DOCSLIB.ORG

An Investigation of 53BP1 in Multiple Myeloma

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An Investigation of 53BP1 in Multiple Myeloma University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2017 An Investigation of 53BP1 in Multiple Myeloma Simms, Justin Simms, J. (2017). An Investigation of 53BP1 in Multiple Myeloma (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/24911 http://hdl.handle.net/11023/4002 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY An Investigation of 53BP1 in Multiple Myeloma by Justin Andrew Simms A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN MEDICAL SCIENCE CALGARY, ALBERTA JULY, 2017 © Justin Andrew Simms 2017 Abstract Currently, multiple myeloma is the second most common hematological malignancy, and as of yet it remains incurable. Although many therapeutic advances have been made in the recent past, there is still room for improvement in the treatment of myeloma. Here, using CRISPR/Cas9 genome editing, we show that a therapeutic combination of proteasome inhibition in combination with PARP inhibition that is in clinical trials depends on the DNA damage response protein 53BP1. These findings contribute to the understanding of the mechanisms behind potential resistance to the combination of proteasome inhibitors with PAPR inhibitors. ii Table of Contents Abstract ............................................................................................................................... ii Table of Contents ............................................................................................................... iii List of Tables .......................................................................................................................v List of Figures and Illustrations ......................................................................................... vi List of Symbols, Abbreviations and Nomenclature ......................................................... viii CHAPTER ONE: INTRODUCTION ..............................................................................12 1.1 Multiple Myeloma .................................................................................................12 1.2 Multiple Myeloma and Genome Instability ...........................................................13 1.3 Bortezomib .............................................................................................................15 1.4 Poly-ADP-Ribose Polymerase Inhibitors ..............................................................16 1.5 Double Stranded Break Repair ..............................................................................17 1.5.1 Canonical non-homologous end joining double strand break repair ...............18 1.5.2 Alternative end joining double strand break repair..........................................19 1.5.3 Homologous recombination double strand break repair ..................................22 1.6 53BP1 recruitment and displacement ....................................................................26 1.6.1 53BP1 Recruitment ..........................................................................................26 1.6.2 53BP1 Displacement/Antagonism ...................................................................27 1.6.2.1 H4K16 acetylation and 53BP1 antagonism .......................................27 1.6.2.2 Ubiquitin and 53BP1 antagonism ......................................................28 1.6.2.3 RIF1 antagonism to facilitate pathway switch ...................................29 1.7 Multiple Myeloma, bortezomib and PARP inhibitors ...........................................30 1.7.1 Previous work from Bahlis lab: Neri et al. 2011 .............................................30 Hypothesized mechanism of action for PI and PARPi combination therapy in MM33 1.8 Experimental Aims: ...............................................................................................38 CHAPTER TWO: MATERIALS AND METHODS ......................................................39 2.1 Antibodies, Plasmids, Primers, and Cell lines: ......................................................39 2.2 Cell culture methods ..............................................................................................41 2.3 Lentiviral infection with sh53BP1 containing LV particles ..................................42 2.4 Cloning of CRISPR/Cas9 Constructs ....................................................................42 2.5 CRISPR/Cas9 packaging of lentiviral plasmids and lentiviral infection: ..............43 2.6 Immunofluorescence Assays .................................................................................44 2.7 Western Blots .........................................................................................................46 2.7.1 Cell lysis buffers ..............................................................................................47 2.7.1.1 RIPA ..................................................................................................47 2.7.1.2 NP-40 (Ines) .......................................................................................47 2.7.1.3 Hypotonic lysis buffer........................................................................47 2.8 RT-PCR and qPCR for transcript expression analysis ..........................................48 2.9 RNA-seq Analysis .................................................................................................48 2.9.1 Sequence Acquisition.......................................................................................48 2.9.2 Sequence Alignment ........................................................................................48 2.9.3 Protein family gene acquisition .......................................................................49 iii 2.10 Surveyor Mutation Detection Assay ......................................................................49 2.11 Cell viability Assays ..............................................................................................50 CHAPTER THREE: ANALYSIS OF MM CELL LINES FOR MUTATIONS IN HISTONES AND DNA REPAIR PROTEINS ........................................................51 CHAPTER FOUR: GENE EDITING USING CRISPR/CAS9.......................................58 4.1 Using shRNA to silence 53BP1 in MM .................................................................58 4.2 Using TALEN to generate 53BP1-/- MM cell lines ...............................................61 4.2.1 TALEN mechanism of action and design to target 53BP1 ..............................61 4.2.2 Detection of mutation by SURVEYOR Mutation Detection assay .................65 4.2.3 Unsuccessful mutation of 53BP1 by TALEN ..................................................66 4.3 Employing the CRISPR/Cas9 genome editing technique to knock-out 53BP1 ....70 4.3.1 CRISPR/Cas9 instead of TALEN? ..................................................................70 4.3.2 CRISPR/Cas9 mechanism of action ................................................................70 4.3.3 Using CRISPR/Cas9 to edit 53BP1 and RNF168 ...........................................73 4.3.3.1 pLENTICRISPRv2 CRISPR/Cas9 of 53BP1 ....................................73 4.3.3.2 pLENTICRISPRv2 targeting RNF168 in OPM2 ..............................85 4.4 Revisiting CRISPR/Cas9 editing of 53BP1 ...........................................................87 4.4.1 Using pSp-Cas9(BB)-2A-GFP to edit 53BP1..................................................87 4.5 Other CRISPR/Cas9 targets that were unsuccessful ..............................................98 4.6 Other CRISPR/Cas9 targets that were successful ................................................101 CHAPTER FIVE: 53BP1 AND MULTIPLE MYELOMA ..........................................103 5.1 High RNF168 expression levels does not correlate with an increase in basal levels of 53BP1 foci in MM ...............................................................................................116 5.2 RNF168 loss does not confer resistance to synergy seen with concomitant treatment of MM with ABT-888 and BTZ ..........................................................................121 5.3 53BP1 is necessary for the synergistic activity of PI and PAPRi in MM............124 CHAPTER SIX: DISCUSSION AND FUTURE DIRECTIONS .................................128 REFERENCES ................................................................................................................131 SUPPLEMENTARY MATERIALS ...................................................................................141 iv List of Tables Table 1-1: Classification of MM by genetic alterations ............................................................... 14 Table 1-2: Known DNA repair pathways ..................................................................................... 25 Table 2-1: List of antibodies used for experiments detailed herein. ............................................. 39 Table 2-2: Cloning primers made to generate CRISPR/Cas9 mediated gene editing. These primers were inserted into pLENTICRISPRv2, pLentiGuide-Puro
Load more

Recommended publications
  • Supplementary Materials
    Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine
    [Show full text]
  • Literature Mining Sustains and Enhances Knowledge Discovery from Omic Studies
    LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES by Rick Matthew Jordan B.S. Biology, University of Pittsburgh, 1996 M.S. Molecular Biology/Biotechnology, East Carolina University, 2001 M.S. Biomedical Informatics, University of Pittsburgh, 2005 Submitted to the Graduate Faculty of School of Medicine in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2016 UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE This dissertation was presented by Rick Matthew Jordan It was defended on December 2, 2015 and approved by Shyam Visweswaran, M.D., Ph.D., Associate Professor Rebecca Jacobson, M.D., M.S., Professor Songjian Lu, Ph.D., Assistant Professor Dissertation Advisor: Vanathi Gopalakrishnan, Ph.D., Associate Professor ii Copyright © by Rick Matthew Jordan 2016 iii LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES Rick Matthew Jordan, M.S. University of Pittsburgh, 2016 Genomic, proteomic and other experimentally generated data from studies of biological systems aiming to discover disease biomarkers are currently analyzed without sufficient supporting evidence from the literature due to complexities associated with automated processing. Extracting prior knowledge about markers associated with biological sample types and disease states from the literature is tedious, and little research has been performed to understand how to use this knowledge to inform the generation of classification models from ‘omic’ data. Using pathway analysis methods to better understand the underlying biology of complex diseases such as breast and lung cancers is state-of-the-art. However, the problem of how to combine literature- mining evidence with pathway analysis evidence is an open problem in biomedical informatics research.
    [Show full text]
  • Regulation of DNA Replication-Coupled Histone Gene Expression
    www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 55), pp: 95005-95022 Review Regulation of DNA replication-coupled histone gene expression Qianyun Mei1,*, Junhua Huang1,*, Wanping Chen1,2, Jie Tang1, Chen Xu1, Qi Yu1, Ying Cheng1, Lixin Ma1,2, Xilan Yu1,2 and Shanshan Li1,2 1Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China 2Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China *These authors have contributed equally to this work Correspondence to: Xilan Yu, email: [email protected] Shanshan Li, email: [email protected] Keywords: DNA replication, histone gene transcription, cell cycle Received: August 08, 2017 Accepted: September 20, 2017 Published: October 16, 2017 Copyright: Mei et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT The expression of core histone genes is cell cycle regulated. Large amounts of histones are required to restore duplicated chromatin during S phase when DNA replication occurs. Over-expression and excess accumulation of histones outside S phase are toxic to cells and therefore cells need to restrict histone expression to S phase. Misregulation of histone gene expression leads to defects in cell cycle progression, genome stability, DNA damage response and transcriptional regulation. Here, we discussed the factors involved in histone gene regulation as well as the underlying mechanism.
    [Show full text]
  • A Mutation in Histone H2B Represents a New Class of Oncogenic Driver
    Author Manuscript Published OnlineFirst on July 23, 2019; DOI: 10.1158/2159-8290.CD-19-0393 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. A Mutation in Histone H2B Represents A New Class Of Oncogenic Driver Richard L. Bennett1, Aditya Bele1, Eliza C. Small2, Christine M. Will2, Behnam Nabet3, Jon A. Oyer2, Xiaoxiao Huang1,9, Rajarshi P. Ghosh4, Adrian T. Grzybowski5, Tao Yu6, Qiao Zhang7, Alberto Riva8, Tanmay P. Lele7, George C. Schatz9, Neil L. Kelleher9 Alexander J. Ruthenburg5, Jan Liphardt4 and Jonathan D. Licht1 * 1 Division of Hematology/Oncology, University of Florida Health Cancer Center, Gainesville, FL 2 Division of Hematology/Oncology, Northwestern University 3 Department of Cancer Biology, Dana Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 4 Department of Bioengineering, Stanford University 5 Department of Molecular Genetics and Cell Biology, The University of Chicago 6 Department of Chemistry, Tennessee Technological University 7 Department of Chemical Engineering, University of Florida 8 Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida 9 Department of Chemistry, Northwestern University, Evanston IL 60208 Running title: Histone mutations in cancer *Corresponding Author: Jonathan D. Licht, MD The University of Florida Health Cancer Center Cancer and Genetics Research Complex, Suite 145 2033 Mowry Road Gainesville, FL 32610 352-273-8143 [email protected] Disclosures: The authors have no conflicts of interest to declare Downloaded from cancerdiscovery.aacrjournals.org on September 27, 2021. © 2019 American Association for Cancer Research. Author Manuscript Published OnlineFirst on July 23, 2019; DOI: 10.1158/2159-8290.CD-19-0393 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
    [Show full text]
  • High-Dose Ionizing Radiation Regulates Gene Expression Changes in the MCF7 Breast Cancer Cell Line
    ANTICANCER RESEARCH 35: 2577-2592 (2015) High-dose Ionizing Radiation Regulates Gene Expression Changes in the MCF7 Breast Cancer Cell Line VALENTINA BRAVATÀ1*, LUIGI MINAFRA1*, GIORGIO RUSSO1, GIUSI IRMA FORTE1, FRANCESCO P. CAMMARATA1, MARILENA RIPAMONTI1, CARLO CASARINO1, GIUSEPPA AUGELLO2, FRANCESCA COSTANTINI2, GIOVANNA BARBIERI2, CRISTINA MESSA1,4,5 and MARIA C. GILARDI1,3,5 1Institute of Bioimaging and Molecular Physiology, National Research Council (IBFM-CNR) -LATO, Cefalù (PA), Italy; 2Institute of Biomedicine and Molecular Immunology “Alberto Monroy”- National Research Council (IBIM-CNR), Palermo, Italy; 3Nuclear Medicine, San Raffaele Scientific Institute, Milan, Italy; 4Nuclear Medicine Center, San Gerardo Hospital, Monza, Italy; 5Department of Health Sciences, Tecnomed Foundation, University of Milano-Bicocca, Milan, Italy Abstract. Background: Intraoperative electron radiation during IOERT boost and exclusive treatments, respectively) therapy (IOERT) is a therapeutic technique which administers by cDNA microarrays. Real-Time Quantitative Reverse a single high dose of ionizing radiation immediately after Transcription PCR (qRT-PCR), immunofluorescence and surgical tumor removal. IOERT induces a strong stress immunoblot experiments were performed to validate response: both tumor and normal cells activating pro- and candidate IOERT biomarkers. We also conducted clonogenic antiproliferative cell signaling pathways. Following treatment, tests and cellular senescence assays to monitor for radiation- several genes and factors are differently modulated, induced effects. Results: The analyses highlighted a producing an imbalance in cell fate decision. However, the transcriptome dependent on the dose delivered and a number contribution of these genes and pathways in conferring of specific key genes that may be proposed as new markers of different cell radiosensitivity and radioresistance needs to be radiosensitivity. Cell and molecular traits observed in MCF7 further investigated, in particular after high-dose treatments.
    [Show full text]
  • Whole-Genome Sequencing Identifies New Genetic Alterations in Meningiomas
    www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 10), pp: 17070-17080 Research Paper Whole-genome sequencing identifies new genetic alterations in meningiomas Mei Tang1,*, Heng Wei2,*, Lu Han1,*, Jiaojiao Deng3, Yuelong Wang3, Meijia Yang1, Yani Tang1, Gang Guo1, Liangxue Zhou3, Aiping Tong1 1The State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China 2College of Life Science, Sichuan University, Chengdu 610064, China 3Department of Neurosurgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China *These authors have contributed equally to the work Correspondence to: Aiping Tong, email: [email protected] Liangxue Zhou, email: [email protected] Keywords: whole-genome sequencing, meningioma, chromosome instability, copy number alteration, mutation Received: October 24, 2016 Accepted: January 13, 2017 Published: February 03, 2017 ABSTRACT The major known genetic contributor to meningioma formation was NF2, which is disrupted by mutation or loss in about 50% of tumors. Besides NF2, several recurrent driver mutations were recently uncovered through next-generation sequencing. Here, we performed whole-genome sequencing across 7 tumor-normal pairs to identify somatic genetic alterations in meningioma. As a result, Chromatin regulators, including multiple histone members, histone-modifying enzymes and several epigenetic regulators, are the major category among all of the identified copy number variants and single nucleotide variants. Notably, all samples contained copy number variants in histone members. Recurrent chromosomal rearrangements were detected on chromosome 22q, 6p21-p22 and 1q21, and most of the histone copy number variants occurred in these regions.
    [Show full text]
  • Expression and Functionality of Histone H2A2C in the Mammary Epithelium
    Universidade de Aveiro Departamento de Química Ano 2012/2013 Fátima Liliana Ribeiro Expressão e funcionalidade da histona H2A2C no Vieira Monteiro epitélio mamário Universidade de Aveiro Departamento de Química Ano 2012/2013 Fátima Liliana Ribeiro Expressão e funcionalidade da histona H2A2C no Vieira Monteiro epitélio mamário Expression and functionality of histone H2A2C in the mammary epithelium Dissertação apresentada à Universidade de Aveiro para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Bioquímica - ramo Clínica, realizada sob a orientação científica da Doutora Luísa Helguero, investigadora auxiliar do Departamento de Química da Universidade de Aveiro, e da Professora Doutora Carmen Jerónimo, Instituto Português de Oncologia do Porto e Departamento de Patologia e Imunologia Molecular do Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto. Apoio financeiro da COMPETE em cooperação com a FEDER e a FCT no âmbito do projecto PTDC/SAU- ONC/118346/2010 (LAH). o júri presidente Doutor Rui Vitorino Investigado auxiliar da Universidade de Aveiro Doutora Isabel Castro Investigadora do Instituto de Biologia Molecular e Celular do Porto Doutora Luisa Helguero Investigadora auxiliar da Universidade de Aveiro Agradecimentos Primeiramente gostaria de agradecer toda a dedicação e apoio prestados pela minha orientadora Doutora Luisa Helguero, que sempre se mostrou disponível para me esclarecer qualquer dúvida. Tenho a certeza de que não poderia ter recebido melhor orientação. À professora Carmen Jerónimo agradeço também todo o apoio prestado e a grande generosidade com que me acolheu no seu grupo de investigação de Epigenética do Cancro no IPO-Porto. Ao Professor Doutor Rui Henrique agradeço o tempo despendido para me tirar qualquer dúvida que me fosse surgindo e também por partilhar diferentes perspectivas que vieram enriquecer o meu trabalho.
    [Show full text]
  • Candidate SNP Analyses Integrated with Mrna Expression and Hormone
    bioRxiv preprint doi: https://doi.org/10.1101/259002; this version posted February 2, 2018. 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. Candidate SNP analyses integrated with mRNA expression and hormone levels reveal influence on mammographic density and breast cancer risk Biong M.1, Suderman M.2,3,4*, Haakensen VD.1,5*, Kulle B.6,7, Berg PR.8, Gram I.T.9,Dumeaux V.9, Ursin G.10,11,12, Helland Å1, H Hallett M.2, Børresen-Dale AL1,5, Kristensen V.N.1,5,13 Affiliations 1Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Montebello 0310, Oslo, Norway 2Goodman Cancer Centre and McGill Centre for Bioinformatics, Montreal, Quebec, 3649 Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada. 3Sackler Program for Epigenetics & Developmental Psychobiology at McGill University, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada. 4Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada. 5Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, NO-0315, Norway 6Epi-Gen, Institute of Clinical Medicine, Akershus University Hospital, University of Oslo Oslo, Norway 7Department of Biostatistics, Institute for Basic Medical Science, University of Oslo, Oslo, Norway 8Centre for Integrative Genetics, The Norwegian University of Life Sciences, Aas, Norway 9Institute of Community Medicine, Faculty of Health Sciences, University of Tromsø, Norway 10Cancer Registry of Norway, Oslo. Norway 11Department of Nutrition, School of Medicine, University of Oslo, Oslo, NO-0315, Norway 12Department of Preventive Medicine University of Southern California, Keck School of Medicine, Los Angeles, CA, USA 1 bioRxiv preprint doi: https://doi.org/10.1101/259002; this version posted February 2, 2018.
    [Show full text]
  • BMC Genetics Biomed Central
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector BMC Genetics BioMed Central Research article Open Access A novel replication-independent histone H2a gene in mouse Hiromi Nishida*, Takahiro Suzuki, Yasuhiro Tomaru and Yoshihide Hayashizaki Address: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Email: Hiromi Nishida* - [email protected]; Takahiro Suzuki - [email protected]; Yasuhiro Tomaru - [email protected]; Yoshihide Hayashizaki - [email protected] * Corresponding author Published: 19 February 2005 Received: 07 October 2004 Accepted: 19 February 2005 BMC Genetics 2005, 6:10 doi:10.1186/1471-2156-6-10 This article is available from: http://www.biomedcentral.com/1471-2156/6/10 © 2005 Nishida et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: An uncharacterized histone H2a-coding transcript (E130307C13) has been cloned from a mouse full-length cDNA library. This transcript is encoded on chromosome 6, approximately 4 kb upstream of a histone H4 gene, Hist4h4. The proteins encoded by this transcript and the human H2afj mRNA isoform-2 have the highest amino acid similarity. In this paper, we characterize it from the expression pattern given by quantitative RT-PCR. Results: Quantitative RT-PCR indicated that the gene that encodes E130307C13 (E130307C13) is regulated in a replication-independent manner, and therefore it is H2afj.
    [Show full text]
  • Cell Cycle Arrest Through Indirect Transcriptional Repression by P53: I Have a DREAM
    Cell Death and Differentiation (2018) 25, 114–132 Official journal of the Cell Death Differentiation Association OPEN www.nature.com/cdd Review Cell cycle arrest through indirect transcriptional repression by p53: I have a DREAM Kurt Engeland1 Activation of the p53 tumor suppressor can lead to cell cycle arrest. The key mechanism of p53-mediated arrest is transcriptional downregulation of many cell cycle genes. In recent years it has become evident that p53-dependent repression is controlled by the p53–p21–DREAM–E2F/CHR pathway (p53–DREAM pathway). DREAM is a transcriptional repressor that binds to E2F or CHR promoter sites. Gene regulation and deregulation by DREAM shares many mechanistic characteristics with the retinoblastoma pRB tumor suppressor that acts through E2F elements. However, because of its binding to E2F and CHR elements, DREAM regulates a larger set of target genes leading to regulatory functions distinct from pRB/E2F. The p53–DREAM pathway controls more than 250 mostly cell cycle-associated genes. The functional spectrum of these pathway targets spans from the G1 phase to the end of mitosis. Consequently, through downregulating the expression of gene products which are essential for progression through the cell cycle, the p53–DREAM pathway participates in the control of all checkpoints from DNA synthesis to cytokinesis including G1/S, G2/M and spindle assembly checkpoints. Therefore, defects in the p53–DREAM pathway contribute to a general loss of checkpoint control. Furthermore, deregulation of DREAM target genes promotes chromosomal instability and aneuploidy of cancer cells. Also, DREAM regulation is abrogated by the human papilloma virus HPV E7 protein linking the p53–DREAM pathway to carcinogenesis by HPV.Another feature of the pathway is that it downregulates many genes involved in DNA repair and telomere maintenance as well as Fanconi anemia.
    [Show full text]
  • Tau Modulates Mrna Transcription, Alternative Polyadenylation Profiles of Hnrnps, Chromatin Remodeling and Spliceosome Complexes
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.16.452616; this version posted July 16, 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. 1 Tau modulates mRNA transcription, alternative 2 polyadenylation profiles of hnRNPs, chromatin remodeling 3 and spliceosome complexes 4 5 Montalbano Mauro1,2, Elizabeth Jaworski3, Stephanie Garcia1,2, Anna Ellsworth1,2, 6 Salome McAllen1,2, Andrew Routh3,4 and Rakez Kayed1,2†. 7 8 1 Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, 9 77555, USA 10 2 Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, 11 Galveston, Texas, 77555, USA 12 3 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 13 77555, USA 14 4Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, 15 Galveston, TX, USA 16 † To whom correspondence should be addressed 17 18 Corresponding Author 19 Rakez Kayed, PhD 20 University of Texas Medical Branch 21 Medical Research Building Room 10.138C 22 301 University Blvd 23 Galveston, TX 77555-1045 24 Phone: 409.772.0138 25 Fax: 409.747.0015 26 e-mail: [email protected] 27 28 Running Title: Tau modulates transcription and alternative polyadenilation processes 29 30 Keywords: Tau, Transcriptomic, Alternative Polyadenilation,
    [Show full text]
  • Autocrine IFN Signaling Inducing Profibrotic Fibroblast Responses By
    Downloaded from http://www.jimmunol.org/ by guest on September 23, 2021 Inducing is online at: average * The Journal of Immunology , 11 of which you can access for free at: 2013; 191:2956-2966; Prepublished online 16 from submission to initial decision 4 weeks from acceptance to publication August 2013; doi: 10.4049/jimmunol.1300376 http://www.jimmunol.org/content/191/6/2956 A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Autocrine IFN Signaling Feng Fang, Kohtaro Ooka, Xiaoyong Sun, Ruchi Shah, Swati Bhattacharyya, Jun Wei and John Varga J Immunol cites 49 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130037 6.DC1 This article http://www.jimmunol.org/content/191/6/2956.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 23, 2021. The Journal of Immunology A Synthetic TLR3 Ligand Mitigates Profibrotic Fibroblast Responses by Inducing Autocrine IFN Signaling Feng Fang,* Kohtaro Ooka,* Xiaoyong Sun,† Ruchi Shah,* Swati Bhattacharyya,* Jun Wei,* and John Varga* Activation of TLR3 by exogenous microbial ligands or endogenous injury-associated ligands leads to production of type I IFN.
    [Show full text]