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The Role of Polyadenylation in Human Papillomavirus Type 16 Late Gene Expression

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The Role of Polyadenylation in Human Papillomavirus Type 16 Late Gene Expression Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 4 The Role of Polyadenylation in Human Papillomavirus Type 16 Late Gene Expression DANIEL ÖBERG ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6206 UPPSALA ISBN 91-554-6141-7 2005 urn:nbn:se:uu:diva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“Young fool... Only now, at the end, do you understand...“ The Emperor, Star Wars eposide VI, The return of the Jedi “It is better to burn out than to fade away” The Kurgan, Highlander "What remains?" cried Ivanhoe; "Glory, maiden, glory! which gilds our sep- ulchre and embalms our name." Ivanhoe to Rebecca, who questions the value of chivalry and has asked what remains for knights when death takes them. (Chapter XXIX) "Chivalry!-why, maiden, she is the nurse of pure and high affection-the stay of the oppressed, the redresser of grievances, the curb of the power of the tyrant-Nobility were but an empty name without her, and liberty finds the best protection in her lance and her sword." Ivanhoe explains to Rebecca the virtues of chivalry. (Chapter XXIX) For my mother, to whom I owe everything Members of the committee Opponent Assistant Prof. Sheila Graham Institute of Virology University of Glasgow Members of the committee Chairman, Prof. Göran Akusjärvi IMBIM Uppsala University Prof. Gerhart Wagner ICM Uppsala University Assistant Prof. Öjar Melefors MTC Karolinska Institutet Stockholm List of manuscripts This thesis is based on the following manuscripts, which in the text are re- ferred by their roman numerals Paper I Collier, B., D. Oberg, X. Zhao, and S. Schwartz. 2002. Specific inactiva- tion of inhibitory sequences in the 5' end of the human papillomavirus type 16 L1 open reading frame results in production of high levels of L1 protein in human epithelial cells. J Virol 76:2739-52. Paper II Oberg, D., B. Collier, X. Zhao, and S. Schwartz. 2003. Mutational inacti- vation of two distinct negative RNA elements in the human papillomavirus type 16 L2 coding region induces production of high levels of L2 in human cells. J Virol 77:11674-84. Paper III Oberg, D., J. Fay, H. Lambkin, S. Schwartz. 2005. A downstream poly- adenylation element in human papillomavirus type 16 encodes multiple GGG-motifs and interacts with hnRNP H. J Virol Submitted. Reprints were made with permission from the publishers Related manuscripts Rollman E, Arnheim L, Collier B, Oberg D, Hall H, Klingstrom J, Dill- ner J, Pastrana DV, Buck CB, Hinkula J, Wahren B, Schwartz S. HPV- 16 L1 genes with inactivated negative RNA elements induce potent immune responses. Virology. 2004 Apr 25;322(1):182-9. Zhao X, Oberg D, Rush M, Fay J, Lambkin H, and S. Schwartz. 2005. A 57-nucleotide upstream early polyadenylation element in human papillo- mavirus type 16 interacts with hFip1, CstF-64, hnRNP C1/C2 and PTB. J Virol, In press. Contents 1 Introduction.................................................................................................... 11 1.1 Virology ................................................................................................. 11 1.2 History of papillomaviruses................................................................... 11 1.3 Human papillomaviruses and cancer..................................................... 12 1.4 Human papillomavirus structure ........................................................... 13 1.5 Papillomavirus life cycle ....................................................................... 15 1.6 Human papillomaviruses and gene expression..................................... 16 1.7 Long control-, early- and late region genomic structure and function. 18 1.7.1 LCR ................................................................................................ 18 1.7.2 The early region ............................................................................. 18 1.7.2.1 E2 and E1 ............................................................................... 19 1.7.2.2 E6 and E7 ............................................................................... 20 1.7.2.3 E5 function and immune defence .......................................... 22 1.7.2.4 E4............................................................................................ 22 1.7.3 The late region................................................................................ 23 1.8 Gene expression..................................................................................... 23 1.8.1 Capping .......................................................................................... 24 1.8.2 Polyadenylation.............................................................................. 24 1.8.3 Splicing........................................................................................... 25 1.8.4 The exon definition model............................................................. 28 1.8.5 Linking mRNA processing and transcription ............................... 29 1.8.6 Nuclear export of mRNA............................................................... 29 1.8.7 Translation...................................................................................... 31 1.8.8 Regulation of mRNA polyadenylation.......................................... 33 1.8.9 Papillomavirus and late polyadenylation ...................................... 36 1.8.10 Papillomavirus early polyadenylation......................................... 38 1.8.11 Negative elements........................................................................ 40 2 Introduction to papers.................................................................................... 42 2.1 Paper I (45)............................................................................................. 42 4.2 Paper II (222) ......................................................................................... 44 2.3 Paper III (223)........................................................................................ 45 3. Future perspectives ....................................................................................... 47 4. Populärvetenskaplig sammanfattning (In Swedish) .................................... 49 5 Acknowledgement ......................................................................................... 51 6 References...................................................................................................... 53 Abbreviations 3’ss 3’splice site, splice acceptor 5’ss 5’splice site, splice donor BPV Bovine papillomavirus C/EBP CCAAT/Enhancer binding protein CBC Cap binding complex CDK Cyklin dependent kinase CF Cleavage factor CMV Cytomegalovirus CPSF Cleavage and polyadenylation specific factor CStF Cleavage stimulatory factor CTD C-terminal domain CTE Constitutive transport element CTL Cytotoxic lymphocyte DSE Downstream element E6AP E6-associated protein EGFR Epidermal growth factor receptor ESS Exonic splicing silencer HDAC Histone deacetylase HIV Human immunodeficiency virus HLA Human leukocyte antigen hnRNP heterogeneous ribonucleo protein HPV Human papillomavirus HSV Herpes simplex virus IgM-mem IgM secretory polyadenylation signal IgM-sec IgM membrane polyadenylation signal ISE Intronic splicing enhancer LCR Long control region MAR Matrix attachment region MHC Major histocompability complex NES Nuclear export signal NK Natural killer cell NMD Nonsense mediated decay NPC Nuclear pore complex NRE Negative regulatory element ORF Open reading frame PABP Poly(A) binding protein pAE Early polyadenylation signal pAL Late polyadenylation signal PAP Poly(A)polymerase POD Promyelocytic leukaemia oncogenic domain PPT Polypyrimidine tract pRB Retinoblastoma protein RRE Rev responsive element RT-PCR Real time PCR snRNP small nuclear ribonucleo protein SV40 Simian virus 40 SVLPA Simian virus 40 late polyadenylation signal USE Upstream element 1 Introduction 1.1 Virology The elucidation of viruses as infectious agents started in the late 19th cen- tury. When the microbial organisms bacteria and fungi were filtered away from fluid shown to transmit certain diseases, the filtered fluid was still found potent to cause the infection. The name “virus”, which is the Latin word for “slimy liquid” or “poison”, was assigned to this invisible agent (89). The 1930s revolutionised the field of virology with the invention of the electron microscope. Electron micrographs on tobacco mosaic virus (TMV) visualised a virus particle for the first time. Other important findings were bacteriophages
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