021 is online at: average * The Journal of Immunology , 25 of which you can access for free at: 2008; 180:5575-5581; ; from submission to initial decision 4 weeks from acceptance to publication J Immunol doi: 10.4049/jimmunol.180.8.5575 http://www.jimmunol.org/content/180/8/5575 Comparison of Proteins Expressed on Secretory Vesicle Membranes and Plasma Membranes of Human Neutrophils Silvia M. Uriarte, David W. Powell, Gregory C. Luerman, Michael L. Merchant, Timothy D. Cummins, Neelakshi R. Jog, Richard A. Ward and Kenneth R. McLeish cites 44 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/2008/04/01/180.8.5575.DC1 This article http://www.jimmunol.org/content/180/8/5575.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 © 2008 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 30, 2021. The Journal of Immunology Comparison of Proteins Expressed on Secretory Vesicle Membranes and Plasma Membranes of Human Neutrophils1 Silvia M.
    [Show full text]