1 Title 1 Loss of PABPC1 Is Compensated by Elevated PABPC4
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Large-Scale Analysis of Genome and Transcriptome Alterations in Multiple Tumors Unveils Novel Cancer-Relevant Splicing Networks
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks Endre Sebestyén,1,5 Babita Singh,1,5 Belén Miñana,1,2 Amadís Pagès,1 Francesca Mateo,3 Miguel Angel Pujana,3 Juan Valcárcel,1,2,4 and Eduardo Eyras1,4 1Universitat Pompeu Fabra, E08003 Barcelona, Spain; 2Centre for Genomic Regulation, E08003 Barcelona, Spain; 3Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), E08908 L’Hospitalet del Llobregat, Spain; 4Catalan Institution for Research and Advanced Studies, E08010 Barcelona, Spain Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled. We system- atically analyzed mutation, copy number, and gene expression patterns of 1348 RNA-binding protein (RBP) genes in 11 solid tumor types, together with alternative splicing changes in these tumors and the enrichment of binding motifs in the alter- natively spliced sequences. Our comprehensive study reveals widespread alterations in the expression of RBP genes, as well as novel mutations and copy number variations in association with multiple alternative splicing changes in cancer drivers and oncogenic pathways. Remarkably, the altered splicing patterns in several tumor types recapitulate those of undifferen- tiated cells. These patterns are predicted to be mainly controlled by MBNL1 and involve multiple cancer drivers, including the mitotic gene NUMA1. We show that NUMA1 alternative splicing induces enhanced cell proliferation and centrosome am- plification in nontumorigenic mammary epithelial cells. -
Sanjay Kumar Gupta
The human CCHC-type Zinc Finger Nucleic Acid Binding Protein (CNBP) binds to the G-rich elements in target mRNA coding sequences and promotes translation Das humane CCHC-Typ-Zinkfinger-Nukleinsäure-Binde-Protein (CNBP) bindet an G-reiche Elemente in der kodierenden Sequenz seiner Ziel-mRNAs und fördert deren Translation Doctoral thesis for a doctoral degree at the Graduate School of Life Sciences, Julius-Maximilians-Universität WürzBurg, Section: Biomedicine suBmitted By Sanjay Kumar Gupta from Varanasi, India WürzBurg, 2016 1 Submitted on: …………………………………………………………..…….. Office stamp Members of the Promotionskomitee: Chairperson: Prof. Dr. Alexander Buchberger Primary Supervisor: Dr. Stefan Juranek Supervisor (Second): Prof. Dr. Utz Fischer Supervisor (Third): Dr. Markus Landthaler Date of Public Defence: …………………………………………….………… Date of Receipt of Certificates: ………………………………………………. 2 Summary The genetic information encoded with in the genes are transcribed and translated to give rise to the functional proteins, which are building block of a cell. At first, it was thought that the regulation of gene expression particularly occurs at the level of transcription By various transcription factors. Recent discoveries have shown the vital role of gene regulation at the level of RNA also known as post-transcriptional gene regulation (PTGR). Apart from non-coding RNAs e.g. micro RNAs, various RNA Binding proteins (RBPs) play essential role in PTGR. RBPs have been implicated in different stages of mRNA life cycle ranging from splicing, processing, transport, localization and decay. In last 20 years studies have shown the presence of hundreds of RBPs across eukaryotic systems many of which are widely conserved. Given the rising numBer of RBPs and their link to human diseases it is quite evident that RBPs have major role in cellular processes and their regulation. -
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. -
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Staufen2 functions in Staufen1-mediated mRNA decay INAUGURAL ARTICLE by binding to itself and its paralog and promoting UPF1 helicase but not ATPase activity Eonyoung Parka,b, Michael L. Gleghorna,b, and Lynne E. Maquata,b,1 aDepartment of Biochemistry and Biophysics, School of Medicine and Dentistry, and bCenter for RNA Biology, University of Rochester, Rochester, NY 14642 This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2011. Edited by Michael R. Botchan, University of California, Berkeley, CA, and approved November 16, 2012 (received for review August 3, 2012) Staufen (STAU)1-mediated mRNA decay (SMD) is a posttranscrip- harbor a STAU1-binding site (SBS) downstream of their normal tional regulatory mechanism in mammals that degrades mRNAs termination codon in a pathway called STAU1-mediated mRNA harboring a STAU1-binding site (SBS) in their 3′-untranslated regions decay or SMD (13, 14), and work published by others indicates (3′ UTRs). We show that SMD involves not only STAU1 but also its that SMD does not involve STAU2 (3, 15). paralog STAU2. STAU2, like STAU1, is a double-stranded RNA-binding According to our current model for SMD, when translation protein that interacts directly with the ATP-dependent RNA helicase terminates upstream of an SBS, recruitment of the nonsense-me- diated mRNA decay (NMD) factor UPF1 to SBS-bound STAU1 up-frameshift 1 (UPF1) to reduce the half-life of SMD targets that form fl an SBS by either intramolecular or intermolecular base-pairing. Com- triggers mRNA decay. SMD in uences a number of cellular pro- pared with STAU1, STAU2 binds ∼10-foldmoreUPF1and∼two- to cesses, including the differentiation of mouse C2C12 myoblasts to myotubes (16), the motility of human HaCaT keratinocytes (17), fivefold more of those SBS-containing mRNAs that were tested, and it and the differentiation of mouse 3T3-L1 preadipocytes to adipo- comparably promotes UPF1 helicase activity, which is critical for SMD. -
Downloaded from the TCGA Data Portal ( Data.Nci.Nih.Gov/Tcga/) (Supplemental Table S1)
bioRxiv preprint doi: https://doi.org/10.1101/023010; this version posted February 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks Endre Sebestyén1,*, Babita Singh1,*, Belén Miñana1,2, Amadís Pagès1, Francesca Mateo3, Miguel Angel Pujana3, Juan Valcárcel1,2,4, Eduardo Eyras1,4,5 1Universitat Pompeu Fabra, Dr. Aiguader 88, E08003 Barcelona, Spain 2Centre for Genomic Regulation, Dr. Aiguader 88, E08003 Barcelona, Spain 3Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), E08908 L’Hospitalet del Llobregat, Spain. 4Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, E08010 Barcelona, Spain *Equal contribution 5Correspondence to: [email protected] Keywords: alternative splicing, RNA binding proteins, splicing networks, cancer 1 bioRxiv preprint doi: https://doi.org/10.1101/023010; this version posted February 11, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled. -
Immunoprecipitation and Mass Spectrometry Defines an Extensive
BRES : 44759 Model7 pp: À 1221ðcol:fig: : NILÞ brain research ] ( ]]]]) ]]]– ]]] Available online at www.sciencedirect.com 121 122 123 124 125 126 www.elsevier.com/locate/brainres 127 128 129 Review 130 131 fi 132 Immunoprecipitation and mass spectrometry de nes 133 – 134 an extensive RBM45 protein protein interaction 135 Q2 136 network 137 138 a a,b a a c 139 Yang Li , Mahlon Collins , Jiyan An , Rachel Geiser , Tony Tegeler , c c c a,b,n 140 Q1 Kristine Tsantilas , Krystine Garcia , Patrick Pirrotte , Robert Bowser 141 aDivisions of Neurology and Neurobiology, Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, 142 Phoenix, AZ 85013, USA 143 bUniversity of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA 144 cCenter for Proteomics, TGen (Translational Genomics Research Institute), Phoenix, AZ 85004, USA 145 146 147 article info abstract 148 149 Article history: The pathological accumulation of RNA-binding proteins (RBPs) within inclusion bodies is a 150 Received 30 January 2016 hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration 151 Received in revised form (FTLD). RBP aggregation results in both toxic gain and loss of normal function. Determining 152 25 February 2016 the protein binding partners and normal functions of disease-associated RBPs is necessary 153 Accepted 28 February 2016 to fully understand molecular mechanisms of RBPs in disease. Herein, we characterized 154 the protein–protein interactions (PPIs) of RBM45, a RBP that localizes to inclusions in ALS/ 155 – fi Keywords: FTLD. Using immunoprecipitation coupled to mass spectrometry (IP MS), we identi ed 132 156 fi RBM45 proteins that speci cally interact with RBM45 within HEK293 cells. -
A SARS-Cov-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing Supplementary Information Supplementary Discussion All SARS-CoV-2 protein and gene functions described in the subnetwork appendices, including the text below and the text found in the individual bait subnetworks, are based on the functions of homologous genes from other coronavirus species. These are mainly from SARS-CoV and MERS-CoV, but when available and applicable other related viruses were used to provide insight into function. The SARS-CoV-2 proteins and genes listed here were designed and researched based on the gene alignments provided by Chan et. al. 1 2020 . Though we are reasonably sure the genes here are well annotated, we want to note that not every protein has been verified to be expressed or functional during SARS-CoV-2 infections, either in vitro or in vivo. In an effort to be as comprehensive and transparent as possible, we are reporting the sub-networks of these functionally unverified proteins along with the other SARS-CoV-2 proteins. In such cases, we have made notes within the text below, and on the corresponding subnetwork figures, and would advise that more caution be taken when examining these proteins and their molecular interactions. Due to practical limits in our sample preparation and data collection process, we were unable to generate data for proteins corresponding to Nsp3, Orf7b, and Nsp16. Therefore these three genes have been left out of the following literature review of the SARS-CoV-2 proteins and the protein-protein interactions (PPIs) identified in this study. -
Genetic and Genomic Analysis of Hyperlipidemia, Obesity and Diabetes Using (C57BL/6J × TALLYHO/Jngj) F2 Mice
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Nutrition Publications and Other Works Nutrition 12-19-2010 Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P. Stewart Marshall University Hyoung Y. Kim University of Tennessee - Knoxville, [email protected] Arnold M. Saxton University of Tennessee - Knoxville, [email protected] Jung H. Kim Marshall University Follow this and additional works at: https://trace.tennessee.edu/utk_nutrpubs Part of the Animal Sciences Commons, and the Nutrition Commons Recommended Citation BMC Genomics 2010, 11:713 doi:10.1186/1471-2164-11-713 This Article is brought to you for free and open access by the Nutrition at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Nutrition Publications and Other Works by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. Stewart et al. BMC Genomics 2010, 11:713 http://www.biomedcentral.com/1471-2164/11/713 RESEARCH ARTICLE Open Access Genetic and genomic analysis of hyperlipidemia, obesity and diabetes using (C57BL/6J × TALLYHO/JngJ) F2 mice Taryn P Stewart1, Hyoung Yon Kim2, Arnold M Saxton3, Jung Han Kim1* Abstract Background: Type 2 diabetes (T2D) is the most common form of diabetes in humans and is closely associated with dyslipidemia and obesity that magnifies the mortality and morbidity related to T2D. The genetic contribution to human T2D and related metabolic disorders is evident, and mostly follows polygenic inheritance. The TALLYHO/ JngJ (TH) mice are a polygenic model for T2D characterized by obesity, hyperinsulinemia, impaired glucose uptake and tolerance, hyperlipidemia, and hyperglycemia. -
Comparative Interactomics Analysis of Different ALS-Associated Proteins
Acta Neuropathol (2016) 132:175–196 DOI 10.1007/s00401-016-1575-8 ORIGINAL PAPER Comparative interactomics analysis of different ALS‑associated proteins identifies converging molecular pathways Anna M. Blokhuis1 · Max Koppers1,2 · Ewout J. N. Groen1,2,9 · Dianne M. A. van den Heuvel1 · Stefano Dini Modigliani4 · Jasper J. Anink5,6 · Katsumi Fumoto1,10 · Femke van Diggelen1 · Anne Snelting1 · Peter Sodaar2 · Bert M. Verheijen1,2 · Jeroen A. A. Demmers7 · Jan H. Veldink2 · Eleonora Aronica5,6 · Irene Bozzoni3 · Jeroen den Hertog8 · Leonard H. van den Berg2 · R. Jeroen Pasterkamp1 Received: 22 January 2016 / Revised: 14 April 2016 / Accepted: 15 April 2016 / Published online: 10 May 2016 © The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Amyotrophic lateral sclerosis (ALS) is a dev- OPTN and UBQLN2, in which mutations caused loss or astating neurological disease with no effective treatment gain of protein interactions. Several of the identified inter- available. An increasing number of genetic causes of ALS actomes showed a high degree of overlap: shared binding are being identified, but how these genetic defects lead to partners of ATXN2, FUS and TDP-43 had roles in RNA motor neuron degeneration and to which extent they affect metabolism; OPTN- and UBQLN2-interacting proteins common cellular pathways remains incompletely under- were related to protein degradation and protein transport, stood. To address these questions, we performed an inter- and C9orf72 interactors function in mitochondria. To con- actomic analysis to identify binding partners of wild-type firm that this overlap is important for ALS pathogenesis, (WT) and ALS-associated mutant versions of ATXN2, we studied fragile X mental retardation protein (FMRP), C9orf72, FUS, OPTN, TDP-43 and UBQLN2 in neuronal one of the common interactors of ATXN2, FUS and TDP- cells. -
PABPC4 293T Cell Transient Overexpression Lysate(Denatured)
Produktinformation Diagnostik & molekulare Diagnostik Laborgeräte & Service Zellkultur & Verbrauchsmaterial Forschungsprodukte & Biochemikalien Weitere Information auf den folgenden Seiten! See the following pages for more information! Lieferung & Zahlungsart Lieferung: frei Haus Bestellung auf Rechnung SZABO-SCANDIC Lieferung: € 10,- HandelsgmbH & Co KG Erstbestellung Vorauskassa Quellenstraße 110, A-1100 Wien T. +43(0)1 489 3961-0 Zuschläge F. +43(0)1 489 3961-7 [email protected] • Mindermengenzuschlag www.szabo-scandic.com • Trockeneiszuschlag • Gefahrgutzuschlag linkedin.com/company/szaboscandic • Expressversand facebook.com/szaboscandic PABPC4 293T Cell Transient Overexpression Lysate(Denatured) Catalog # : H00008761-T01 規格 : [ 100 uL ] List All Specification Application Image Transfected 293T Western Blot Cell Line: Plasmid: pCMV-PABPC4 full-length Host: Human Theoretical MW 72.71 (kDa): Quality Control Transient overexpression cell lysate was tested with Anti-PABPC4 Testing: antibody (H00008761-B01) by Western Blots. SDS-PAGE Gel PABPC4 transfected lysate. Western Blot Lane 1: PABPC4 transfected lysate ( 72.71 KDa) Lane 2: Non-transfected lysate. Storage Buffer: 1X Sample Buffer (50 mM Tris-HCl, 2% SDS, 10% glycerol, 300 mM 2- mercaptoethanol, 0.01% Bromophenol blue) Storage Store at -80°C. Aliquot to avoid repeated freezing and thawing. Instruction: MSDS: Download Applications Page 1 of 2 2016/5/22 Western Blot Gene Information Entrez GeneID: 8761 GeneBank BC071591.1 Accession#: Protein AAH71591.1 Accession#: Gene Name: PABPC4 Gene Alias: APP-1,APP1,FLJ43938,PABP4,iPABP Gene poly(A) binding protein, cytoplasmic 4 (inducible form) Description: Omim ID: 603407 Gene Ontology: Hyperlink Gene Summary: Poly(A)-binding proteins (PABPs) bind to the poly(A) tail present at the 3-prime ends of most eukaryotic mRNAs. -
Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins
Biomolecules 2015, 5, 1441-1466; doi:10.3390/biom5031441 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Article Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins Rebecca Bish 1,†, Nerea Cuevas-Polo 1,†, Zhe Cheng 1, Dolores Hambardzumyan 2, Mathias Munschauer 3, Markus Landthaler 3 and Christine Vogel 1,* 1 Center for Genomics and Systems Biology, Department of Biology, New York University, 12 Waverly Place, New York, NY 10003, USA; E-Mails: [email protected] (R.B.); [email protected] (N.C.-P.); [email protected] (Z.C.) 2 The Cleveland Clinic, Department of Neurosciences, Lerner Research Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA; E-Mail: [email protected] 3 RNA Biology and Post-Transcriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, Robert-Rössle-Str. 10, Berlin 13092, Germany; E-Mails: [email protected] (M.M.); [email protected] (M.L.) † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-212-998-3976; Fax: +1-212-995-4015. Academic Editor: André P. Gerber Received: 10 May 2015 / Accepted: 15 June 2015 / Published: 15 July 2015 Abstract: DDX6 (p54/RCK) is a human RNA helicase with central roles in mRNA decay and translation repression. To help our understanding of how DDX6 performs these multiple functions, we conducted the first unbiased, large-scale study to map the DDX6-centric protein-protein interactome using immunoprecipitation and mass spectrometry. Using DDX6 as bait, we identify a high-confidence and high-quality set of protein interaction partners which are enriched for functions in RNA metabolism and ribosomal proteins. -
RAB9 Antibody (R32125)
RAB9 Antibody (R32125) Catalog No. Formulation Size R32125 0.5mg/ml if reconstituted with 0.2ml sterile DI water 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human, Mouse, Rat Format Antigen affinity purified Clonality Polyclonal (rabbit origin) Isotype Rabbit IgG Purity Antigen affinity Buffer Lyophilized from 1X PBS with 2.5% BSA and 0.025% sodium azide UniProt P51151 Applications Western blot : 0.1-0.5ug/ml Limitations This RAB9 antibody is available for research use only. Western blot testing of 1) rat brain, 2) mouse brain, 3) human HeLa and 4) human MCF7 lysate with RAB9 antibody. Expected/observed molecular weight: ~23 kDa. Description Ras-related protein Rab-9A, also called RAB9, is a protein that in humans is encoded by the RAB9A gene. This gene is mapped to Xp22.2. RAB9 has been localized to components of the endocytic/exocytic pathway and has been implicated in recycling of membrane receptors. It has been found that downregulation of RAB9A gene expression in HeLa cells induced severe cell vacuolation. RAB9A GTPase is directly bound by TIP47 in its active, GTP-bound conformation. Moreover, RAB9A increases the affinity of TIP47 for its cargo. What’s more, this gene may involved in the transport of proteins between the endosomes and the trans Golgi network. RAB9A has been shown to interact with RABEPK and TIP47. Application Notes Optimal dilution of the RAB9 antibody should be determined by the researcher. Immunogen Amino acids KDATNVAAAFEEAVRRVLATEDRSDHLIQTDTVNLHRK of human RAB9A were used as the immunogen for the RAB9 antibody. Storage After reconstitution, the RAB9 antibody can be stored for up to one month at 4oC.