Skip to main content Accessibility help
×
Hostname: page-component-77c89778f8-5wvtr Total loading time: 0 Render date: 2024-07-18T23:36:08.937Z Has data issue: false hasContentIssue false

31 - Identification and potential function of viral microRNAs

from V - MicroRNAs in disease biology

Published online by Cambridge University Press:  22 August 2009

Finn Grey
Affiliation:
Vaccine & Gene Therapy Institute Oregon Health & Sciences University Portland, OR 97201 USA
Alec J. Hirsch
Affiliation:
Vaccine & Gene Therapy Institute Oregon Health & Sciences University Portland, OR 97201 USA
Jay A. Nelson
Affiliation:
Vaccine & Gene Therapy Institute Oregon Health & Sciences University Portland, OR 97201 USA
Get access

Summary

The discovery of RNA interference (RNAi) and microRNAs (miRNAs) is undoubtedly one of the most significant recent advances in the field of biology. miRNAs were initially identified in Caenorhabditis elegans with the discovery of a small RNA, lin-4, that was shown to regulate the heterochronic gene lin-14 (Lee et al., 1993; Wightman et al., 1993). Further investigations led to the identification of a second small RNA, let-7, that played a similar role in regulation of developmental genes (Reinhart et al., 2000). Subsequent studies using extensive cloning strategies and bioinformatics methods have identified hundreds of miRNA genes in plants and animals suggesting that post-transcriptional regulation through expression of small RNAs is an evolutionarily conserved and common mechanism of gene regulation (Bartel, 2004; Pfeffer et al., 2004; Pfeffer et al., 2005). More recent studies have revealed that a surprisingly large percentage of genes in higher organisms may be regulated by miRNAs (Brennecke et al., 2005; Grün et al., 2005; Krek et al., 2005; Lewis et al., 2005; Xie et al., 2005). Given the widespread prevalence and influential effects of miRNAs on gene expression it is unsurprising that viruses exploit RNAi pathways by expressing their own small RNAs. In this chapter we will review what is currently known about virally encoded miRNAs, including examination of their expression, genomic position and degree of evolutionary conservation between related viruses. We will also discuss the potential functions of viral miRNAs.

Type
Chapter
Information
MicroRNAs
From Basic Science to Disease Biology
, pp. 405 - 426
Publisher: Cambridge University Press
Print publication year: 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Andersson, M. G., Haasnoot, P. C., Xu, N.et al. (2005). Suppression of RNA interference by adenovirus virus-associated RNA. Journal of Virology, 79, 9556–9565.Google Scholar
Aparicio, O., Razquin, N., Zaratiegui, M., Narvaiza, I. and Fortes, P. (2006). Adenovirus virus-associated RNA is processed to functional interfering RNAs involved in virus production. Journal of Virology, 80, 1376–1384.Google Scholar
Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116, 281–297.Google Scholar
Bennasser, Y., Le, S. Y., Benkirane, M. and Jeang, K. T. (2005). Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing. Immunity, 22, 607–619.Google Scholar
Bentwich, I., Avniel, A., Karov, Y.et al. (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nature Genetics, 37, 766–770.Google Scholar
Berezikov, E., Guryev, V., Belt, J.et al. (2005). Phylogenetic shadowing and computational identification of human microRNA genes. Cell, 120, 21–24.Google Scholar
Bowden, R. J., Simas, J. P., Davis, A. J. and Efstathiou, S. (1997). Murine gammaherpesvirus 68 encodes tRNA-like sequences which are expressed during latency. Journal of General Virology, 78, 1675–1687.Google Scholar
Branco, F. J. and Fraser, N. W. (2005). Herpes simplex virus type 1 latency-associated transcript expression protects trigeminal ganglion neurons from apoptosis. Journal of Virology, 79, 9019–9025.Google Scholar
Brennecke, J., Stark, A., Russell, R. B. and Cohen, S. M. (2005). Principles of microRNA-target recognition. Public Library of Science Biology, 3, e85.Google Scholar
Cai, X. and Cullen, B. R. (2006). Transcriptional origin of Kaposi's sarcoma-associated herpesvirus microRNAs. Journal of Virology, 80, 2234–2242.Google Scholar
Cai, X., Lu, S., Zhang, Z.et al. (2005). Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proceedings of the National Academy of Sciences USA, 102, 5570–5575.Google Scholar
Courcelle, C. T., Courcelle, J., Prichard, M. N. and Mocarski, E. S. (2001). Requirement for uracil-DNA glycosylase during the transition to late-phase cytomegalovirus DNA replication. Journal of Virology, 75, 7592–7601.Google Scholar
DeMarchi, J. M., Schmidt, C. A. and Kaplan, A. S. (1980). Patterns of transcription of human cytomegalovirus in permissively infected cells. Journal of Virology, 35, 277–286.Google Scholar
Dunn, W., Chou, C., Li, H.et al. (2003). Functional profiling of a human cytomegalovirus genome. Proceedings of the National Academy of Sciences USA, 100, 14 223–14 228.Google Scholar
Dunn, W., Trang, P., Zhong, Q.et al. (2005). Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cellular Microbiology, 7, 1684–1695.Google Scholar
Farh, K. K., Grimson, A., Jan, C.et al. (2005). The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science, 310, 1817–1821.Google Scholar
Furnari, F. B., Adams, M. D. and Pagano, J. S. (1992). Regulation of the Epstein–Barr virus DNA polymerase gene. Journal of Virology, 66, 2837–2845.Google Scholar
Goldmacher, V. S., Bartle, L. M., Skaletskaya, A.et al. (1999). A cytomegalovirus-encoded mitochondria-localized inhibitor of apoptosis structurally unrelated to Bcl-2. Proceedings of the National Academy of Sciences USA, 96, 12 536–12 541.Google Scholar
Grey, F., Antoniewicz, A., Allen, E.et al. (2005). Identification and characterization of human cytomegalovirus-encoded microRNAs. Journal of Virology, 79, 12 095–12 099.Google Scholar
Grun, D., Wang, Y. L., Langenberger, D., Gunsalus, K. C. and Rajewsky, N. (2005). MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. Public Library of Science Computer Biology, 1, e13.Google Scholar
Jopling, C. L., Yi, M., Lancaster, A. M., Lemon, S. M. and Sarnow, P. (2005). Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA. Science, 309, 1577–1581.Google Scholar
Krek, A., Grun, D., Poy, M. N.et al. (2005). Combinatorial microRNA target predictions. Nature Genetics, 37, 495–500.Google Scholar
Lecellier, C. H., Dunoyer, P., Arar, K.et al. (2005). A cellular microRNA mediates antiviral defense in human cells. Science, 308, 557–560.Google Scholar
Lee, R. C., Feinbaum, R. L. and Ambros, V. (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843–854.Google Scholar
Lewis, B. P., Burge, C. B. and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15–20.Google Scholar
Lim, L. P., Lau, N. C., Weinstein, E. G.et al. (2003). The microRNAs of Caenorhabditis elegans. Genes & Development, 17, 991–1008.Google Scholar
Lu, S. and Cullen, B. R. (2004). Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and microRNA biogenesis. Journal of Virology, 78, 12 868–12 876.Google Scholar
McCormick, C. and Ganem, D. (2005). The kaposin B protein of KSHV activates the p38/MK2 pathway and stabilizes cytokine mRNAs. Science, 307, 739–741.Google Scholar
Moore, P. and Chang, Y. (2001). Kaposi's sarcoma-associated Herpesvirus. Fields Virology, 2, 2803–2831.Google Scholar
Omoto, S. and Fujii, Y. R. (2005). Regulation of human immunodeficiency virus 1 transcription by nef microRNA. Journal of General Virology, 86, 751–755.Google Scholar
Omoto, S., Ito, M., Tsutsumi, Y.et al. (2004). HIV-1 nef suppression by virally encoded microRNA. Retrovirology, 1, 44.Google Scholar
Pasquinelli, A. E., Reinhart, B. J., Slack, F.et al. (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature, 408, 86–89.Google Scholar
Patterson, C. E. and Shenk, T. (1999). Human cytomegalovirus UL36 protein is dispensable for viral replication in cultured cells. Journal of Virology, 73, 7126–7131.Google Scholar
Pearce, M., Matsumura, S. and Wilson, A. C. (2005). Transcripts encoding K12, v-FLIP, v-cyclin, and the microRNA cluster of Kaposi's sarcoma-associated herpesvirus originate from a common promoter. Journal of Virology, 79, 14 457–14 464.Google Scholar
Pfeffer, S., Zavolan, M., Grasser, F. A.et al. (2004). Identification of virus-encoded microRNAs. Science, 304, 734–736.Google Scholar
Pfeffer, S., Sewer, A., Lagos-Quintana, M.et al. (2005). Identification of microRNAs of the herpesvirus family. Nature Methods, 2, 269–276.Google Scholar
Prichard, M. N., Duke, G. M. and Mocarski, E. S. (1996). Human cytomegalovirus uracil DNA glycosylase is required for the normal temporal regulation of both DNA synthesis and viral replication. Journal of Virology, 70, 3018–3025.Google Scholar
Reinhart, B. J., Slack, F. J., Basson, M.et al. (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403, 901–906.Google Scholar
Roizman, B. and Pellet, E. (2001). The family Herpesviridae: a brief introduction. Fields Virology, 2, 2381–2397.Google Scholar
Samols, M. A., Hu, J., Skalsky, R. L. and Renne, R. (2005). Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. Journal of Virology, 79, 9301–9305.Google Scholar
Sano, M., Kato, Y. and Taira, K. (2006). Sequence-specific interference by small RNAs derived from adenovirus VAI RNA. Federation of European Biological Sciences Letters, 580, 1553–1564.Google Scholar
Shenk, T. (2001). Adenoviridae: the viruses and their replication. Fields Virology, 2, 2265–2326.Google Scholar
Simas, J. P., Bowden, R. J., Paige, V. and Efstathiou, S. (1998). Four tRNA-like sequences and a serpin homologue encoded by murine gammaherpesvirus 68 are dispensable for lytic replication in vitro and latency in vivo. Journal of General Virology, 79, 149–153.Google Scholar
Skaletskaya, A., Bartle, L. M., Chittenden, T.et al. (2001). A cytomegalovirus-encoded inhibitor of apoptosis that suppresses caspase-8 activation. Proceedings of the National Academy of Sciences USA, 98, 7829–7834.Google Scholar
Smith, P. R., Jesus, O., Turner, D.et al. (2000). Structure and coding content of CST (BART) family RNAs of Epstein–Barr virus. Journal of Virology, 74, 3082–3092.Google Scholar
Stark, A., Brennecke, J., Bushati, N., Russell, R. B. and Cohen, S. M. (2005). Animal microRNAs confer robustness to gene expression and have a significant impact on 3′ UTR evolution. Cell, 123, 1133–1146.Google Scholar
Sullivan, C. S. and Ganem, D. (2005). MicroRNAs and viral infection. Molecular Cell, 20, 3–7.Google Scholar
Sullivan, C. S., Grundhoff, A. T., Tevethia, S., Pipas, J. M. and Ganem, D. (2005). SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature, 435, 682–686.Google Scholar
Thompson, R. L. and Sawtell, N. M. (2001). Herpes simplex virus type 1 latency-associated transcript gene promotes neuronal survival. Journal of Virology, 75, 6660–6675.Google Scholar
Wathen, M. W. and Stinski, M. F. (1982). Temporal patterns of human cytomegalovirus transcription: mapping the viral RNAs synthesized at immediate early, early, and late times after infection. Journal of Virology, 41, 462–477.Google Scholar
Wightman, B., Ha, I. and Ruvkun, G. (1993). Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75, 855–862.Google Scholar
Xie, X., Lu, J., Kulbokas, E. J.et al. (2005). Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature, 434, 338–345.Google Scholar
Yu, D., Silva, M. C. and Shenk, T. (2003). Functional map of human cytomegalovirus AD169 defined by global mutational analysis. Proceedings of the National Academy of Sciences USA, 100, 12 396–12 401.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×