DOCSLIB.ORG

Nucleotide Excision Repair: Interplay Between Nuclear Compartmentalization, Histone Modifications and Signaling

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nucleotide Excision Repair: Interplay Between Nuclear Compartmentalization, Histone Modifications and Signaling Nucleotide Excision Repair: Interplay between nuclear compartmentalization, histone modifications and signaling Dissertation zur Erlangung des Grades "Doktor der Naturwissenschaften" am Fachbereich Biologie der Johannes Gutenberg-Universität in Mainz Shalaka Chitale geb. am 20.06.1988 in Pune, India Mainz, 2017 Tag der mündlichen Prüfung: 20.06.2017 1 1 Table of Contents SUMMARY 4 ZUSSAMENFASSUNG 5 INTRODUCTION 7 THE NEED FOR EFFICIENT DNA REPAIR: 7 TYPES OF DNA DAMAGE: 7 Double strand break repair 9 Mismatch repair 10 Base excision repair 11 Nucleotide excision repair 12 DNA REPAIR IN THE CONTEXT OF CHROMATIN 17 Mechanisms of regulation of chromatin structure at site of DNA damage 18 Histone modifications: 19 ATP dependent Chromatin remodeling 22 SPATIAL NUCLEAR ORGANIZATION OF NER 23 REFERENCES 26 AIMS OF THE STUDY 34 ZRF1 MEDIATES REMODELING OF E3 LIGASES AT DNA LESION SITES DURING NUCLEOTIDE EXCISION REPAIR 35 INTRODUCTION 36 RESULTS 38 DISCUSSION 52 MATERIALS AND METHODS 57 AUTHOR CONTRIBUTION 63 REFERENCES 63 NUCLEAR ORGANIZATION OF NUCLEOTIDE EXCISION REPAIR IS MEDIATED BY RING1B DEPENDENT H2A-UBIQUITYLATION 69 SUMMARY 70 INTRODUCTION 70 RESULTS 72 NER is partially routed to the nucleolus and involves reorganization of chromatin 72 DDB2 causes repositioning of chromatin to the vicinity of the nucleolus 77 Nucleolar repositioning requires presence of a functional UV-RING1B complex and H2A-K119 ubiquitylation 80 ZRF1 is present in the nucleolus and facilitates relocalization of chromatin 85 DISCUSSION 88 EXPERIMENTAL PROCEDURES 90 REFERENCES 93 SUPPLEMENTARY FIGURES 97 DICER AND ZRF1 CONTRIBUTE TO CHROMATIN DECONDENSATION DURING NUCLEOTIDE EXCISION REPAIR 106 ABSTRACT 107 INTRODUCTION 108 MATERIALS AND METHODS 109 RESULTS 113 2 DICER is essential for nucleotide excision repair and is recruited to DNA damage sites 113 DICER interacts with ZRF1 and its recruitment to chromatin is dependent on ZRF1 115 DICER and ZRF1 interactions with chromatin are RNA dependent 116 DICER and ZRF1 are required for chromatin decondensation after UV damage 117 DICER and ZRF1 mediated decondensation requires PARP activity 124 DISCUSSION 127 REFERENCES 129 SUPPLEMENTARY DATA 133 XPA RECRUITMENT TO DNA DAMAGE SITES IS MEDIATED BY DICER AND MMSET-CATALYZED DIMETHYLATION OF H4K20 138 INTRODUCTION 139 RESULTS 141 DICER is associated with setting of H4K20me2 during NER 141 H4K20me2 is catalyzed by MMSET during NER 144 MMSET is recruited to chromatin by DICER 147 H4K20me2 provides a tethering platform for XPA recruitment 148 DISCUSSION 151 REFERENCES 153 SUPPLEMENTARY FIGURES: 156 DISCUSSION: 160 UBIQUITIN SIGNALING IN THE NER PATHWAY. 162 COMPARTMENTALIZATION OF CELLULAR PROCESSES: HOW IS NER COMPARTMENTALIZED? HOW UNIVERSAL ARE METHODS OF CHROMATIN COMPARTMENTALIZATION USED IN NER? 182 CHROMATIN ACCESSIBILITY DURING NER: NOVEL PLAYERS REGULATING CHROMATIN ACCESSIBILITY AND THEIR IMPLICATION IN MAINTENANCE OF CELLULAR CHROMATIN CONFORMATION 188 SIGNALING THROUGH HISTONE MODIFICATIONS 190 REFERENCES 192 ACKNOWLEDGEMENTS 194 3 Summary Maintaining the integrity of genetic information is one of the crucial functions of the cell. Depending on the type of DNA damage, there are several repair pathways dedicated to a quick and efficient repair of the damage. A major source of DNA damage is exposure to UV light, which causes formation of 6’-4’photoproducts and pyrimidine dimers. These are bulky DNA adducts that cause distortion of the helix structure. Such lesions are repaired by Nucleotide Excision Repair (NER). Nucleotide Excision Repair occurs by two sub-pathways, depending on the genomic location of the lesion. Transcription coupled NER (TC-NER) repairs lesions in actively transcribed genes, which global genomic NER (GG-NER) can repair all types of lesions. These two pathways differ in their recognition step. Lesion recognition is followed by verification of damage, excision of the damaged strand, and refilling of the gap by DNA synthesis. An important unanswered question in the field of NER is how the removal of lesions occurs in the context of chromatin structure. Recognition of lesions in heterochromatin requires a decondensation of chromatin to enable access by repair factors. Additionally, lesion recognition requires cascades of recruitment of the various proteins, in a tightly regulated and synchronized manner. We show that the recognition step during GG-NER consists of a ZRF1-DICER-MMSET axis linking lesion recognition via DDB2 to lesion verification via XPA followed by subsequent repair. ZRF1 recognizes the H2AK119 ub mark set by the UV-RING1B complex. This results in translocation of the lesion to the nucleolus, and remodeling of the complex to the UV-CUL4A complex. Formation of this complex enables the next phase of ubiquitylation that regulates NER repair proteins. ZRF1 in turn also contributed to chromatin decondensation through recruitment of DICER. DICER enables relaxation of chromatin structure in a PARP1 dependent manner. It also recruits MMSET, which sets the H4K20me2 mark. This histone mark serves as a tethering platform for recruitment of XPA, a core NER component which is essential for further repair to take place. Thus, we have discovered a novel and essential function for these proteins in NER. 4 Zussamenfassung FACHBEREICH BIOLOGIE DER JOHANNES GUTENBERG-UNIVERSITÄT MAINZ Nr. / 20 Zusammenfassung der Dissertation von __Shalaka Chitale Thema: Eine wesentliche Aufgabe der Zelle ist es die Integrität ihrer DNA zu schützen, um die darin enthaltene genetische Information zu erhalten. Abhängig von der Art der DNA-Schädigung werden in der Zelle unterschiedliche DNA-Reparaturmechanismen angeschaltet, die eine schnelle und effiziente Reparatur des Schadens gewährleisten. Eine der zahlreichen zellulären DNA Reparaturmechanismen ist die Nukleotidexzisionsreparatur (NER), welche unterschiedliche Schäden wie zum Beispiel Cyclobutanpyrimidin Dimere (CPD) und 6-4 Photoprodukte repariert, die nach der Bestrahlung mit UV Licht entstehen. In Säugerzellen werden in der NER Schäden durch zwei unterschiedliche Mechanismen repariert. Schäden in transkribierten genomischen Bereichen werden durch die sogenannte transcription-coupled NER (TC-NER) repariert, alle anderen genomische Bereiche werden durch global genomic NER (GG-NER) repariert. Diese beiden DNA Reparaturmechanismen unterscheiden sich lediglich in der Schadenserkennung. In deren Anschluss nutzen TC-NER und GG-NER einen gemeinsamen Mechanismus zur Verifizierung, zur Exzsion des Schadens und zur Auffüllung der entstandenen etwa 30 Nukleotide umfassenden Lücke durch DNA Synthese. Wie NER im Kontext der Chromatinstruktur verläuft ist eine bislang noch offene Frage. Die Schadenserkennung im Heterochromatin benötigt eine Dekondensierung bzw. Öffnung der Chromatinkonformation, um die Rekrutierung von DNA Reparaturfaktoren zu ermöglichen. Ausserdem werden während der Schadenserkennung unterschiedliche Proteinkomplexe in einer synchronisierten bzw. zeitlich festgelegten Folge zur DNA-Läsion rekrutiert. In der vorliegenden Arbeit wird gezeigt, dass während der GG-NER die Schadenserkennung durch das Zusammenspiel der Faktoren ZRF1, DICER und MMSET mit dem DNA Reparturerkennungsfaktor DDB2 geprägt ist, welches die Rekrutierung des DNA Reparaturfaktors XPA ermöglicht. Dabei bindet ZRF1 mono- ubiquitiniertes histone H2A (H2A-K119-Ub), welches durch den UV-RING1B Komplex katalysiert wird. Derart modifiziertes Chromatin wird zum Nukleolus transloziert, wo durch molekulares Remodeling der UV-RING1B Komplex in den UV-CUL4A Komplex umgebaut wird. Die Herstellung des UV-CUL4A Komplexes leitet dann die nächste Phase von Ubiquitinierungsreaktionen ein, welche wiederum nachfolgende Reparaturreaktionen regulieren. Weiterhin ist ZRF1 an der Chromatin-Dekondensierung beteiligt, da es über die Rekruiterung von DICER eine PARP1-abhängige Relaxation der Chromatin-Konformation hervorruft. DICER wiederum ist für die Rekruiterung des Methyltransferase MMSET essentiell, welche ein Methylierung am Histone H4 (H4K20me2) bedingt. Diese Histonmodifizierung dient als eine Art 5 Bindeplattform für den Reparaturfaktor XPA, eine der Hauptkomponenten der NER. Zusammengenommen konnte eine neue und essentielle Funktion der obengenannten Proteine bzw. deren Zusammenspiel während der NER entdeckt werden. Genehmigt vom 1. Gutachter / von der 1. Gutachterin _______________________________________ (Unterschrift) 6 Introduction The need for efficient DNA repair: One of the major biological discoveries in recent times, has been the central dogma that governs all biological systems. DNA uses a specific sequence of the four bases A,T,G,C to encode genetic information, this information is transmitted via RNA, and thus leads to formation of the specific proteins needed by an organism to survive. Considering the major role of DNA as a repository of the genetic information of an organism, maintaining the sequence integrity of DNA is one of the major functions of a cell. DNA is under threat from a variety of internal and external agents, that can directly or indirectly lead to changes in the DNA sequence. Persistent DNA damage can lead to mutations, cell cycle stalling and ultimately even cell death. Thus, the cell has devised a variety of pathways to ensure efficient repair of its DNA. Types of DNA damage: DNA damage can occur due to a variety of endogenous and exogenous factors. Depending on the type of damage, the cell has evolved a corresponding variety of repair pathways that repair the damage. (Table 1) (reviewed in De Bont and van Larebeke,
Load more

Recommended publications
  • Genetic Variations Associated with Resistance to Doxorubicin and Paclitaxel in Breast Cancer
    GENETIC VARIATIONS ASSOCIATED WITH RESISTANCE TO DOXORUBICIN AND PACLITAXEL IN BREAST CANCER by Irada Ibrahim-zada A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto © Copyright by Irada Ibrahim-zada 2010 ii Genetic variations associated with resistance to doxorubicin and paclitaxel in breast cancer Irada Ibrahim-zada Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto 2010 Abstract Anthracycline- and taxane-based regimens have been the mainstay in treating breast cancer patients using chemotherapy. Yet, the genetic make-up of patients and their tumors may have a strong impact on tumor sensitivity to these agents and to treatment outcome. This study represents a new paradigm assimilating bioinformatic tools with in vitro model systems to discover novel genetic variations that may be associated with chemotherapy response in breast cancer. This innovative paradigm integrates drug response data for the NCI60 cell line panel with genome-wide Affymetrix SNP data in order to identify genetic variations associated with drug resistance. This genome wide association study has led to the discovery of 59 candidate loci that may play critical roles in breast tumor sensitivity to doxorubicin and paclitaxel. 16 of them were mapped within well-characterized genes (three related to doxorubicin and 13 to paclitaxel). Further in silico characterization and in vitro functional analysis validated their differential expression in resistant cancer cell lines treated with the drug of interest (over-expression of RORA and DSG1, and under-expression of FRMD6, SGCD, SNTG1, LPHN2 and DCT). iii Interestingly, three and six genes associated with doxorubicin and paclitaxel resistance, respectively, are involved in the apoptotic process in cells.
    [Show full text]
  • ZRF1-‐Mediated Transcriptional Regulation in Acute Myeloid Leukemia
    ZRF1-mediated transcriptional regulation in acute myeloid leukemia Santiago Demajo Meseguer TESI DOCTORAL UPF / 2013 Aquesta tesi ha estat realitzada sota la direcció del Dr. Luciano Di Croce Departament de Regulació Gènica, Cèl·lules Mare i Càncer Centre de Regulació Genòmica (CRG) Barcelona, desembre de 2013 TABLE OF CONTENTS ABSTRACT ....................................................................................................... 5 INTRODUCTION ...........................................................................................11 1. ACUTE MYELOID LEUKEMIA................................................................................13 1.1 Leukemia ........................................................................................................ 13 1.2 Acute myeloid leukemia (AML)............................................................. 14 1.3 Differentiation therapy in AML............................................................. 15 2. RETINOIC ACID SIGNALING PATHWAY ..............................................................19 2.1 RA metabolism and signaling................................................................ 19 2.2 Role of RA in differentiation, apoptosis and proliferation........ 20 2.3 RA molecular mechanism........................................................................ 22 2.4 Disruption of RA signaling: the example of PML-RARα.............. 23 3. CHROMATIN AND EPIGENETICS IN TRANSCRIPTION ......................................27 3.1 Chromatin structure.................................................................................
    [Show full text]
  • Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
    Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing
    [Show full text]
  • DNAJC2 Rabbit Pab
    Leader in Biomolecular Solutions for Life Science DNAJC2 Rabbit pAb Catalog No.: A4633 Basic Information Background Catalog No. This gene is a member of the M-phase phosphoprotein (MPP) family. The gene encodes A4633 a phosphoprotein with a J domain and a Myb DNA-binding domain which localizes to both the nucleus and the cytosol. The protein is capable of forming a heterodimeric Observed MW complex that associates with ribosomes, acting as a molecular chaperone for nascent 72kDa polypeptide chains as they exit the ribosome. This protein was identified as a leukemia- associated antigen and expression of the gene is upregulated in leukemic blasts. Also, Calculated MW chromosomal aberrations involving this gene are associated with primary head and 65kDa/71kDa neck squamous cell tumors. This gene has a pseudogene on chromosome 6. Alternatively spliced variants which encode different protein isoforms have been Category described. Primary antibody Applications WB Cross-Reactivity Human, Mouse Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 27000 Q99543 Immunogen Recombinant fusion protein containing a sequence corresponding to amino acids 1-140 of human DNAJC2 (NP_055192.1). Synonyms DNAJC2;MPHOSPH11;MPP11;ZRF1;ZUO1 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts of various cell lines, using DNAJC2 antibody (A4633) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane.
    [Show full text]
  • Genetic Insight Into the Domain Structure and Functions of Dicer-Type Ribonucleases
    International Journal of Molecular Sciences Review Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases Kinga Ciechanowska, Maria Pokornowska and Anna Kurzy ´nska-Kokorniak* Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; [email protected] (K.C.); [email protected] (M.P.) * Correspondence: [email protected]; Tel.: +48-61-852-85-03 (ext. 1264) Abstract: Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.
    [Show full text]
  • [KO Validated] DNAJC2 Rabbit Pab
    Leader in Biomolecular Solutions for Life Science [KO Validated] DNAJC2 Rabbit pAb Catalog No.: A19954 KO Validated Basic Information Background Catalog No. This gene is a member of the M-phase phosphoprotein (MPP) family. The gene encodes A19954 a phosphoprotein with a J domain and a Myb DNA-binding domain which localizes to both the nucleus and the cytosol. The protein is capable of forming a heterodimeric Observed MW complex that associates with ribosomes, acting as a molecular chaperone for nascent 80KDa polypeptide chains as they exit the ribosome. This protein was identified as a leukemia- associated antigen and expression of the gene is upregulated in leukemic blasts. Also, Calculated MW chromosomal aberrations involving this gene are associated with primary head and 65kDa/71kDa neck squamous cell tumors. This gene has a pseudogene on chromosome 6. Alternatively spliced variants which encode different protein isoforms have been Category described. Primary antibody Applications WB Cross-Reactivity Human, Mouse Recommended Dilutions Immunogen Information WB 1:500 - 1:2000 Gene ID Swiss Prot 27000 Q99543 Immunogen Recombinant protein of human DNAJC2. Synonyms DNAJC2;MPHOSPH11;MPP11;ZRF1;ZUO1 Contact Product Information www.abclonal.com Source Isotype Purification Rabbit IgG Affinity purification Storage Store at -20℃. Avoid freeze / thaw cycles. Buffer: PBS with 0.02% sodium azide,50% glycerol,pH7.3. Validation Data Western blot analysis of extracts from normal (control) and DNAJC2 knockout (KO) 293T cells, using DNAJC2 antibody (A19954) at 1:1000 dilution. Secondary antibody: HRP Goat Anti-Rabbit IgG (H+L) (AS014) at 1:10000 dilution. Lysates/proteins: 25ug per lane. Blocking buffer: 3% nonfat dry milk in TBST.
    [Show full text]
  • Functions of RING1B and ZRF1 in Ubiquitin-Mediated Regulation of Nucleotide Excision Repair
    Functions of RING1B and ZRF1 in ubiquitin-mediated regulation of Nucleotide Excision Repair Dissertation zur Erlangung des Grades "Doktor der Naturwissenschaften" am Fachbereich Biologie der Johannes Gutenberg-Universität in Mainz Ekaterina Gracheva geb. am 21.04.1989 in Khabarovsk, Russland Mainz, 2016 Dekan: Prof. Dr. Hans Zischler 1. Berichterstatter: 2. Berichterstatter: Tag der mündlichen Prüfung: 28.07.2016 1 This work is dedicated to my late mother 1 Index of contents Index of figures 6 Index of tables 8 Index of abbreviations 9 Summary 1 Zusammenfassung 2 Introduction 3 DNA Repair Pathways 3 Types of DNA damage 3 Repair of double strand breaks 4 Mismatch repair 7 Base excision repair 7 Nucleotide excision repair 7 Regulation of DNA repair by posttranslational modifications 15 Phosphorylation 15 PARylation 16 Ubiquitination 16 SUMOylation 20 Regulation of NER by posttranslational modifications 20 Phosphorylation in NER 20 PARylation in NER 21 Ubiquitination in NER 21 2 Chromatin reorganization in DNA repair 25 Incorporation of histone variants 25 Posttranslational modifications of histones 26 Acetylation 26 Methylation 26 Ubiquitination 27 PRC1 complex 28 Deubiquitination of H2A 29 ATP-dependent chromatin remodeling 30 Chromatin reorganization in NER 31 Aims of the study 34 Materials and methods 35 Cell culture 35 Cell line production 35 U2OS-shRING1B 35 shRNA and siRNA mediated gene knockdown 35 shRNA transduction 35 siRNA transfectrion 36 Transfections 37 Genotoxic treatment and enzymatic inhibition 38 Biochemical methods 39
    [Show full text]
  • Human Untagged Clone – SC311107 | Origene
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for SC311107 DNAJC2 (NM_014377) Human Untagged Clone Product data: Product Type: Expression Plasmids Product Name: DNAJC2 (NM_014377) Human Untagged Clone Tag: Tag Free Symbol: DNAJC2 Synonyms: MPHOSPH11; MPP11; ZRF1; ZUO1 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 DNAJC2 (NM_014377) Human Untagged Clone – SC311107 Fully Sequenced ORF: >NCBI ORF sequence for NM_014377, the custom clone sequence may differ by one or more nucleotides ATGCTGCTTCTGCCAAGCGCCGCGGACGGCCGGGGCACCGCCATCACCCACGCTCTGACCTCTGCCTCTA CACTCTGTCAAGTTGAACCTGTGGGAAGATGGTTTGAAGCTTTTGTTAAGAGGAGAAACAGAAATGCTTC TGCCTCTTTTCAGGAACTGGAGGATAAGAAAGAGTTATCCGAGGAATCAGAAGATGAAGAATTGCAGTTG GAAGAGTTTCCCATGCTGAAAACACTTGATCCCAAAGACTGGAAGAACCAAGATCATTATGCAGTTCTTG GACTTGGCCATGTGAGATACAAGGCTACACAGAGACAGATCAAAGCAGCTCATAAAGCAATGGTTTTAAA ACATCACCCAGACAAACGGAAAGCAGCTGGTGAACCAATAAAAGAAGGAGATAATGACTACTTCACTTGC ATAACTAAAGCTTATGAAATGTTATCTGATCCAGTGAAAAGACGAGCATTTAACAGTGTAGATCCTACTT TTGATAACTCAGTTCCTTCTAAAAGTGAAGCAAAGGATAATTTCTTCGAAGTGTTTACCCCAGTGTTTGA AAGGAATTCCAGATGGTCAAATAAAAAAAATGTTCCTAAACTTGGTGATATGAATTCATCATTTGAAGAT GTAGATATATTTTATTCTTTCTGGTATAATTTTGATTCTTGGAGAGAATTTTCTTATTTAGATGAAGAAG
    [Show full text]
  • Primepcr™Assay Validation Report
    PrimePCR™Assay Validation Report Gene Information Gene Name DnaJ (Hsp40) homolog, subfamily C, member 2 Gene Symbol DNAJC2 Organism Human Gene Summary This gene is a member of the M-phase phosphoprotein (MPP) family. The gene encodes a phosphoprotein with a J domain and a Myb DNA-binding domain which localizes to both the nucleus and the cytosol. The protein is capable of forming a heterodimeric complex that associates with ribosomes acting as a molecular chaperone for nascent polypeptide chains as they exit the ribosome. This protein was identified as a leukemia-associated antigen and expression of the gene is upregulated in leukemic blasts. Also chromosomal aberrations involving this gene are associated with primary head and neck squamous cell tumors. This gene has a pseudogene on chromosome 6. Alternatively spliced variants which encode different protein isoforms have been described. Gene Aliases MPHOSPH11, MPP11, ZRF1, ZUO1 RefSeq Accession No. NC_000007.13, NT_007933.15 UniGene ID Hs.558476 Ensembl Gene ID ENSG00000105821 Entrez Gene ID 27000 Assay Information Unique Assay ID qHsaCEP0058275 Assay Type Probe - Validation information is for the primer pair using SYBR® Green detection Detected Coding Transcript(s) ENST00000249270, ENST00000379263, ENST00000426036, ENST00000454277, ENST00000412522 Amplicon Context Sequence ACTGCATAATGATCTTGGTTCTTCCAGTCTTTGGGATCAAGTGTTTTCAGCATGG GAAACTCTTCCAACTGCAATTCTTCATCTTCTGATTCCTCGGATAACTCTTTCTTA TCCT Amplicon Length (bp) 85 Chromosome Location 7:102978239-102982305 Assay Design Exonic Purification
    [Show full text]
  • Role of Chromatin Regulators Atring1 and Atzrf1 in Arabidopsis Growth and Development Qiannan Wang
    Role of chromatin regulators AtRING1 and AtZRF1 in Arabidopsis growth and development Qiannan Wang To cite this version: Qiannan Wang. Role of chromatin regulators AtRING1 and AtZRF1 in Arabidopsis growth and development. Vegetal Biology. Université de Strasbourg, 2018. English. NNT : 2018STRAJ129. tel-02310659 HAL Id: tel-02310659 https://tel.archives-ouvertes.fr/tel-02310659 Submitted on 10 Oct 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ [Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS] THÈSE présentée par : [Qiannan WANG] soutenue le : 14 Décembre 2018 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Aspects Moléculaires et Cellulaires de la Biologie Investigation du mécanisme fonctionnel des gènes AtRING1 et AtZRF1 dans la régulation de la croissance et du développement chez les plantes THÈSE dirigée par : [M. SHEN Wen-Hui] Directeur de Recherche CNRS, Université de Strasbourg RAPPORTEURS : [Mme. PROBST Aline] Directeur de Recherche CNRS, Université Clermont Auvergne [Mme. DELARUE Marianne] Professeur, Université Paris-Sud, Université Evry et, Université Paris-Saclay AUTRES MEMBRES DU JURY : [M. OTTEN Léon] Professeur, Université de Strasbourg ACKNOWLEDGMENTS First, I would like to express my sincere gratitude to my supervisor, Dr.
    [Show full text]
  • High-Density Single Nucleotide Polymorphism Array Analysis and ASXL1 Gene Mutation Screening in Chronic Myeloid Leukemia During Disease Progression
    Leukemia (2010) 24, 1139–1145 & 2010 Macmillan Publishers Limited All rights reserved 0887-6924/10 www.nature.com/leu ORIGINAL ARTICLE High-density single nucleotide polymorphism array analysis and ASXL1 gene mutation screening in chronic myeloid leukemia during disease progression J Boultwood1, J Perry1, R Zaman1, C Fernandez-Santamaria1, T Littlewood1, R Kusec2, A Pellagatti1, L Wang3, RE Clark3 and JS Wainscoat1 1LRF Molecular Haematology Unit, NDCLS, University of Oxford, John Radcliffe Hospital, Oxford, UK; 2Department of Clinical Sciences, Department of Haematology, University Hospital Merkur, Zagreb, Croatia and 3University Department of Haematology, Royal Liverpool University Hospital, Liverpool, UK We have undertaken a genome-wide single nucleotide poly- patients not treated with imatinib and also in those who have morphism (SNP) array analysis of 41 chronic myeloid leukemia become resistant to the drug.6,7 (CML) patients. In total, 44 regions of uniparental disomy (UPD) Although it is recognized that cytogenetic and molecular 43 Mb were identified in 24 of 32 patients in chronic phase (CP), and 21 regions of UPD 43 Mb were identified in 13 of 21 patients changes occur in the majority of CML patients during evolution in blast crisis (BC). Chromosome 8 had the highest frequency of to BC, the molecular events responsible for leukemic transfor- UPD regions in both CP and BC samples. Eight recurrent regions mation remain unclear. It has been suggested that BCR/ABL may of UPD were observed among the 41 patients, with chromosome have a direct or an indirect role in promoting genomic instability 8 showing the highest frequency. Ten regions of copy number and 60–80% of patients with CML develop additional non- change (CNC) 43 Mb were observed in 4 of 21 patients in BC, random chromosomal abnormalities involving chromosomes 8, whereas none were observed in CP.
    [Show full text]
  • A Master Autoantigen-Ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 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. A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases Julia Y. Wang1*, Michael W. Roehrl1, Victor B. Roehrl1, and Michael H. Roehrl2* 1 Curandis, New York, USA 2 Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA * Correspondence: [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.30.454526; this version posted August 4, 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. Abstract Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer.
    [Show full text]