DOCSLIB.ORG

Supplemental Information Figure S1. Genome-Wide Alternative Splicing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplemental Information Figure S1. Genome-Wide Alternative Splicing Supplemental information Figure S1. Genome-wide alternative splicing events affected by inducible expression SRSF3 in mouse MEF3T3 cells. To examine the effects of SRSF3 (SRp20) on genome-wide RNA splicing in mouse cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in MEF3T3 mouse fibroblasts with or without ectopically inducible expression of SRp20. (A–C) Clustered heat maps for the top events regulated by SRSF3 identified by ExonHit splice arrays. SRSF3-targeted genes in three experimental repeats consist of 65 evidenced splicing events (A), 74 novel splicing events (B) and 11 genes with expression changes (C), with a threshold of ≥2-fold changes (p<0.01) in log2 as determined by a B/E method and FDR cutoff of 0.1 for gene expression change and 0.2 for splicing alternation. Individual gene names and event ID are indicated on the right. Event ID specifies individual splicing events being detailed in Supplementary Table S1-S3. MEF3T3 cells with an empty vector transfection were included as vector controls. Color key scales in log2 values are indicated at the bottom of each panel. The full list of B/E ratio analysis result is available at NCBI GEO (http://www.ncbi.nlm.nih.gov/geo/) (accession number GSE60147). Figure S2. Isoform profiling of mouse Ilf3 and human ILF3. (A) Diagrams of RNA isoforms of mouse Ilf3. Mouse Ilf3 consists of 22 exons and 21 introns, which produces 6 spliced isoforms of mRNAs by alternative splicing as illustrated. (B) Diagrams of splice isoforms of human ILF3. Human ILF3 gene consists of 21 exons (boxes) and 20 introns (lines between boxes), which produce 8 splice isoforms of mRNAs by alternative splicing as depicted. Isoform 7 and 8 are two novel isoforms identified in this study. ILF3 Isoform-3, previously reported as TCP80 was not detectable in our study. Diagrams do not reflect exon/intron scale. (C) Profiling of human ILF3 protein isoforms in U2OS cells. U2OS cells with (lanes 1-5) or without (lanes 6-8) transfection by Myc/Flag-tagged ILF3 isoform-1 (pCMV6-ILF3 isoform-1), isoform-7 (pJR16), isoform-8 (pJR15), isoform-7 and -8, or an empty vector were blotted by 1 an anti-ILF-3 antibody (Ab) or by anti-Myc antibody. All ectopically expressed ILF3 protein isoforms have an additional 31 amino acid (aa) residues as a C-terminal Myc/FLAG tag and were immunoblotted with anti-ILF3 or anti-Myc antibody. U2OS cells transfected with 40 nM of si-SRSF3 (a SRSF3-specific siRNA) or si-NS (a non-targeting siRNA) or without (none) siRNA were served for endogenous ILF3 detection by Western blotting. ILF3 isoform profile (1, 2/5, 7 and 8) is indicated on the left. hnRNP K served as a sample loading control. *, endogenous isoform 7 without a tag in lane 7. Exp, exposure. (D-E) Knockdown of SRSF1 expression in U2OS cells does not affect alternative splicing of ILF3 RNA. Total cell protein extract and total RNA from U2OS cells transfected with 40 nM of si-SRSF1 or si-NS twice at a 48 h interval were examined, respectively, by Western blotting for SRSF1 knockdown efficiency (D) and by RT-PCR for production of ILF3 isoforms with the primer pairs used in Figure 2A (E) Figure S3. Roles of RBM5 and RBM39 in alternative RNA splicing of ILF3. (A-B) RBM5 and RBM39 are not downstream targets of SRSF3. SRSF3 in HEK293T cells were knocked down twice in a 48 h interval with 40 nM of a non-specific si-NS or a SRSF3-specific si-SRSF3. Total protein extract and total cell RNA were prepared at 24 h after the last time of siRNA treatment. The knockdown efficiency of SRSF3 in HEK293 was examined by Western blot analysis (A). The knockdown of SRSF3 on RBM5 and RBM39 RNA expression was examined by RT-qPCR (B). (C-D) RBM5 and RBM39 in alternative ILF3 RNA splicing and ILF3 isoform-2 production. Total RNA prepared from HEK293T cells with or without twice knockdown of RBM5 or RBM39 expression by the indicated siRNA (C) as described above was examined by RT-PCR for alternative RNA splicing of ILF3 with the indicated primer pairs (a, b, c, d and e, see Figure 2A). The detected ILF3 isoforms were indicated on the gel right (D). Triplicates in each experiment were repeated twice. Figure S4. Expression of ILF3 isoform-1 and -2 in WI-38 fibroblast cells is regulated by SRSF3 and is important for cell growth. (A) Ectopic expression of SRSF3 in WI-38 cells reduces the expression of suppressive ILF3 isoform-5. Total RNA extracted from WI-38 cells 48 h after the second transfection 2 with a SRSF3 expression vector was examined by RT-PCR with an ILF3-specific primer pair. RT, reverse transcription. (B) Ectopic expression of ILF3 isoform-1 and -2 in WI-38 cells promotes cell proliferation. A total of 1 x 105 WI-38 cells in each well of a 12-well plate were transfected twice in a 48- h interval by reverse transfection with 1 μg FLAG-ILF3 isoform-1 in combination with 1 μg FLAG- tagged ILF3 isoform-2 or an empty control vector pFLAG-CMV-5.1 (2 μg). The cells were counted on day 4 from the first transfection and cell numbers from each group were statistically analyzed with a student t-test. The ectopic expression of ILF3 isoform-1 and -2 was examined by Western blot with an anti-FLAG antibody and is shown above the bar graph. Figure S5. Effects of human ILF3 isoform-1, -2, -5 and -7 at ectopic expression on the growth of NIH/3T3 cells. (A) Effects of transient expression of ILF3 isoforms on cell growth. NIH 3T3 cells at 5 x 105/well were seeded into a 6-well plate and reversely transfected immediately with 2 μg of FLAG-ILF3 isoform-1 (pCMV6-ILF3), -2 (pJR9), -5 (pJR18), or -7 (pJR16), or a control vector (pSB21). The cells at 24 h were passed and reversely transfected again with the same amount of each plasmid. The cell counts were obtained at 96 h after the first transfection. (B) Effects of stable expression of ILF3 isoforms on cell growth. NIH 3T3 cells stably transfected with FLAG-ILF3 isoform-1, -2, -5, -7 or pSB21 plasmid at 2.5 x 105 per well were seeded into a 6- well plate and passed once on Day 3. The total cell counts were obtained on Day 5. Below each bar graph are individual FLAG-tagged ILF3 isoforms blotted by an anti- FLAG antibody. (C) Effects of ectopic transient expression of ILF3 isoform-1 and -2 on U2OS cell growth. The cell counts were obtained at 96 h after twice transfection of individual plasmids. Figure. S6. Stable expression of human ILF3 isoform-2 in MEF3T3 cells promotes cell cycle progression. MEF3T3 cells stably transfected by pJR19 encoding FLAG-ILF3 isoform-2 or an empty vector. The cells at 2 x 105 cells per well were seeded into a 6-well plate in DMEM medium containing 10% calf serum for 24 h, synchronized by starvation for 48 h in DMEM medium containing 0.1% calf 3 serum, and collected at the indicated duration of serum stimulation in DMEM medium containing 10% calf serum for cell cycle flow cytometry. Figure S7. SRSF3 regulates RNA splicing of human ILF3 minigene. (A) Diagram of an ILF3 minigene from its exon 16 to exon 19 under CMV IE promoter control (arrow), with its splicing directions and the primers (short lines) used for detection of alternative 3’ ss selection in the exon 18. (B) Examination of ILF3 minigene splicing in U2OS cells. U2OS cells were cotransfected by 2 μg of pJR8 and 40 nM of si-SRSF3 or NS siRNA. After 48 h of transfection, total cell RNA was extracted for RT- PCR analysis by oJR51 (pJR plasmid-specific primer) and oJR26 in the ILF3 exon 18 to examine ILF3 isoform-2 and -5 splicing in the minigene expression. Table S1. Genes with evidence splicing events (p<0.01, fold change >2). spliceEventId: EHT (ExonHit company) nomenclature used in array design; p-value (SR vs Vec): Statistical analysis of SRSF3 overexpression (SR) vs control (Vec) group; Fold-Change (SR vs. Vec): The fold change of the F1 vs F2 ratio between SRSF3 overexpression (SR) vs control (Vec) group; F1 to F2 Ratio - SR 1.CEL: The ratio of expression level between isoform F1 and F2; entrezId: Entrez Gene Number; formId: Splice event ID (above) appended with F1 or F2; Accession: NCBI/Genbank accession # used for event design; net bp delta: Size (bp) of splice event; Gene name: Entrez Gene name; spliceEventName: Type of splice event, see Table S1. Table S2. Genes with predicted novel splicing events. Splice Event Id: EHT (ExonHit company) nomenclature used in array design; p-value (SR vs Vec): Statistical analysis of SRSF3 overexpression (SR) vs control (Vec) group; Fold-Change (SR vs Vec): The fold change of the ratio of exon inclusion vs exon exclusion between SR vs Vec group; SR 1.CEL: The ratio of expression levels between exon inclusion and exon exclusion in SR 1 sample; entrezId: Entrez Gene Number; Chromosome start: Position on chromosome of event start; Chromosome end: Position on 4 chromosome of event end; Orientation: Orientation of probe set on chromosome; Accessions/descriptions at: NCBI/Genbank accession number used for predicted event design. Predicted net bp delta: Predicted size (bp) change caused by alternative splicing in a transcript. Table S3. Genes with expression level changes. Table S4. DNA/RNA oligonucleotides used in this study.
Load more

Recommended publications
  • Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
    Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3.
    [Show full text]
  • Structural Basis for DEAH-Helicase Activation by G-Patch Proteins
    Structural basis for DEAH-helicase activation by G-patch proteins Michael K. Studera, Lazar Ivanovica, Marco E. Webera, Sabrina Martia, and Stefanie Jonasa,1 aInstitute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland Edited by Joseph D. Puglisi, Stanford University School of Medicine, Stanford, CA, and approved February 21, 2020 (received for review August 12, 2019) RNA helicases of the DEAH/RHA family are involved in many essential RNA bases are stacked in the RNA binding channel between a long cellular processes, such as splicing or ribosome biogenesis, where β-hairpin in RecA2 (β14 to β15 in hsDHX15/scPrp43; SI Appendix, they remodel large RNA–protein complexes to facilitate transitions Fig. S1) and a conserved loop in RecA1 (termed “Hook-turn”). to the next intermediate. DEAH helicases couple adenosine tri- This means that during progression into the open state, the phosphate (ATP) hydrolysis to conformational changes of their β-hairpin and two other RNA-binding patches in RecA2 (termed catalytic core. This movement results in translocation along RNA, “Hook-loop” and “motif V”; SI Appendix, Fig. S1) have to shift 1 which is held in place by auxiliary C-terminal domains. The activity nucleotide (nt) toward the 5′ end of the RNA. Thus, when the of DEAH proteins is strongly enhanced by the large and diverse RecA domains close back up, at the start of the next hydrolysis class of G-patch activators. Despite their central roles in RNA me- cycle, the RNA is pushed by 1 nt through the RNA channel.
    [Show full text]
  • RBM5/LUCA-15 Tumour Suppression by Control of Apoptosis and the Cell
    Review Article TheScientificWorldJOURNAL (2002) 2, 1885–1890 ISSN 1537-744X; DOI 10.1100/tsw.2002.859 RBM5/LUCA-15 —Tumour Suppression by Control of Apoptosis and the Cell Cycle? Mirna Mourtada-Maarabouni1 and Gwyn T. Williams2 School of Life Sciences, Keele University, Keele, Staffs, ST5 5BG, U.K. 1 2 TEL: 44 1782 583679, FAX 44 1782 583516; TEL: 44 1782 583032, FAX: 44 1782 583516 E-mail: [email protected]; [email protected] Received March 19, 2002; Revised May 17, 2002; Accepted May 17, 2002; Published July 4, 2002 The candidate tumour suppressor gene, LUCA-15, maps to the lung cancer tumour suppressor locus 3p21.3. The LUCA-15 gene locus encodes at least four alternatively spliced transcripts, which have been shown to function as regulators of apoptosis, a fact that may have a major significance in tumour regulation. This review highlights evidence that implicates the LUCA-15 locus in the control of apoptosis and cell proliferation, and reports observations that significantly strengthen the case for tumour suppressor activity by this gene. KEY WORDS: T-lymphocytes, LUCA-15, RNA-binding proteins, cell death, cell proliferation DOMAINS: cell death, cell cycle, oncology, gene regulation INTRODUCTION The molecular control of cancer is complex. Cancer genes are involved in the dysregulation of a whole range of normal cellular systemic processes including cell proliferation[1], cell-cell communication[2], DNA repair[3], chromosome stability[4], tumour invasion, motility and metastasis[5,6], apoptosis[7], and others. Despite impressive progress in recent years in understanding the molecular basis of cancer, many crucial genes remain to be identified.
    [Show full text]
  • Insight Into the Role of Alternative Splicing Within the Rbm10v1 Exon 10 Tandem Donor Site
    Tessier et al. BMC Research Notes (2015) 8:46 DOI 10.1186/s13104-015-0983-5 SHORT REPORT Open Access Insight into the role of alternative splicing within the RBM10v1 exon 10 tandem donor site Sarah J Tessier1, Julie J Loiselle2, Anne McBain3, Celine Pullen1, Benjamin W Koenderink4, Justin G Roy5 and Leslie C Sutherland1,2,4,5,6,7* Abstract Background: RBM10 is an RNA binding protein involved in the regulation of transcription, alternative splicing and message stabilization. Mutations in RBM10, which maps to the X chromosome, are associated with TARP syndrome, lung and pancreatic cancers. Two predominant isoforms of RBM10 exist, RBM10v1 and RBM10v2. Both variants have alternate isoforms that differ by one valine residue, at amino acid 354 (RBM10v1) or 277 (RBM10v2). It was recently observed that a novel point mutation at amino acid 354 of RBM10v1, replacing valine with glutamic acid, correlated with preferential expression of an exon 11 inclusion variant of the proliferation regulatory protein NUMB, which is upregulated in lung cancer. Findings: We demonstrate, using the GLC20 male-derived small cell lung cancer cell line - confirmed to have only one X chromosome - that the two (+/−) valine isoforms of RBM10v1 and RBM10v2 result from alternative splicing. Protein modeling of the RNA Recognition Motif (RRM) within which the alteration occurs, shows that the presence of valine inhibits the formation of one of the two α-helices associated with RRM tertiary structure, whereas the absence of valine supports the α-helical configuration. We then show 2-fold elevated expression of the transcripts encoding the minus valine RBM10v1 isoform in GLC20 cells, compared to those encoding the plus valine isoform.
    [Show full text]
  • 3P21.3 Tumor Suppressor Gene H37/Luca15/RBM5 Inhibits Growth of Human Lung Cancer Cells Through Cell Cycle Arrest Andapoptosis
    Research Article 3p21.3 Tumor Suppressor Gene H37/Luca15/RBM5 Inhibits Growth of Human Lung Cancer Cells through Cell Cycle Arrest andApoptosis Juliana J. Oh, Ali Razfar, Idolina Delgado, Rebecca A. Reed, Anna Malkina, Baher Boctor, and Dennis J. Slamon Division of Hematology/Oncology, University of California at Los Angeles School of Medicine, Los Angeles, California Abstract 3p21.3 TSGs play a role in preventing lung cancer initiation. Deletion at chromosome 3p21.3 is the earliest and the most Thus, isolation and characterization of the 3p TSGs could be a first frequently observed genetic alteration in lung cancer, suggest- step toward developing new targeted treatments and diagnostic ing that the region contains tumor suppressor gene(s) (TSG). tools for lung cancer. Accordingly, the search for TSGs in this Identification of those genes may lead to the development region has been the focus of extensive research over the past two both of biomarkers to identify high-risk individuals and novel decades, and many genes mapping to this region have recently therapeutics. Previously, we cloned the H37/Luca15/RBM5 been characterized (3–9). The two most prominent genes, already gene from 3p21.3 and showed its TSG characteristics. To being evaluated for clinical utility, are fus-1 (phase I clinical trial; investigate the physiologic function of H37 in the lung and its refs. 10, 11) and RASSF-1A (epigenetic biomarker; refs. 12, 13). mechanism of tumor suppression, we have stably transfected We previously showed that the H37 gene (also called Luca15 or H37 into A549 non–small cell lung cancer cells. A549/H37 cells RBM5; refs.
    [Show full text]
  • Oncoscore: a Novel, Internet-Based Tool to Assess the Oncogenic Potential of Genes
    www.nature.com/scientificreports OPEN OncoScore: a novel, Internet- based tool to assess the oncogenic potential of genes Received: 06 July 2016 Rocco Piazza1, Daniele Ramazzotti2, Roberta Spinelli1, Alessandra Pirola3, Luca De Sano4, Accepted: 15 March 2017 Pierangelo Ferrari3, Vera Magistroni1, Nicoletta Cordani1, Nitesh Sharma5 & Published: 07 April 2017 Carlo Gambacorti-Passerini1 The complicated, evolving landscape of cancer mutations poses a formidable challenge to identify cancer genes among the large lists of mutations typically generated in NGS experiments. The ability to prioritize these variants is therefore of paramount importance. To address this issue we developed OncoScore, a text-mining tool that ranks genes according to their association with cancer, based on available biomedical literature. Receiver operating characteristic curve and the area under the curve (AUC) metrics on manually curated datasets confirmed the excellent discriminating capability of OncoScore (OncoScore cut-off threshold = 21.09; AUC = 90.3%, 95% CI: 88.1–92.5%), indicating that OncoScore provides useful results in cases where an efficient prioritization of cancer-associated genes is needed. The huge amount of data emerging from NGS projects is bringing a revolution in molecular medicine, leading to the discovery of a large number of new somatic alterations that are associated with the onset and/or progression of cancer. However, researchers are facing a formidable challenge in prioritizing cancer genes among the variants generated by NGS experiments. Despite the development of a significant number of tools devoted to cancer driver prediction, limited effort has been dedicated to tools able to generate a gene-centered Oncogenic Score based on the evidence already available in the scientific literature.
    [Show full text]
  • Analysis of Rbm5 and Rbm10 Expression Throughout H9c2 Skeletal and Cardiac Muscle Cell Differentiation
    ANALYSIS OF RBM5 AND RBM10 EXPRESSION THROUGHOUT H9C2 SKELETAL AND CARDIAC MUSCLE CELL DIFFERENTIATION by Julie Jennifer Loiselle A thesis submitted in partial fulfillment of the requirements for the degree of Master of Sciences (MSc) in Biology School of Graduate Studies Laurentian University Sudbury, Ontario © Julie Loiselle, 2013 THESIS DEFENCE COMMITTEE/COMITÉ DE SOUTENANCE DE THÈSE Laurentian Université/Université Laurentienne School of Graduate Studies/École des études supérieures Title of Thesis Titre de la thèse ANALYSIS OF RBM5 AND RBM10 EXPRESSION THROUGHOUT H9C2 SKELETAL AND CARDIAC MUSCLE CELL DIFFERENTIATION Name of Candidate Nom du candidat Loiselle, Julie Jennifer Degree Diplôme Master of Science Department/Program Date of Defence Département/Programme Biology Date de la soutenance July 15, 2013 APPROVED/APPROUVÉ Thesis Examiners/Examinateurs de thèse: Dr. Leslie Sutherland (Supervisor/Directrice de thèse) Dr. Céline Boudreau-Larivière (Committee member/Membre du comité) Dr. Éric Gauthier (Committee member/Membre du comité) Approved for the School of Graduate Studies Dr. Mazen Saleh Approuvé pour l’École des études supérieures (Committee member/Membre du comité) Dr. David Lesbarrères M. David Lesbarrères Dr. David A. Hood Director, School of Graduate Studies (External Examiner/Examinateur externe) Directeur, École des études supérieures ACCESSIBILITY CLAUSE AND PERMISSION TO USE I, Julie Jennifer Loiselle, hereby grant to Laurentian University and/or its agents the non-exclusive license to archive and make accessible my thesis, dissertation, or project report in whole or in part in all forms of media, now or for the duration of my copyright ownership. I retain all other ownership rights to the copyright of the thesis, dissertation or project report.
    [Show full text]
  • Autoregulation of RBM10 and Cross-Regulation of RBM10/RBM5
    Nucleic Acids Research, 2017 1 doi: 10.1093/nar/gkx508 Autoregulation of RBM10 and cross-regulation of RBM10/RBM5 via alternative splicing-coupled nonsense-mediated decay Yue Sun 1,2,3, Yufang Bao3,†, Wenjian Han4,†, Fan Song3, Xianfeng Shen3, Jiawei Zhao3, Ji Zuo3,DavidSaffen2,3,5, Wei Chen6, Zefeng Wang4,XintianYou7,* and Yongbo Wang3,* 1School of Life Sciences, Fudan University, Shanghai 200438, China, 2Institutes of Brain Science, Fudan University, Shanghai 200032, China, 3Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China, 4Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Science, Shanghai 200031, China, 5State Key Laboratory for Medical Neurobiology, Fudan University, Shanghai 200032, China, 6Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China and 7Zuse Institute Berlin, Takustrasse 7, Berlin 14195, Germany Received December 06, 2016; Revised May 25, 2017; Editorial Decision May 26, 2017; Accepted May 27, 2017 ABSTRACT INTRODUCTION Mutations in the spliceosomal RNA binding protein Alternative splicing (AS) is a key molecular mechanism un- RBM10 cause TARP syndrome and are frequently derlying transcriptomic and proteomic diversity in eukary- observed in lung adenocarcinoma (LUAD). We have otic cells (1–3). AS plays critical roles in both normal and previously shown that RBM10 enhances exon skip- disease contexts (4–7). In addition to generating protein iso- forms with distinct functions (8) and functionally impor- ping of its target genes, including its paralog RBM5. tant non-coding RNAs (9,10), AS also produces mRNA Here, we report that RBM10 negatively regulates its variants that are substrates for nonsense-mediated mRNA own mRNA and protein expression and that of RBM5 decay (NMD) (11).
    [Show full text]
  • UNIVERSITY of CALIFORNIA, SAN DIEGO Measuring
    UNIVERSITY OF CALIFORNIA, SAN DIEGO Measuring and Correlating Blood and Brain Gene Expression Levels: Assays, Inbred Mouse Strain Comparisons, and Applications to Human Disease Assessment A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Biomedical Sciences by Mary Elizabeth Winn Committee in charge: Professor Nicholas J Schork, Chair Professor Gene Yeo, Co-Chair Professor Eric Courchesne Professor Ron Kuczenski Professor Sanford Shattil 2011 Copyright Mary Elizabeth Winn, 2011 All rights reserved. 2 The dissertation of Mary Elizabeth Winn is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California, San Diego 2011 iii DEDICATION To my parents, Dennis E. Winn II and Ann M. Winn, to my siblings, Jessica A. Winn and Stephen J. Winn, and to all who have supported me throughout this journey. iv TABLE OF CONTENTS Signature Page iii Dedication iv Table of Contents v List of Figures viii List of Tables x Acknowledgements xiii Vita xvi Abstract of Dissertation xix Chapter 1 Introduction and Background 1 INTRODUCTION 2 Translational Genomics, Genome-wide Expression Analysis, and Biomarker Discovery 2 Neuropsychiatric Diseases, Tissue Accessibility and Blood-based Gene Expression 4 Mouse Models of Human Disease 5 Microarray Gene Expression Profiling and Globin Reduction 7 Finding and Accessible Surrogate Tissue for Neural Tissue 9 Genetic Background Effect Analysis 11 SPECIFIC AIMS 12 ENUMERATION OF CHAPTERS
    [Show full text]
  • Dynamics of Alternative Splicing During Somatic Cell Reprogramming Reveals Functions for RNA-Binding Proteins CPSF3, Hnrnp UL1 and TIA1
    bioRxiv preprint doi: https://doi.org/10.1101/2020.09.17.299867; this version posted September 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1 and TIA1 Claudia Vivori1,2, Panagiotis Papasaikas1,#, Ralph Stadhouders1,##, Bruno Di Stefano1,%, Clara Berenguer Balaguer1,%%, Serena Generoso1,2, Anna Mallol1, José Luis Sardina1,%%, Bernhard Payer1,2, Thomas Graf1,2 and Juan Valcárcel1,2,3* 1 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain 2 Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain 3 Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain * Correspondence to [email protected] # Current address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66 / Swiss Institute of Bioinformatics, 4058 Basel, Switzerland ## Current address: Departments of Pulmonary Medicine and Cell Biology, Erasmus MC, Rotterdam, The Netherlands % Current address: Department of Molecular Biology, Massachusetts General Hospital / Center for Regenera- tive Medicine / Center for Cancer Research, Massachusetts General Hospital / Harvard Medical School, Boston, MA, USA / Department of Stem Cell and Regenerative Biology / Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA %% Current address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.17.299867; this version posted September 18, 2020.
    [Show full text]
  • Atlas Journal
    Atlas of Genetics and Cytogenetics in Oncology and Haematology Home Genes Leukemias Solid Tumours Cancer-Prone Deep Insight Portal Teaching X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA Atlas Journal Atlas Journal versus Atlas Database: the accumulation of the issues of the Journal constitutes the body of the Database/Text-Book. TABLE OF CONTENTS Volume 11, Number 3, Jul-Sep 2007 Previous Issue / Next Issue Genes MSH6 (mutS homolog 6 (E. Coli)) (2p16). Sreeparna Banerjee. Atlas Genet Cytogenet Oncol Haematol 2006; 9 11 (3): 289-297. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/MSH6ID344ch2p16.html LDB1 (10q24). Takeshi Setogawa, Testu Akiyama. Atlas Genet Cytogenet Oncol Haematol 2006; 11 (3): 298-301.[Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/LDB1ID41135ch10q24.html INTS6 (integrator complex subunit 6) (13q14.3). Ilse Wieland. Atlas Genet Cytogenet Oncol Haematol 2006; 11 (3): 302-306.[Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/INTS6ID40287ch13q14.html EPHA7 (EPH receptor A7) (6q16.1). Haruhiko Sugimura, Hiroki Mori, Tomoyasu Bunai, Masaya Suzuki. Atlas Genet Cytogenet Oncol Haematol 2007; 11 (3): 307-312. [Full Text] [PDF] Atlas Genet Cytogenet Oncol Haematol 2007;3 -I URL : http://atlasgeneticsoncology.org/Genes/EPHA7ID40466ch6q16.html RNASET2 (ribonuclease T2) (6q27). Francesco Acquati, Paola Campomenosi. Atlas Genet Cytogenet Oncol Haematol 2007; 11 (3): 313-317. [Full Text] [PDF] URL : http://atlasgeneticsoncology.org/Genes/RNASET2ID518ch6q27.html RHOB (ras homolog gene family, member B) (2p24.1). Minzhou Huang, Lisa D Laury-Kleintop, George Prendergast. Atlas Genet Cytogenet Oncol Haematol 2007; 11 (3): 318-323.
    [Show full text]
  • Structural Basis for the Recognition of Spliceosomal Smn/B/B' Proteins By
    RESEARCH ARTICLE Structural basis for the recognition of spliceosomal SmN/B/B’ proteins by the RBM5 OCRE domain in splicing regulation Andre´ Moura˜ o1,2†, Sophie Bonnal3†, Komal Soni1,2†, Lisa Warner1,2†, Re´ my Bordonne´ 4, Juan Valca´ rcel3,5*, Michael Sattler1,2* 1Institute of Structural Biology, Helmholtz Zentrum Mu¨ nchen, Neuherberg, Germany; 2Biomolecular NMR and Center for Integrated Protein Science Munich, Department Chemie, Technische Universita¨ t Mu¨ nchen, Garching, Germany; 3Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Centre de Regulacio´ Geno`mica, Barcelona, Spain; 4Institut de Ge´ne´tique Mole´culaire de Montpellier, CNRS-UMR5535, Universite´ de Montpellier, Montpellier, France; 5Institucio´ Catalana de Recerca i Estudis Avanc¸ats, Barcelona, Spain Abstract The multi-domain splicing factor RBM5 regulates the balance between antagonistic isoforms of the apoptosis-control genes FAS/CD95, Caspase-2 and AID. An OCRE (OCtamer REpeat of aromatic residues) domain found in RBM5 is important for alternative splicing regulation and mediates interactions with components of the U4/U6.U5 tri-snRNP. We show that the RBM5 OCRE domain adopts a unique b–sheet fold. NMR and biochemical experiments demonstrate that the OCRE domain directly binds to the proline-rich C-terminal tail of the essential snRNP core proteins SmN/B/B’. The NMR structure of an OCRE-SmN peptide complex reveals a specific *For correspondence: recognition of poly-proline helical motifs in SmN/B/B’. Mutation of conserved aromatic residues [email protected] (JVa´); impairs binding to the Sm proteins in vitro and compromises RBM5-mediated alternative splicing [email protected] regulation of FAS/CD95.
    [Show full text]