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  • Review Article
  • Published:

Regulation of human papillomavirus gene expression by splicing and polyadenylation

Nature Reviews Microbiology volume 11, pages 239–251 (2013)Cite this article

Subjects

Key Points

  • Human papillomaviruses (HPVs) are small DNA tumour viruses that are present in more than 99% of all cervical cancers.

  • The majority of studies discussed in this Review were carried out on HPV type 16 (HPV-16), which is the most common HPV type in the human population, as well as the HPV type most commonly associated with cancer.

  • The HPV life cycle is strictly dependent on the differentiation stage of the infected keratinocyte and can be divided into an early and a late stage.

  • The switch from early to late gene expression is regulated at the level of transcription, splicing and polyadenylation.

  • HPVs make extensive use of alternative RNA splicing and alternative polyadenylation to regulate expression of their genes and to prevent premature expression of the late proteins, which are highly immunogenic.

  • Alternative splicing and polyadenylation of HPV mRNAs is tightly regulated by positive and negative cis-acting RNA elements that interact with cellular serine–arginine-rich (SR) proteins and/or heterogeneous nuclear ribonucleoproteins (hnRNPs).

  • The most common strategy for evaluating HPV-16 gene regulation is to use subgenomic expression plasmids, but future studies will need to confirm the relevance of these observations in the context of the full HPV-16 genome.

Abstract

Human papillomaviruses (HPVs) are small DNA tumour viruses that are present in more than 99% of all cervical cancers. The ability of these viruses to cause disease is partly attributed to the strict coordination of viral gene expression with the differentiation stage of the infected cell. HPV gene expression is regulated temporally at the level of RNA splicing and polyadenylation, and a dysregulated gene expression programme allows some HPV types to establish long-term persistence, which is a risk factor for cancer. In this Review, we summarize the role of splicing and polyadenylation in the regulation of HPV gene expression and discuss the viral and cellular factors that control these processes.

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Figure 1: The human papillomavirus type 16 life cycle.
Figure 2: The human papillomavirus type 16 genome and representative mRNAs.
Figure 3: Regulation of human papillomavirus type 16 early splice sites and the early polyadenylation signal.
Figure 4: Human papillomavirus type 16 E2 protein inhibits the early polyadenylation signal to induce late gene expression.
Figure 5: Regulation of human papillomavirus type 16 late splice sites to control production of late mRNAs.
Figure 6: The papillomavirus late 3′ UTR contains regulatory RNA elements.

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References

  1. zur Hausen, H. Papillomaviruses and cancer: from basic studies to clinical application. Nature Rev. Cancer 2, 342–350 (2002).

    Article  CAS  Google Scholar 

  2. Bernard, H. U. et al. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 401, 70–79 (2010).

    Article  CAS  PubMed  Google Scholar 

  3. Bouvard, V. et al. A review of human carcinogens—part B: biological agents. Lancet Oncol. 10, 321–322 (2009).

    Article  PubMed  Google Scholar 

  4. Bosch, F. X., Lorincz, A., Munoz, N. & Meijer, C. J. The causal relation between human papillomavirus and cervical cancer. J. Clin. Pathol. 55, 244–265 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Walboomers, J. M. et al. Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J. Pathol. 189, 12–19 (1999).

    Article  CAS  PubMed  Google Scholar 

  6. Parkin, D. M., Bray, F. I. & Devesa, S. S. Cancer burden in the year 2000. The global picture. Eur. J. Cancer 37 (Suppl. 8), 24–66 (2001).

    Google Scholar 

  7. Chow, L. T., Broker, T. R. & Steinberg, B. M. The natural history of human papillomavirus infections of the mucosal epithelia. APMIS 118, 422–449 (2010).

    Article  CAS  PubMed  Google Scholar 

  8. Stanley, M. A. Epithelial cell responses to infection with human papillomaviruses. Clin. Microbiol. Rev. 25, 215–222 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Doorbar, J. The papillomavirus life cycle. J. Clin. Virol. 32 (Suppl. 1), S7–S15 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. Moody, C. A. & Laimins, L. A. Human papillomavirus oncoproteins: pathways to transformation. Nature Rev. Cancer 10, 550–560 (2010).

    Article  CAS  Google Scholar 

  11. Bodily, J. & Laimins, L. A. Persistence of human papillomavirus infection: keys to malignant progression. Trends Microbiol. 19, 33–29 (2011).

    Article  CAS  PubMed  Google Scholar 

  12. Stenlund, A. Initiation of DNA replication: lessons from viral initiator proteins-. Nature Rev. Mol. Cell Biol. 4, 777–785 (2003).

    Article  CAS  Google Scholar 

  13. Münger, K. & Howley, P. Human papillomavirus immortalization and transformation functions. Virus Res. 89, 213–228 (2002).

    Article  PubMed  Google Scholar 

  14. Pim, D., Massimi, P. & Banks, L. Alternatively spliced HPV-18 E6* protein inhibits E6 mediated degradation of p53 and suppresses transformed cell growth. Oncogene 15, 257–264 (1997).

    Article  CAS  PubMed  Google Scholar 

  15. Venuti, A. et al. Papillomavirus E5: the smallest oncoprotein with many functions. Mol. Cancer 10, 140 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. DiMaio, D. & Liao, J. B. Human papillomavirus and cervical cancer. Adv. Virus Res. 66, 125–159 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Bernard, H. U. Gene expression of genital human papillomaviruses and considerations on potential antiviral approaches. Antivir. Ther. 7, 219–237 (2002).

    CAS  PubMed  Google Scholar 

  18. Thierry, F. Transcriptional regulation of the papillomavirus oncogenes by cellular and viral transcription factors in cervical carcinoma. Virology 384, 375–379 (2009).

    Article  CAS  PubMed  Google Scholar 

  19. McBride, A. A. Replication and partitioning of papillomavirus genomes. Adv. Virus Res. 72, 155–205 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Doorbar, J., Ely, S., Sterling, J., McLean, C. & Crawford, L. Specific interaction between HPV-16 E1–E4 and cytokeratins results in collapse of the epithelial cell intermediate filament network. Nature 352, 824–827 (1991).

    Article  CAS  PubMed  Google Scholar 

  21. Moscicki, A. B. et al. Updating the natural history of human papillomavirus and anogenital cancers. Vaccine 30 (Suppl. 5), F24–F33 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Schwartz, S. HPV-16 RNA processing. Front. Biosci. 13, 5880–5891 (2008).

    Article  CAS  PubMed  Google Scholar 

  23. Zheng, Z. M. & Baker, C. C. Papillomavirus genome structure, expression, and posttranscriptional regulation. Front. Biosci. 11, 2286–2302 (2006). A comprehensive review of papillomavirus RNA processing, in particular for BPV-1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Graham, S. V. Papillomavirus 3′ UTR regulatory elements. Front. Biosci. 13, 5646–5663 (2008).

    Article  CAS  PubMed  Google Scholar 

  25. Kozak, M. Regulation of translation inititation in eucaryotic systems. Annu. Rev. Cell Biol. 8, 197–225 (1992).

    Article  CAS  PubMed  Google Scholar 

  26. Orru, B., Cunniffe, C., Ryan, F. & Schwartz, S. Development and validation of a novel reporter assay for human papillomavirus type 16 late gene expression. J. Virol. Meth. 183, 106–116 (2012).

    Article  CAS  Google Scholar 

  27. Zhao, X., Rush, M. & Schwartz, S. Identification of an hnRNP A1 dependent splicing silencer in the HPV-16 L1 coding region that prevents premature expression of the late L1 gene. J. Virol. 78, 10888–10905 (2004). A study that identifies an hnRNP A1-depdendent splicing silencer which suppresses splicing of HPV-16 late mRNAs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lambert, P. F. et al. Using an imortalised cell line to study the HPV life cycle in organotypic “raft” cultures. Methods Mol. Med. 119, 141–155 (2005).

    CAS  PubMed  Google Scholar 

  29. Meyers, C. & Laimins, L. A. In vitro systems for the study and propagation of human papillomaviruses. Curr. Top. Microbiol. Immunol. 186, 199–215 (1994).

    CAS  PubMed  Google Scholar 

  30. Wang, H. K., Duffy, A. A., Broker, T. R. & Chow, L. T. Robust production and passaging of infectious HPV in squamous epithelium of primary human keratinocytes. Genes Dev. 23, 181–194 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Surviladze, Z., Dziduszko, A. & Ozbun, M. A. Essential roles for soluble virion-associated heparan sulfonated proteoglycans and growth factors in human papillomavirus infections. PLoS Pathog. 8, e1002519 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Schiller, J. T., Day, P. M. & Kines, R. C. Current understanding of the mechanism of HPV infection. Gynecol. Oncol. 118 (Suppl.1), S12–S17 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Baker, C. & Calef, C. in Human Papillomaviruses 1997: A Compilation and Analysis of Nucleic Acid and Amino Acid Sequences (eds Billakanti, S. R., Calef, C. E., Farmer, A. D., Halpern, A. L. & Myers, G. L.) 3–10 (Theoretical Biology and Biophysics, 1997).

    Google Scholar 

  34. Doorbar, J. et al. Detection of novel splicing patterns in a HPV16-containing keratinocyte cell line. Virology 178, 254–262 (1990).

    Article  CAS  PubMed  Google Scholar 

  35. Grassmann, K., Rapp, B., Maschek, H., Petry, K. U. & Iftner, T. Identification of a differentiation-inducible promoter in the E7 open reading frame of human papillomavirus type 16 (HPV-16) in raft cultures of a new cell line containing high copy numbers of episomal HPV-16 DNA. J. Virol. 70, 2339–2349 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Milligan, S. G., Veerapraditsin, T., Ahamet, B., Mole, S. & Graham, S. V. Analysis of novel human papillomavirus type 16 late mRNAs in differentiated W12 cervical epithelial cells. Virology 360, 172–181 (2007).

    Article  CAS  PubMed  Google Scholar 

  37. Zheng, Z. M., Tao, M., Yamanegi, K., Bodaghi, S. & Xiao, W. Splicing of a cap-proximal human papillomavirus 16 E6E7 intron promotes E7 expression, but can be restrained by distance of the intron from its RNA 5′ cap. J. Mol. Biol. 337, 1091–1108 (2004).

    Article  CAS  PubMed  Google Scholar 

  38. Tang, S., Tao, M., McCoy, J. P. & Zheng, Z.-M. The E7 oncoprotein is translated from spliced E6*I transcripts in high-risk human papillomavirus type 16- or 18-positive cervical cancer cell lines via translation reinitiation. J. Virol. 80, 4249–4263 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Belaguli, N. S., Pater, M. M. & Pater, A. Splice sites of human papillomavirus type 16 E6 gene or heterologous gene required for transformation by E7 and accumulation of E7 RNA. J. Med. Virol. 47, 445–453 (1995).

    Article  CAS  PubMed  Google Scholar 

  40. Cheng, S., Schmidt-Grimminger, D.-C., Murant, T., Broker, T. R. & Chow, L. T. Differentiation-dependent up-regulation of the human papillomavirus E7 gene reactivates cellular DNA replication in suprabasal differentiated keratinocytes. Genes Dev. 9, 2335–2349 (1995).

    Article  CAS  PubMed  Google Scholar 

  41. Remm, M., Remm, A. & Ustav, M. Human papillomavirus type 18 E1 protein is translated from polycistronic mRNA by a discontinuous scanning mechanism. J. Virol. 73, 3062–3070 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Stacey, S. N. et al. Translation of the human papillomavirus type 16 E7 oncoprotein from bicistronic mRNA is independent of splicing events within the E6 open reading frame. J. Virol. 69, 7023–7031 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Filippova, M. et al. The large and small isoforms of human papillomavirus type 16 E6 bind to and differentially affect procaspase 8 stability and activity. J. Virol. 81, 4116–4129 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Rosenberger, S., De-Castro Arce, J., Langbein, L., Steenbergen, R. D. M. & Rösl, F. Alternative splicing of human papillomavirus type-16 E6/E6* early mRNA is coupled to EGF signaling via Erk1/2 activation. Proc. Natl Acad. Sci. USA 107, 7006–7011 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Han, S. P., Tang, Y. H. & Smith, R. Functional diversity of the hnRNPs: past, present and perspectives. Biochem. J. 430, 379–392 (2010).

    Article  CAS  PubMed  Google Scholar 

  46. Bodaghi, S., Jia, R. & Zheng, Z. M. Human papillomavirus type 16 E2 and E6 are RNA-binding proteins and inhibit in vitro splicing of pre-mRNAs with suboptimal splice sites. Virology 386, 32–43 (2009).

    Article  CAS  PubMed  Google Scholar 

  47. Ajiro, M., Jia, R., Zhang, L., Liu, X. & Zheng, Z. M. Intron definition and a branch site adenosine at nt 385 control RNA splicing of HPV16 E6*I and E7 expression. PLoS ONE 7, e46412 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Lopez-Urrutia, E. et al. A few nucleotide polymorphisms are sufficient to recruit nuclear factors differentially to the intron 1 of HPV-16 intratypic variants. Virus Res. 166, 43–53 (2012).

    Article  CAS  PubMed  Google Scholar 

  49. Schmitt, M. et al. Diagnosing cervical cancer and high-grade precursors by HPV-16 transcription patterns. Cancer Res. 70, 249–256 (2010).

    Article  CAS  PubMed  Google Scholar 

  50. Rush, M., Zhao, X. & Schwartz, S. A splicing enhancer in the E4 coding region of human papillomavirus type 16 is required for early mRNA splicing and polyadenylation as well as inhibition of premature late gene expression. J. Virol. 79, 12002–12015 (2005). This article identifies an essential splicing enhancer for the most commonly used HPV-16 3′ splice site, SA3358.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Somberg, M. & Schwartz, S. Multiple ASF/SF2 sites in the HPV-16 E4-coding region promote splicing to the most commonly used 3′-splice site on the HPV-16 genome. J. Virol. 84, 8219–8230 (2010). This investigation establishes that SRSF1-binding sites are required for splicing to the most commonly used HPV-16 3′ splice site, SA3358.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Tranell, A., Fenyö, E. M. & Schwartz, S. Serine- and arginine-rich proteins 55 and 75 (SRp55 and SRp75) induce production of HIV-1 vpr mRNA by inhibiting the 5′-splice site of exon 3. J. Biol. Chem. 285, 31537–31547 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Ozbun, M. A. Human papillomavirus type 31b infection of human keratinocytes and the onset of early transcription. J. Virol. 76, 11291–11300 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Klumpp, D., Stubenrauch, F. & Laimins, L. A. Differential effects of the splice acceptor at nucleotide 3295 of human papillomavirus 31 on stable and transient viral replication. J. Virol. 71, 8186–8194 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Cartegni, L., Wang, J., Zhu, Z., Zhang, M. Q. & Krainer, A. R. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res. 31, 3568–3571 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Jia, R. et al. Control of the papillomavirus early-to-late switch by differentially expressed SRp20. J. Virol. 83, 167–180 (2009). A study linking the expression levels of cellular SRSF3 to the early–late switch in BPV-1 gene expression.

    Article  CAS  PubMed  Google Scholar 

  57. Somberg, M. et al. SRp30c activates human papillomavirus type 16 L1 mRNA expression via a bimodal mechanism. J. Gen. Virol. 92, 2411–2421 (2011).

    Article  CAS  PubMed  Google Scholar 

  58. Karni, R. et al. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nature Struct. Mol. Biol. 14, 185–193 (2007).

    Article  CAS  Google Scholar 

  59. Fay, J., Kelehan, P., Lambkin, H. & Schwartz, S. Increased expression of cellular RNA-binding proteins in HPV-induced neoplasia and cervical cancer. J. Med. Virol. 81, 897–907 (2009).

    Article  CAS  PubMed  Google Scholar 

  60. Mole, S. et al. RNA splicing factors regulated by HPV16 during cervical tumour progression. J. Pathol. 219, 383–391 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Mole, S., Milligan, S. G. & Graham, S. V. Human papillomavirus type 16 E2 protein transcriptionally activates the promoter of a key cellular splicing factor, SF2/ASF. J. Virol. 83, 357–367 (2009). This work demonstrates that HPV-16 E2 enhances the expression of the cellular splicing factor SRSF1, which in turn might affect HPV-16 mRNA splicing.

    Article  CAS  PubMed  Google Scholar 

  62. Xue, Y. et al. HPV16 E2 is an immediate early marker of viral infection, preceding E7 expression in precursor structures of cervical carcinoma. Cancer Res. 70, 5316–5325 (2010).

    Article  CAS  PubMed  Google Scholar 

  63. Spink, K. M. & Laimins, L. A. Induction of the human papillomavirus type 31 late promoter requires differentiation but not DNA amplification. J. Virol. 79, 4918–4926 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Deng, W. et al. mRNA splicing regulates human papillomavirus type 11 E1 protein production and DNA replication. J. Virol. 77, 10213–10226 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Mannik, A., Runkorg, K., Jaanson, N., Ustav, M. & Ustav, E. Induction of the bovine papillomavirus origin “onion skin”-type DNA replication at high E1 protein concentrations in vivo. J. Virol. 76, 5835–5845 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Hubert, W. G. & Laimins, L. A. Human papillomavirus type 31 replication modes during the early phases of the viral life cycle depend on transcriptional and posttranscriptional regulation of E1 and E2 expression. J. Virol. 76, 2263–2273 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Fertey, J. et al. Interaction of the papillomavirus E8^E2C protein with the cellular CHD6 protein contributes to transcriptional repression. J. Virol. 84, 9505–9515 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Lace, M. J., Anson, J. R., Thomas, G. S., Turek, L. P. & Haugen, T. H. The E8^E2 gene product of human papillomavirus type 16 represses early transcription and replication but is dispensable for viral plasmid persistence in keratinocytes. J. Virol. 82, 10841–10853 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Zhao, X. et al. A 57 nucleotide upstream early polyadenylation element in human papillomavirus type 16 interacts with hFip1, CstF-64, hnRNP C1/C2 and PTB. J. Virol. 79, 4270–4288 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Andrew, E. M. & DiMaio, D. Hierarchy of polyadenylation site usage by bovine papillomavirus in transformed cells. J. Virol. 67, 7705–7710 (1993).

    Google Scholar 

  71. Terhune, S. S., Hubert, W. G., Thomas, J. T. & Laimins, L. A. Early polyadenylation signals of human papillomavirus type 31 negatively regulate capsid gene expression. J. Virol. 75, 8147–8157 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Terhune, S. S., Milcarek, C. & Laimins, L. A. Regulation of human papillomavirus 31 polyadenylation during the differentiation-dependent life cycle. J. Virol. 73, 7185–7192 (1999). A report describing RNA elements that are found in the HPV-31 L2 coding region and bind CSTF64 to stimulate polyadenylation at the upstream pAE signal.

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Kaufmann, I., Martin, G., Friedlein, A., Langen, H. & Keller, W. Human Fip1 is a subunit of CPSF that binds to U-rich elements and stimulates poly(A) polymerase. EMBO J. 23, 616–626 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Lace, M. J. et al. Human papillomavirus (HPV) type 18 induces extended growth in primary human cervical, tonsillar, or foreskin keratinocytes more effectively than other high-risk mucosal HPVs. J. Virol. 83, 11784–11794 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Jeon, S., Allen-Hoffmann, B. L. & Lambert, P. F. Integration of human papillomavirus type 16 into the human genome correlates with a selective growth advantage of cells. J. Virol. 69, 2989–2997 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Jeon, S. & Lambert, P. F. Integration of human papillomavirus type 16 DNA into the human genome leads to increased stability of E6 and E7 mRNAs: implications for cervical carcinogenesis. Proc. Natl Acad. Sci. USA 92, 1654–1658 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Häfner, N. et al. Integration of the HPV-16 genome does not invariably result in high levels of viral oncogene transcripts. Oncogene 27, 1610–1617 (2008).

    Article  PubMed  CAS  Google Scholar 

  78. Tan, W. & Schwartz, S. The Rev protein of human immunodeficiency virus type 1 counteracts the effect of an AU-rich negative element in the human papillomavirus type 1 late 3′ untranslated region. J. Virol. 69, 2932–2945 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Lace, M. J. et al. Upstream regulatory region alterations found in human papillomavirus type 16 (HPV-16) isolates from cervical carcinomas increase transcription, ori function, and HPV immortalization capacity in culture. J. Virol. 83, 7457–7466 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Oberg, D., Fay, J., Lambkin, H. & Schwartz, S. A downstream polyadenylation element in human papillomavirus type 16 encodes multiple GGG-motifs and interacts with hnRNPH. J. Virol. 79, 9254–9269 (2005). This work identifies RNA elements that are present in the HPV-16 L2 coding region and bind hnRNP H and CSTF64 to enhance polyadenylation at pAE.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  81. Baker, C. C. & Noe, J. S. Transcriptional termination between bovine papillomavirus type 1 (BPV-1) early and late polyadenylation sites blocks late transcription in BPV-1-transformed cells. J. Virol. 63, 3529–3534 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. Kanopka, A., Mühlemann, O. & Akusjärvi, G. Inhibition by SR proteins of splicing of a regulated adenovirus pre-mRNA. Nature 381, 535–538 (1996).

    Article  CAS  PubMed  Google Scholar 

  83. Somberg, M. et al. Adenovirus E4orf4 induces HPV-16 late L1 mRNA production. Virology 383, 279–290 (2009).

    Article  CAS  PubMed  Google Scholar 

  84. Johansson, C. et al. HPV-16 E2 contributes to induction of HPV-16 late gene expression by inhibiting early polyadenylation. EMBO J. 13, 3212–3227 (2012). A demonstration that the HPV-16 E2 protein can activate HPV-16 late gene expression by inhibiting the viral pAE signal.

    Article  CAS  Google Scholar 

  85. Nemeroff, M. E., Barabino, S. M., Li, Y., Keller, W. & Krug, R. M. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3′ end formation of cellular pre-mRNAs. Mol. Cell 1, 991–1000 (1998).

    Article  CAS  PubMed  Google Scholar 

  86. Backström Winquist, E. et al. Inefficient splicing of segment 7 and 8 mRNAs is an inherent property of influenza virus A/Brevig Mission/1918/1 (H1N1) that causes elevated expression of NS1 protein. Virology 422, 46–58 (2011).

    Article  PubMed  CAS  Google Scholar 

  87. Somberg, M., Zhao, X., Fröhlich, M., Evander, M. & Schwartz, S. PTB induces HPV-16 late gene expression by interfering with splicing inhibitory elements at the major late 5′-splice site SD3632. J. Virol. 82, 3665–3678 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Ozbun, M. A. & Meyers, C. Characterization of late gene transcripts expressed during vegetative replication of human papillomavirus type 31b. J. Virol. 71, 5161–5172 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Tomita, Y. & Simizu, B. Translational properties of the human papillomavirus type-6 L1-coding mRNA. Gene 133, 223–225 (1993).

    Article  CAS  PubMed  Google Scholar 

  90. Kanopka, A. et al. Regulation of adenovirus alternative RNA splicing by dephosphorylation of SR proteins. Nature 393, 185–187 (1998).

    Article  CAS  PubMed  Google Scholar 

  91. Zhao, X., Fay, J., Lambkin, H. & Schwartz, S. Identification of a 17-nucleotide splicing enhancer in HPV-16 L1 that counteracts the effect of multiple hnRNP A1-binding splicing silencers. Virology 369, 351–363 (2007).

    Article  CAS  PubMed  Google Scholar 

  92. Jacquenet, S. et al. A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H. J. Biol. Chem. 276, 40464–40475 (2001).

    Article  CAS  PubMed  Google Scholar 

  93. Zhao, X. & Schwartz, S. Inhibition of HPV-16 L1 expression from L1 cDNAs correlates with the presence of hnRNP A1 binding sites in the L1 coding region. Virus Genes 36, 45–53 (2008).

    Article  PubMed  CAS  Google Scholar 

  94. Zhao, X., Rush, M., Carlsson, A. & Schwartz, S. The presence of inhibitory RNA elements in the late 3′-untranslated region is a conserved property of human papillomaviruses. Virus Res. 125, 135–144 (2007).

    Article  CAS  PubMed  Google Scholar 

  95. Furth, P. A. & Baker, C. C. An element in the bovine papillomavirus late 3′ untranslated region reduces polyadenylated cytoplasmic RNA levels. J. Virol. 65, 5806–5812 (1991). The first report of inhibitory RNA elements in the BPV-1 lUTR.

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Kennedy, I. M., Haddow, J. K. & Clements, J. B. Analysis of human papillomavirus type 16 late mRNA 3′ processing signals in vitro and in vivo. J. Virol. 64, 1825–1829 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Kennedy, I. M., Haddow, J. K. & Clements, J. B. A negative regulatory element in the human papillomavirus type 16 genome acts at the level of late mRNA stability. J. Virol. 65, 2093–2097 (1991). The initial report describing inhibitory RNA elements in the HPV-16 lUTR.

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Cumming, S. A. et al. The human papillomavirus type 31 untranslated region contains a complex bipartite negative regulatory element. J. Virol. 76, 5993–6003 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Sokolowski, M., Zhao, C., Tan, W. & Schwartz, S. AU-rich mRNA instability elements on human papillomavirus type 1 late mRNAs and c-fos mRNAs interact with the same cellular factors. Oncogene 15, 2303–2319 (1997).

    Article  CAS  PubMed  Google Scholar 

  100. Wiklund, L., Sokolowski, M., Carlsson, A., Rush, M. & Schwartz, S. Inhibition of translation by UAUUUAU and UAUUUUUAU motifs of the AU-rich RNA instability in the HPV-1 late 3′ untranslated region. J. Biol. Chem. 277, 40462–40471 (2002). A paper establishing that the HPV-1 lUTR inhibits mRNA translation.

    Article  CAS  PubMed  Google Scholar 

  101. Sokolowski, M., Furneaux, H. & Schwartz, S. The inhibitory activity of the AU-rich RNA element in the human papillomavirus type 1 late 3′ untranslated region correlates with its affinity for the elav-like HuR protein. J. Virol. 73, 1080–1091 (1999). This study shows that in vitro binding of cellular HuR to the AU-rich RNA element in the HPV-1 lUTR correlates with its inhibitory activity.

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Sokolowski, M. & Schwartz, S. Heterogeneous nuclear ribonucleoprotein C binds exclusively to the functionally important UUUUU-motifs in the human papillomavirus type-1 AU-rich inhibitory element. Virus Res. 73, 163–175 (2001).

    Article  CAS  PubMed  Google Scholar 

  103. Cumming, S. A., Chuen-Im, T., Zhang, J. & Graham, S. V. The RNA stability regulator HuR regulates L1 protein expression in vivo in differentiating cervical epithelial cells. Virology 383, 142–149 (2009).

    Article  CAS  PubMed  Google Scholar 

  104. Fan, X. C. & Steitz, J. A. Overexpression of HuR, a nuclear–cytoplasmic shuttling protein, increases the in vivo stability of ARE-containing mRNAs. EMBO J. 17, 3448–3460 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Carlsson, A. & Schwartz, S. Inhibitory activity of the human papillomavirus type 1 AU-rich element correlates inversely with the levels of the elav-like HuR protein in the cell cytoplasm. Arch. Virol. 145, 491–503 (2000).

    Article  CAS  PubMed  Google Scholar 

  106. Barksdale, S. K. & Baker, C. C. The human immunodeficiency virus type 1 Rev protein and the Rev-responsive element counteract the effect of an inhibitory 5′ splice site in a 3′ untranslated region. Mol. Cell. Biol. 15, 2962–2971 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Tan, W., Felber, B. K., Zolotukhin, A. S., Pavlakis, G. N. & Schwartz, S. Efficient expression of the human papillomavirus type 16 L1 protein in epithelial cells by using Rev and the Rev-responsive element of human immunodeficiency virus or the cis-acting transactivation element of simian retrovirus type 1. J. Virol. 69, 5607–5620 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  108. McPhillips, M. G. et al. SF2/ASF binds the human papillomavirus type 16 late RNA control element and is regulated during differentiation of virus-infected epithelial cells. J. Virol. 78, 10598–10605 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Cheunim, T., Zhang, J., Milligan, S. G., McPhillips, M. G. & Graham, S. V. The alternative splicing factor hnRNP A1 is up-regulated during virus-infected epithelial cell differentiation and binds the human papillomavirus type 16 late regulatory element. Virus Res. 131, 189–198 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Furth, P. A., Choe, W. T., Rex, J. H., Byrne, J. C. & Baker, C. C. Sequences homologous to 5′ splice sites are required for the inhibitory activity of papillomavirus late 3′ untranslated regions. Mol. Cell. Biol. 14, 5278–5289 (1994). The first demonstration that binding of U1snRNP to the BPV-1 and HPV-16 lUTRs inhibits late gene expression by inhibiting the pAL signal.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Gunderson, S. I., Polycarpou-Schwarz, M. & Mattaj, I. W. U1 snRNP inhibits pre-mRNA polyadenylation through a direct interaction between U1 70K and poly(A) polymerase. Mol. Cell 1, 255–264 (1998).

    Article  CAS  PubMed  Google Scholar 

  112. Cumming, S. A., McPhillips, M. G., Veerapraditsin, T., Milligan, S. G. & Graham, S. V. Activity of the human papillomavirus type 16 late negative regulatory element is partly due to four weak consensus 5′ splice sites that bind a U1 snRNP-like complex. J. Virol. 77, 5167–5177 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Goraczniak, R. & Gunderson, S. I. The regulatory element in the 3′ untranslated region of human papillomavirus 16 inhibits expression by binding CUG binding protein 1. J. Biol. Chem. 283, 2286–2296 (2008).

    Article  CAS  PubMed  Google Scholar 

  114. Collier, B., Öberg, D., Zhao, X. & Schwartz, S. Specific inactivation 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, 2739–2752 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Leder, C., Kleinschmidt, J. A., Wiethe, C. & Müller, M. Enhancement of capsid gene expression: preparing the human papillomavirus type 16 major structural gene L1 for DNA vaccination purposes. J. Virol. 75, 9201–9209 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Heino, P., Dillner, J. & Schwartz, S. Human papillomavirus type 16 capsid proteins produced from recombinant Semliki Forest virus assemble into virus like particles. Virology 214, 349–359 (1995).

    Article  CAS  PubMed  Google Scholar 

  117. Sokolowski, M., Tan, W., Jellne, M. & Schwartz, S. mRNA instability elements in the human papillomavirus type 16 L2 coding region. J. Virol. 72, 1504–1515 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Mori, S. et al. Inhibitory cis-element-mediated decay of human papillomavirus type 16 L1-transcript in undifferentiated cells. Mol. Cell. Biochem. 288, 47–57 (2006).

    Article  CAS  PubMed  Google Scholar 

  119. Afonina, E., Neumann, M. & Pavlakis, G. N. Preferential binding of poly(A)-binding protein 1 to an inhibitory RNA element in the human immunodeficiency virus type 1 gag mRNA. J. Biol. Chem. 272, 2307–2311 (1997).

    Article  CAS  PubMed  Google Scholar 

  120. Zhou, W. et al. Multiple RNA splicing and the presence of cryptic RNA splice donor and acceptor sites may contribute to low expression levels and poor immunogenicity of potential DNA vaccines containing the env gene of equine infectious anemia virus (EIAV). Vet. Microbiol. 88, 127–151 (2002).

    Article  CAS  PubMed  Google Scholar 

  121. Berg, M., DiFatta, J., Hoiczyk, E., Schlegel, R. & Ketner, G. Viable adenovirus vaccine prototypes: high-level production of a papillomavirus capsid antigen from the major late transcription unit. Proc. Natl Acad. Sci. USA 102, 4590–4595 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Oberg, D., Collier, B., Zhao, X. & Schwartz, S. Mutational inactivation 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, 11674–11684 (2003).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  123. Rollman, E. et al. HPV-16 L1 genes with inactivated negative RNA elements induce potent immune responses. Virology 322, 182–189 (2004).

    Article  CAS  PubMed  Google Scholar 

  124. Kudla, G., Lipinski, L., Caffin, F., Helwak, A. & Zylicz, M. High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol. 4, 933–942 (2006).

    Article  CAS  Google Scholar 

  125. Wang, X. M., Jansen, K. U. & McClements, W. L. DNA replicative functions of highly-expressed, codon-optimized human papillomavirus proteins E1 and E2. J. Virol. Methods 108, 83–90 (2003).

    Article  CAS  PubMed  Google Scholar 

  126. Disbrow, G. L., Sunitha, I., Baker, C. C., Hanover, J. & Schlegel, R. Codon optimization of the HPV-16 E5 gene enhances protein expression. Virology 311, 105–114 (2003).

    Article  CAS  PubMed  Google Scholar 

  127. Lin, C.-T. et al. A DNA vaccine encoding a codon-optimised human papillomavirus type 16 E6 gene enhances CTL response and anti-tumor activity. J. Biomed. Sci. 13, 481–488 (2006).

    Article  CAS  PubMed  Google Scholar 

  128. Liu, W. J. et al. Codon modified human papillomavirus type 16 E7 DNA vaccine enhances cytotoxic T-lymphocyte induction and anti-tumour activity. Virology 301, 43–52 (2002).

    Article  CAS  PubMed  Google Scholar 

  129. Gu, W. et al. tRNASer(CGA) differentially regulates expression of wild-type and codon-modified papillomavirus L1 genes. Nucleic Acids Res. 32, 4448–4461 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Zhao, K. N., Gu, W., Fang, N. X., Saunders, N. A. & Frazer, I. H. Gene codon composition determines differentiation-dependent expression of a viral capsid gene in keratinocytes in vitro and in vivo. Mol. Cell. Biol. 19, 8643–8655 (2005).

    Article  CAS  Google Scholar 

  131. Collier, B., Goobar-Larsson, L., Sokolowski, M. & Schwartz, S. Translational inhibition in vitro of human papillomavirus type 16 L2 mRNA mediated through interaction with heterogenous ribonucleoprotein K and poly(rC)-binding proteins 1 and 2. J. Biol. Chem. 273, 22648–22656 (1998).

    Article  CAS  PubMed  Google Scholar 

  132. Cartegni, L., Chew, S. L. & Krainer, A. R. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nature Rev. Genet. 3, 285–298 (2002).

    Article  CAS  PubMed  Google Scholar 

  133. Chen, M. & Manley, J. L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nature Rev. Mol. Cell Biol. 11, 741–754 (2009).

    Article  CAS  Google Scholar 

  134. Long, J. C. & Caceres, J. F. The SR protein family of splicing factors: master regulators of gene expression. Biochem. J. 417, 15–27 (2009).

    Article  CAS  PubMed  Google Scholar 

  135. Manley, J. L. & Krainer, A. R. A rationale nomenclature for serine/argininge-rich protein splicing factors (SR proteins). Genes Dev. 24, 1073–1074 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. MacDonald, C. C. & McMahon, K. W. Tissue-specific mechanisms of alternative polyadenylation: testis, brain, and beyond. Wiley Interdiscip. Rev. RNA 3, 494–501 (2010).

    Article  CAS  Google Scholar 

  137. Singh, R. K. & Cooper, T. A. Pre-mRNA splicing in disease and therapeutics. Trends Mol. Med. 18, 472–482 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Keren, H., Lev-Maor, G. & Ast, G. Alternative splicing and evolution: diversification, exon definition and function. Nature Rev. Genet. 11, 345–355 (2010).

    Article  CAS  PubMed  Google Scholar 

  139. Stolzfus, C. M. & Madsen, J. M. Role of viral splicing elements and cellular RNA binding proteins in regulation of HIV-1 alternative RNA splicing. Curr. HIV Res. 1, 43–55 (2006).

    Article  Google Scholar 

  140. Zheng, Z. M. Regulation of alternative RNA splicing by exon definition and exon sequences in viral and mammalian gene expression. J. Biomed. Sci. 11, 278–294 (2004).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Research in the Schwartz laboratory is sponsored by the Swedish Research Council–Scientific Council for Medicine and Health and by the Swedish cancer society, Cancerfonden.

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  1. Department of Laboratory Medicine, Section of Medical Microbiology, Lund University, BMC-B13, room B1314c, Lund, 221 84, Sweden

    Cecilia Johansson & Stefan Schwartz

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  1. Cecilia Johansson
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Glossary

Cutaneous epithelium

The stratified epithelium of the skin.

Mucosal epithelium

The stratified epithelium in mucosa.

Episomal

Pertaining to a DNA molecule: able to exist and replicate autonomously.

Exons

Sequences that form the mRNA molecule when the introns have been removed by pre-mRNA splicing.

Introns

Sequences that are spliced out of the pre-mRNA molecule; following this splicing, the mature mRNA molecule consists of exons only.

Splice sites

RNA sequences that mark the borders between exons and introns; the splicing machinery cleaves the RNA at these sequences to splice exons together.

Organotypic cell culture

A culture technique in which cells are grown in a three-dimensional environment.

Kozak start codon

A translational start codon (AUG) that occurs in a context which is efficiently recognized by ribosomes. This context is characterized by a purine at position −3 in relation to the A residue in AUG, and a G at position +4.

ERK1–ERK2 pathway

(Extracellular signal-regulated kinase 1–extracellular signal-regulated kinase 2 pathway). A signalling pathway that is often dysregulated in human cancers.

Heterogeneous nuclear ribonucleoprotein

An RNA-binding protein that shuttles between the nucleus and cytoplasm and is involved in the regulation of cellular RNA processing. Many of the proteins in this family are very abundant.

Splicing enhancer

A cis-acting RNA sequence that interacts with RNA-binding proteins to promote the use of a particular splice site.

SR protein

(serine–arginine-rich protein). A modular splicing-regulatory protein consisting of one or more amino-terminal RNA-binding domains and a carboxy-terminal arginine- and serine-rich domain.

Polyadenylation complex

A multiprotein complex that forms on the polyadenylation signal, AAUAAA, in the pre-mRNA to execute the cleavage and polyadenylation reaction at the polyadenylation site.

Splicing silencers

Cis-acting RNA sequences that interact with RNA-binding proteins to repress the use of certain splice sites.

Spliceosome

A complex nuclear machinery that executes splicing to remove introns. It contains five U-rich small nuclear RNAs and more than 150 proteins.

FOS 3′ UTR RNA instability element

A short, AU-rich RNA sequence in the 3′ UTR of the FOS mRNA; this sequence promotes mRNA degradation and confers a short half-life to the FOS mRNA.

Heat shock protein 70

A family of heat stress-induced cellular proteins encoded by GC-rich mRNAs.

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Johansson, C., Schwartz, S. Regulation of human papillomavirus gene expression by splicing and polyadenylation. Nat Rev Microbiol 11, 239–251 (2013). https://doi.org/10.1038/nrmicro2984

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