Deep RNA Sequencing Analysis of Readthrough Gene Fusions in Human
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Old Data and Friends Improve with Age: Advancements with the Updated Tools of Genenetwork
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.24.445383; this version posted May 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. Old data and friends improve with age: Advancements with the updated tools of GeneNetwork Alisha Chunduri1, David G. Ashbrook2 1Department of Biotechnology, Chaitanya Bharathi Institute of Technology, Hyderabad 500075, India 2Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA Abstract Understanding gene-by-environment interactions is important across biology, particularly behaviour. Families of isogenic strains are excellently placed, as the same genome can be tested in multiple environments. The BXD’s recent expansion to 140 strains makes them the largest family of murine isogenic genomes, and therefore give great power to detect QTL. Indefinite reproducible genometypes can be leveraged; old data can be reanalysed with emerging tools to produce novel biological insights. To highlight the importance of reanalyses, we obtained drug- and behavioural-phenotypes from Philip et al. 2010, and reanalysed their data with new genotypes from sequencing, and new models (GEMMA and R/qtl2). We discover QTL on chromosomes 3, 5, 9, 11, and 14, not found in the original study. We narrowed down the candidate genes based on their ability to alter gene expression and/or protein function, using cis-eQTL analysis, and variants predicted to be deleterious. Co-expression analysis (‘gene friends’) and human PheWAS were used to further narrow candidates. -
Supporting Information for Proteomics DOI 10.1002/Pmic.200400896
Supporting Information for Proteomics DOI 10.1002/pmic.200400896 Odette Prat, Frdric Berenguer, Vronique Malard, Emmanuelle Tavan, Nicole Sage, Grard Steinmetz and Eric Quemeneur Transcriptomic and proteomic responses of human renal HEK293 cells to uranium toxicity ª 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Table 1 : Differentially expressed genes in HEK293 cells treated with uranium at CI50 , CI30 and CI20. GENE ID GENE DESCRIPTION CI50 CI30 CI20 AANAT arylalkylamine N-acetyltransferase 1.66 AASDHPPT aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase -1.73 ABCC8 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 2.96 2.9 ABCF2 ATP-binding cassette, sub-family F (GCN20), member 2 1.86 ACAT2 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) -2.47 ACTB actin, beta -2.12 ACTR2 ARP2 actin-related protein 2 homolog (yeast) -1.94 ADAR adenosine deaminase, RNA-specific 1.87 1.92 ADNP activity-dependent neuroprotector -1.03 ADPRTL1 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1.48 2.31 2.1 AKAP1 A kinase (PRKA) anchor protein 1 1.59 AKR1C3 aldo-keto reductase family 1, member C3 -1.37 (3-alpha hydroxysteroid dehydrogenase, type II) ALS2CR3 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3 -1.21 APBB1 amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65) 4.41 APC adenomatosis polyposis coli -1.66 APP amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) -1.32 APPBP1 amyloid beta precursor -
Of GTP-Binding Proteins: ARF, ARL, and SAR Proteins
Published Online: 27 February, 2006 | Supp Info: http://doi.org/10.1083/jcb.200512057 JCB: COMMENT Downloaded from jcb.rupress.org on May 9, 2019 <doi>10.1083/jcb.200512057</doi><aid>200512057</aid>Nomenclature for the human Arf family of GTP-binding proteins: ARF, ARL, and SAR proteins Richard A. Kahn,1 Jacqueline Cherfi ls,2 Marek Elias,3 Ruth C. Lovering,4 Sean Munro,5 and Annette Schurmann6 1Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322 2Laboratoire d’Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifi que, 91198 Gif-sur-Yvette, France 3Department of Plant Physiology, Faculty of Science, Charles University, 128 44 Prague 2, Czech Republic 4Human Genome Organisation Gene Nomenclature Committee, Galton Laboratory, Department of Biology, University College London, London NW1 2HE, United Kingdom 5Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom 6Department of Pharmacology, German Institute of Human Nutrition Potsdam-Rehbrücke, D-14558 Nuthetal, Germany The Ras superfamily is comprised of at least four large they have been found to be ubiquitous regulators of membrane families of regulatory guanosine triphosphate–binding traffi c and phospholipid metabolism in eukaryotic cells (for re- views and discussion of Arf actions see Nie et al., 2003; Burd proteins, including the Arfs. The Arf family includes three et al., 2004; Kahn, 2004). Arfs are soluble proteins that translocate different groups of proteins: the Arfs, Arf-like (Arls), and onto membranes in concert with their activation, or GTP bind- SARs. Several Arf family members have been very highly ing. The biological actions of Arfs are thought to occur on mem- conserved throughout eukaryotic evolution and have branes and to result from their specifi c interactions with a large orthologues in evolutionally diverse species. -
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. -
NUFIP1 Sirna (H): Sc-105367
SANTA CRUZ BIOTECHNOLOGY, INC. NUFIP1 siRNA (h): sc-105367 BACKGROUND STORAGE AND RESUSPENSION NUFIP1 (nuclear fragile X mental retardation-interacting protein 1) is a 495 Store lyophilized siRNA duplex at -20° C with desiccant. Stable for at least amino acid protein that localizes to the nucleus and can interact with FMR1 one year from the date of shipment. Once resuspended, store at -20° C, (fragile X mental retardation protein) and BRCA1, a breast and ovarian-specific avoid contact with RNAses and repeated freeze thaw cycles. tumor suppressor. Through its interaction with FMR1, NUFIP1 is thought to Resuspend lyophilized siRNA duplex in 330 µl of the RNAse-free water shuttle specific mRNPs to active neuronal synapses, thereby regulating the provided. Resuspension of the siRNA duplex in 330 µl of RNAse-free water translation of synaptic plasticity-related mRNA. The close interaction of makes a 10 µM solution in a 10 µM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM NUFIP1 with FMR1, a protein that is essential for proper dendritic spine matu- EDTA buffered solution. ration, suggests close involvement in neuronal development. Interaction of NUFIP1 with BRCA1 results in the formation of a complex which binds the APPLICATIONS positive elongation factor P-TEFb, thus stimulating RNA polymerase II (pol II) transcription. When associated with BRAC1, NUFIP1 acts as a transcriptional NUFIP1 siRNA (h) is recommended for the inhibition of NUFIP1 expression in activator contributing to tumor suppressor gene expression. NUFIP1 contains human cells. one C2H2-type zinc finger and is expressed throughout the body. SUPPORT REAGENTS REFERENCES For optimal siRNA transfection efficiency, Santa Cruz Biotechnology’s 1. -
Bppart and Bpmax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model
BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, and Hamidreza Chitsaz ∗ Department of Computer Science, Colorado State University Abstract A few elite classes of RNA-RNA interaction (RRI), with complex roles in cellular functions such as miRNA-target and lncRNAs in human health, have already been studied. Accordingly, RRI bioinfor- matics tools tailored for those elite classes have been proposed in the last decade. Interestingly, there are somewhat unnoticed mRNA-mRNA interactions in the literature with potentially drastic biological roles. Hence, there is a need for high-throughput generic RRI bioinformatics tools. We revisit our RRI partition function algorithm, piRNA, which happens to be the most comprehensive and computationally-intensive thermodynamic model for RRI. We propose simpler models that are shown to retain the vast majority of the thermodynamic information that piRNA captures. We simplify the energy model and instead consider only weighted base pair counting to obtain BPPart for Base-pair Partition function and BPMax for Base-pair Maximization which are 225 and 1350 faster ◦ × × than piRNA, with a correlation of 0.855 and 0.836 with piRNA at 37 C on 50,500 experimentally charac- terized RRIs. This correlation increases to 0.920 and 0.904, respectively, at 180◦C. − Finally, we apply our algorithm BPPart to discover two disease-related RNAs, SNORD3D and TRAF3, and hypothesize their potential roles in Parkinson's disease and Cerebral Autosomal Dominant Arteri- opathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL). 1 Introduction Since mid 1990s with the advent of RNA interference discovery, RNA-RNA interaction (RRI) has moved to the spotlight in modern, post-genome biology. -
Detection of Aneuploidies by Paralogous Sequence Quantification S Deutsch, U Choudhury, G Merla, C Howald, a Sylvan, S E Antonarakis
908 J Med Genet: first published as 10.1136/jmg.2004.023184 on 9 December 2004. Downloaded from ORIGINAL ARTICLE Detection of aneuploidies by paralogous sequence quantification S Deutsch, U Choudhury, G Merla, C Howald, A Sylvan, S E Antonarakis ............................................................................................................................... J Med Genet 2004;41:908–915. doi: 10.1136/jmg.2004.023184 Background: Chromosomal aneuploidies are a common cause of congenital disorders associated with cognitive impairment and multiple dysmorphic features. Pre-natal diagnosis of aneuploidies is most See end of article for commonly performed by the karyotyping of fetal cells obtained by amniocentesis or chorionic villus authors’ affiliations sampling, but this method is labour intensive and requires about 14 days to complete. ....................... Methods: We have developed a PCR based method for the detection of targeted chromosome number Correspondence to: abnormalities termed paralogous sequence quantification (PSQ), based on the use of paralogous genes. Professor Stylianos E Paralogous sequences have a high degree of sequence identity, but accumulate nucleotide substitutions in Antonarakis, Department a locus specific manner. These sequence differences, which we term paralogous sequence mismatches of Genetic Medicine and Development, University of (PSMs), can be quantified using pyrosequencing technology, to estimate the relative dosage between Geneva Medical School, different chromosomes. We designed 10 assays for the detection of trisomies of chromosomes 13, 18, and GE 1211, Geneva, 21 and sex chromosome aneuploidies. Switzerland; Stylianos. antonarakis@medecine. Results: We evaluated the performance of this method on 175 DNAs, highly enriched for abnormal unige.ch samples. A correct and unambiguous diagnosis was given for 119 out of 120 aneuploid samples as well as for all the controls. -
To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants
Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin. -
Leukaemia Section
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(4;9)(q21.22;p24) SEC31A/JAK2 Julie Sanford Biggerstaff Idaho Cytogenetics Diagnostic Laboratory, Boise, ID 83706, USA; [email protected] Published in Atlas Database: April 2017 Online updated version : http://AtlasGeneticsOncology.org/Anomalies/t0409q21p24ID1682.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/68905/04-2017-t0409q21p24ID1682.pdf DOI: 10.4267/2042/68905 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2018 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract Cytogenetics Review on t(4;9)(q21.22;p24) SEC31A/JAK2, with data on clinics, and the genes involved. Cytogenetics morphological KEYWORDS JAK2 breakapart (commonly available). Chromosome 4; chromosome 9; translocation; SEC31A; JAK2; Hodgkin Lymphoma Genes involved and Clinics and pathology proteins SEC31A (SEC31 homolog A, COPII Disease coat complex component) Hodgkin Lymphoma Location Phenotype/cell stem origin 4q21.22 Hodgkin and Reed-Sternberg cells, which derive DNA/RNA from pre-apoptotic crippled germinal center (GC) B- gene is 72,606 bp with 25 exons; transcribed from cells, are positive for CD30, CD15, CD40 and the - strand; coding region is 62,863 bp with 24 IRF4/MUM1 exons Epidemiology Protein Hodgkin lymphoma itself is common, but this 1166 amnio acids. Protein transport protein SEC31A particular translocation may be rare within the is ubiquitously expressed and forms part of the coat disorder. However, it is not often assayed for; found protein complex II (COPII) which is comprised of at in 2/131 cHL cases examined: a M/31 with nodular least four other proteins in addition to SEC31A this sclerosis cHL, alive 60 mths after diagnosis; and a complex is involved in formation of transport M/83 with lymphocyte-depleted cHL who died at vesicles from the ER to Golgi. -
UNIVERSITY of CALIFORNIA, IRVINE Combinatorial Regulation By
UNIVERSITY OF CALIFORNIA, IRVINE Combinatorial regulation by maternal transcription factors during activation of the endoderm gene regulatory network DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biological Sciences by Kitt D. Paraiso Dissertation Committee: Professor Ken W.Y. Cho, Chair Associate Professor Olivier Cinquin Professor Thomas Schilling 2018 Chapter 4 © 2017 Elsevier Ltd. © 2018 Kitt D. Paraiso DEDICATION To the incredibly intelligent and talented people, who in one way or another, helped complete this thesis. ii TABLE OF CONTENTS Page LIST OF FIGURES vii LIST OF TABLES ix LIST OF ABBREVIATIONS X ACKNOWLEDGEMENTS xi CURRICULUM VITAE xii ABSTRACT OF THE DISSERTATION xiv CHAPTER 1: Maternal transcription factors during early endoderm formation in 1 Xenopus Transcription factors co-regulate in a cell type-specific manner 2 Otx1 is expressed in a variety of cell lineages 4 Maternal otx1 in the endodermal conteXt 5 Establishment of enhancers by maternal transcription factors 9 Uncovering the endodermal gene regulatory network 12 Zygotic genome activation and temporal control of gene eXpression 14 The role of maternal transcription factors in early development 18 References 19 CHAPTER 2: Assembly of maternal transcription factors initiates the emergence 26 of tissue-specific zygotic cis-regulatory regions Introduction 28 Identification of maternal vegetally-localized transcription factors 31 Vegt and OtX1 combinatorially regulate the endodermal 33 transcriptome iii -
PRODUCT SPECIFICATION Product Datasheet
Product Datasheet QPrEST PRODUCT SPECIFICATION Product Name QPrEST K1841 Mass Spectrometry Protein Standard Product Number QPrEST29029 Protein Name Uncharacterized protein KIAA1841 Uniprot ID Q6NSI8 Gene KIAA1841 Product Description Stable isotope-labeled standard for absolute protein quantification of Uncharacterized protein KIAA1841. Lys (13C and 15N) and Arg (13C and 15N) metabolically labeled recombinant human protein fragment. Application Absolute protein quantification using mass spectrometry Sequence (excluding EQCIQYCHKNMNAIVATPCNMNCINANLLTRIADLFSHNEVDDLKDKKDK fusion tag) FKSKLFCKKIERLFDPEYLNPDSRSNAA Theoretical MW 26883 Da including N-terminal His6ABP fusion tag Fusion Tag A purification and quantification tag (QTag) consisting of a hexahistidine sequence followed by an Albumin Binding Protein (ABP) domain derived from Streptococcal Protein G. Expression Host Escherichia coli LysA ArgA BL21(DE3) Purification IMAC purification Purity >90% as determined by Bioanalyzer Protein 230 Purity Assay Isotopic Incorporation >99% Concentration >5 μM after reconstitution in 100 μl H20 Concentration Concentration determined by LC-MS/MS using a highly pure amino acid analyzed internal Determination reference (QTag), CV ≤10%. Amount >0.5 nmol per vial, two vials supplied. Formulation Lyophilized in 100 mM Tris-HCl 5% Trehalose, pH 8.0 Instructions for Spin vial before opening. Add 100 μL ultrapure H2O to the vial. Vortex thoroughly and spin Reconstitution down. For further dilution, see Application Protocol. Shipping Shipped at ambient temperature Storage Lyophilized product shall be stored at -20°C. See COA for expiry date. Reconstituted product can be stored at -20°C for up to 4 weeks. Avoid repeated freeze-thaw cycles. Notes For research use only Product of Sweden. For research use only. Not intended for pharmaceutical development, diagnostic, therapeutic or any in vivo use. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase