References

Amen, M.A. and A. Griffiths, 2011. Identification and expression analysis of Herpes B virus-encoded small RNAs. J. Virol., 85: 7296-7311.
PubMed  |  

Bakre, A., P. Mitchell, J.K. Coleman, L.P. Jones and G. Saavedra et al., 2012. Respiratory syncytial virus modifies microRNAs regulating host genes that affect virus replication. J. General Virol., 93: 2346-2356.
PubMed  |  

Bartel, D.P., 2004. MicroRNAs: Genomics, biogenesis, mechanism and function. Cell, 116: 281-297.
PubMed  |  Direct Link  |  

Boss, I.W. and R. Renne, 2010. Viral miRNAs: Tools for immune evasion. Curr. Opin. Microbiol., 13: 540-545.
PubMed  |  

Boss, I.W. and R. Renne, 2011. Viral miRNAs and immune evasion. Biochim. Biophys. Acta (BBA)-Gene Regulatory Mech., 1809: 708-714.
CrossRef  |  PubMed  |  

Buck, A.H., J. Santoyo-Lopez, K.A. Robertson, D.S. Kumar, M. Reczko and P. Ghazal, 2007. Discrete clusters of virus-encoded micrornas are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J. Virol., 81: 13761-13770.
PubMed  |  

Burnside, J., E. Bernberg, A. Anderson, C. Lu and B.C. Meyers et al., 2006. Marek's disease virus encodes microRNAs that map to meq and the latency-associated transcript. J. Virol., 80: 8778-8786.
PubMed  |  

Cai, X. and B.R. Cullen, 2006. Transcriptional origin of Kaposi's Sarcoma-associated herpesvirus MicroRNAs. J. Virol., 80: 2234-2242.
CrossRef  |  

Cai, X., A. Schafer, S. Lu, J.P. Bilello and R.C. Desrosiers et al., 2006. Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog., Vol. 2. 10.1371/journal.ppat.0020023

Cai, X., S. Lu, Z. Zhang, C.M. Gonzalez, B. Damania and B.R. Cullen, 2005. Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc. Natl. Acad. Sci. USA., 102: 5570-5575.
CrossRef  |  PubMed  |  

Carl Jr., J.W., J. Trgovcich and S. Hannenhalli, 2013. Widespread evidence of viral miRNAs targeting host pathways. BMC Bioinform., Vol. 14. 10.1186/1471-2105-14-S2-S3

Carrington, J.C. and V. Ambros, 2003. Role of micro RNAs in plant and animal development. Science, 301: 336-338.
CrossRef  |  

Cazalla, D., M. Xie and J.A. Steitz, 2011. A primate herpesvirus uses the integrator complex to generate viral microRNAs. Mol. Cell, 43: 982-992.
CrossRef  |  PubMed  |  Direct Link  |  

Diebel, K.W., A.L. Smith and L.F. van Dyk, 2009. Mature and functional viral miRNAs transcribed from novel RNA polymerase III promoters. RNA, 16: 170-185.
CrossRef  |  Direct Link  |  

Dunn, W., P. Trang, Q. Zhong, E. Yang, C. van Belle and F. Liu, 2005. Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol., 7: 1684-1695.
PubMed  |  

Gee, G.V., M.L. Stanifer, B.C. Christensen, W.J. Atwood and D. Ugolini et al., 2010. SV40 associated miRNAs are not detectable in mesotheliomas. Br. J. Cancer, 103: 885-888.
PubMed  |  

Geeleher, P., S.R. Huang, E.R. Gamazon, A. Golden and C. Seoighe, 2012. The regulatory effect of miRNAs is a heritable genetic trait in humans. Genom., Vol. 13. 10.1186/1471-2164-13-383

Glazov, E.A., P.F. Horwood, W. Assavalapsakul, K. Kongsuwan, R.W. Mitchell, N. Mitter and T.J. Mahony, 2010. Characterization of microRNAs encoded by the bovine herpesvirus 1 genome. J. Gen. Virol., 91: 32-41.
PubMed  |  

Gottwein, E. and B.R. Cullen, 2008. Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe., 3: 375-387.
PubMed  |  

Grundhoff, A. and C.S. Sullivan, 2011. Virus-encoded microRNAs. Virology, 411: 325-343.
CrossRef  |  PubMed  |  

Halford, W.P., C.D. Kemp, J.A. Isler, D.J. Davido and P.A. Schaffer, 2001. ICP0, ICP4, or VP16 expressed from adenovirus vectors induces reactivation of latent herpes simplex virus type 1 in primary cultures of latently infected trigeminal ganglion cells. J. Virol., 75: 6143-6153.
CrossRef  |  Direct Link  |  

Han, Y., Y. Liu, Y. Gui and Z. Cai, 2013. Inducing cell proliferation inhibition and apoptosis via silencing dicer, Drosha and Exportin 5 in urothelial carcinoma of the bladder. J. Surg. Oncol., 107: 201-205.
PubMed  |  

Hoffmann, T.W., G. Duverlie and A. Bengrine, 2012. MicroRNAs and hepatitis C virus: Toward the end of miR-122 supremacy. Virol. J. 10.1186/1743-422X-9-109

Jeang, K.T., 2012. RNAi in the regulation of mammalian viral infections. BMC Biol., Vol. 10. 10.1186/1741-7007-10-58

Jin, W.B., F.L. Wu, D. Kong and A.G. Guo, 2007. HBV-encoded microRNA candidate and its target. Comput. Biol. Chem., 31: 124-126.
CrossRef  |  PubMed  |  Direct Link  |  

Jurak, I., M.F. Kramer, J.C. Mellor, A.L. van Lint, F.P. Roth, D.M. Knipe and D.M. Coen, 2010. Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2. J. Virol., 84: 4659-4672.
PubMed  |  

Kincaid, R.P., J.M. Burke and C.S. Sullivan, 2012. From the cover: RNA virus microRNA that mimics a B-cell oncomiR. Proc. Natl. Acad. Sci. USA., 109: 3077-3082.
Direct Link  |  

Klase, Z.A., G.C. Sampey and F. Kashanchi, 2013. Retrovirus infected cells contain viral microRNAs. Retrovirology, Vol. 10. 10.1186/1742-4690-10-15

Koshiol, J., M.L. Gulley, Y. Zhao, M. Rubagotti and F.M. Marincola et al., 2011. Epstein-Barr virus microRNAs and lung cancer. Br. J. Cancer, 105: 320-326.
PubMed  |  

Kramer, M.F., I. Jurak, J.M. Pesola, S. Boissel, D.M. Knipe and D.M. Coen, 2011. Herpes simplex virus 1 microRNAs expressed abundantly during latent infection are not essential for latency in mouse trigeminal ganglia. Virology, 417: 239-247.
PubMed  |  

Kumar, S., F.A. Ansari and V. Scaria, 2009. Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features. Virol. J., Vol. 6. 10.1186/1743-422X-6-129

Landgraf, P., M. Rusu, R. Sheridan, A. Sewer and N. Iovino et al., 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129: 1401-1414.
CrossRef  |  PubMed  |  

Lee, R.C., R.L. Feinbaum and V. Ambros, 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75: 843-854.
CrossRef  |  Direct Link  |  

Leisegang, M.S., R. Martin, A.S. Ramirez and M.T. Bohnsack, 2012. Exportin t and Exportin 5: tRNA and miRNA biogenesis- and beyond. Biol. Chem., 393: 599-604.
CrossRef  |  PubMed  |  

Li, Z., C.S. Yang, K. Nakashima and T.M. Rana, 2011. Small RNA-mediated regulation of iPS cell generation. EMBO J., 30: 823-834.
CrossRef  |  PubMed  |  

Liang, D., Y. Gao, X. Lin, Z. He, Q. Zhao, Q. Deng and K. Lan, 2011. A human herpesvirus miRNA attenuates interferon signaling and contributes to maintenance of viral latency by targeting IKKepsilon. Cell Res., 21: 793-806.
CrossRef  |  PubMed  |  

Libri, V., A. Helwak, P. Miesen, D. Santhakumar and J.G. Borger et al., 2011. Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target. Proc. Natl. Acad. Sci. USA., 109: 279-284.
PubMed  |  

Lin, J. and B.R. Cullen, 2007. Analysis of the interaction of primate retroviruses with the human RNA interference machinery. J. Virol., 81: 12218-12226.
PubMed  |  

Lin, Y.T., R.P. Kincaid, D. Arasappan, S.E. Dowd, S.P. Hunicke-Smith and C.S. Sullivan, 2010. Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA, 16: 1540-1558.
PubMed  |  

Lin, Z. and E.K. Flemington, 2011. miRNAs in the pathogenesis of oncogenic human viruses. Cancer Lett., 305: 186-199.
PubMed  |  

Lo, A.K., K.F. To, K.W. Lo, R.W. Lung, J.W. Hui, G. Liao and S.D. Hayward, 2007. Modulation of LMP1 protein expression by EBV-encoded microRNAs. Proc. Natl. Acad. Sci. USA., 104: 16164-16169.
PubMed  |  

Meshesha, M.K., I. Veksler-Lublinsky, O. Isakov, I. Reichenstein and N. Shomron et al., 2012. The microRNA Transcriptome of Human Cytomegalovirus (HCMV). Open Virol. J., 6: 38-48.
Direct Link  |  

Morgan, R., A. Anderson, E. Bernberg, S. Kamboj and E. Huang et al., 2008. Sequence conservation and differential expression of Marek's disease virus microRNAs. J. Virol., 82: 12213-12220.
PubMed  |  

Murphy, E., J. Vanicek, H. Robins, T. Shenk and A.J. Levine, 2008. Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency. Proc. Natl. Acad. Sci. USA., 105: 5453-5458.
CrossRef  |  PubMed  |  Direct Link  |  

Omoto, S. and Y.R. Fujii, 2005. Regulation of human immunodeficiency virus 1 transcription by nef microRNA. J. Gen. Virol., 86: 751-755.
Direct Link  |  

Omoto, S., M. Ito, Y. Tsutsumi, Y. Ichikawa and H. Okuyama et al., 2004. HIV-1 nef suppression by virally encoded microRNA. Retrovirology, Vol. 1. 10.1186/1742-4690-1-44

Orom, U.A., F.C. Nielsen and A.H. Lund, 2008. MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell, 30: 460-471.
PubMed  |  

Ouellet, D.L., I. Plante, P. Landry, C. Barat and M.E. Janelle et al., 2008. Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res., 36: 2353-2365.
PubMed  |  

Ouellet, D.L., J. Vigneault-Edwards, K. Letourneau, L.A. Gobeil and I. Plante et al., 2013. Regulation of host gene expression by HIV-1 TAR microRNAs. Retrovirology, Vol. 10. 10.1186/1742-4690-10-86

Pfeffer, S., A. Sewer, M. Lagos-Quintana, R. Sheridan and C. Sander et al., 2005. Identification of microRNAs of the herpesvirus family. Nat. Methods, 2: 269-276.
CrossRef  |  

Pfeffer, S., M. Zavolan, F.A. Grasser, M. Chien and J.J. Russo et al., 2004. Identification of virus-encoded MicroRNAs. Science, 304: 734-736.
CrossRef  |  

Rachamadugu, R., J.Y. Lee, A. Wooming and B.W. Kong, 2009. Identification and expression analysis of infectious laryngotracheitis virus encoding microRNAs. Virus Genes, 39: 301-308.
PubMed  |  

Reese, T.A., J. Xia, L.S. Johnson, X. Zhou, W. Zhang and H.W. Virgin, 2010. Identification of novel microRNA-like molecules generated from herpesvirus and host tRNA transcripts. J. Virol., 84: 10344-10353.
PubMed  |  

Riley, K.J., G.S. Rabinowitz and J.A. Steitz, 2010. Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression. J. Virol., 84: 5148-5157.
Direct Link  |  

Rosewick, N., M. Momont, K. Durkin, H. Takeda and F. Caiment et al., 2013. Deep sequencing reveals abundant noncanonical retroviral microRNAs in B-cell leukemia/lymphoma. Proc. Natl. Acad. Sci. USA., 110: 2306-2311.
PubMed  |  

Sarid, R. and S.J. Gao, 2011. Viruses and human cancer: From detection to causality. Cancer Lett., 305: 218-227.
PubMed  |  

Scaria, V., M. Hariharan, S. Maiti, B. Pillai and S.K. Brahmachari, 2006. Host-virus interaction: A new role for microRNAs. Retrovirology, Vol. 3. 10.1186/1742-4690-3-68

Schafer, A., X. Cai, J.P. Bilello, R.C. Desrosiers and B.R. Cullen, 2007. Cloning and analysis of microRNAs encoded by the primate gamma-herpesvirus rhesus monkey rhadinovirus. Virology, 364: 21-27.
PubMed  |  

Seo, G.J., C.J. Chen and C.S. Sullivan, 2009. Merkel cell polyomavirus encodes a microRNA with the ability to autoregulate viral gene expression. Virology, 383: 183-187.
CrossRef  |  Direct Link  |  

Seo, G.J., L.H. Fink, B. O'Hara, W.J. Atwood and C.S. Sullivan, 2008. Evolutionarily conserved function of a viral microRNA. J. Virol., 82: 9823-9828.
CrossRef  |  Direct Link  |  

Shapiro, J.S., R.A. Langlois, A.M. Pham and B.R. tenOever, 2012. Evidence for a cytoplasmic microprocessor of pri-miRNAs. RNA, 18: 1338-1346.
CrossRef  |  Direct Link  |  

Shapshak, P., 2012. Molecule of the month HIV-1 Tat and miRNA. Bioinformation, 8: 1123-1124.
Direct Link  |  

Shimakami, T., D. Yamane, R.K. Jangra, B.J. Kempf, C. Spaniel, D.J. Barton and S.M. Lemon, 2012. Stabilization of hepatitis C virus RNA by an Ago2-miR-122 complex. Proc. Natl. Acad. Sci. USA., 109: 941-946.
CrossRef  |  Direct Link  |  

Sisk, J.M., J.E. Clements and K.W. Witwer, 2012. miRNA profiles of monocyte-lineage cells are consistent with complicated roles in HIV-1 restriction. Viruses, 4: 1844-1864.
CrossRef  |  Direct Link  |  

Slezak-Prochazka, I., S. Durmus, B.J. Kroesen and A. van den Berg, 2010. MicroRNAs, macrocontrol: Regulation of miRNA processing. RNA, 16: 1087-1095.
CrossRef  |  Direct Link  |  

Song, L., H. Liu, S. Gao, W. Jiang and W. Huang, 2010. Cellular micrornas inhibit replication of the h1n1 influenza a virus in infected cells. J. Virol., 84: 8849-8860.
Direct Link  |  

Stark, T.J., J.D. Arnold, D.H. Spector and G.W. Yeo, 2011. High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection. J. Virol., 86: 226-235.
CrossRef  |  Direct Link  |  

Steitz, J., S. Borah, D. Cazalla, V. Fok and R. Lytle et al., 2010. Noncoding RNPs of viral origin. Cold Spring Harbor Perspect. Biol., Vol. 3. 10.1101/cshperspect.a005165

Sullivan, C.S., A.T. Grundhoff, S. Tevethia, J.M. Pipas and D. Ganem, 2005. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature, 435: 682-686.
CrossRef  |  Direct Link  |  

Sun, J., M. Li, Z. Li, J. Xue and X. Lan et al., 2013. Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis. BMC Genomics, Vol. 14. 10.1186/1471-2164-14-42

Tang, S., A.S. Bertke, A. Patel, K. Wang, J.I. Cohen and P.R. Krause, 2008. An acutely and latently expressed herpes simplex virus 2 viral microRNA inhibits expression of ICP34.5, a viral neurovirulence factor. Proc. Natl. Acad. Sci. USA., 105: 10931-10936.
CrossRef  |  Direct Link  |  

Umbach, J.L. and B.R. Cullen, 2009. The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev., 23: 1151-1164.
CrossRef  |  Direct Link  |  

Umbach, J.L. and B.R. Cullen, 2010. In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J. Virol., 84: 695-703.
CrossRef  |  Direct Link  |  

Umbach, J.L., M.A. Nagel, R.J. Cohrs, D.H. Gilden and B.R. Cullen, 2009. Analysis of human alphaherpesvirus microRNA expression in latently infected human trigeminal ganglia. J. Virol., 83: 10677-10683.
CrossRef  |  Direct Link  |  

Umbach, J.L., M.F. Kramer, I. Jurak, H.W. Karnowski, D.M. Coen and B.R. Cullen, 2008. MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature, 454: 780-783.
CrossRef  |  

Vasudevan, S., Y. Tong and J.A. Steitz, 2008. Cell cycle control of microRNA-mediated translation regulation. Cell Cycle, 7: 1545-1549.
CrossRef  |  

Veksler-Lublinsky, I., Y. Shemer-Avni, E. Meiri, Z. Bentwich, K. Kedem and M. Ziv-Ukelson, 2012. Finding quasi-modules of human and viral miRNAs: A case study of human cytomegalovirus (HCMV). BMC Bioinform., Vol. 13. 10.1186/1471-2105-13-322

Waidner, L.A., R.W. Morgan, A.S. Anderson, E.L. Bernberg and S. Kamboj et al., 2009. MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific. Virology, 388: 128-136.
CrossRef  |  

Wang, Y., V. Brahmakshatriya, B. Lupiani, S.M. Reddy and B. Soibam et al., 2012. Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers. BMC Genomics, Vol. 13. 10.1186/1471-2164-13-278

Wightman, B., I. Ha and G. Ruvkun, 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75: 855-862.
CrossRef  |  PubMed  |  

Witkowski, W. and B. Verhasselt, 2013. Contributions of HIV-1 Nef to immune dysregulation in HIV-infected patients: A therapeutic target? Expert Opin. Ther. Targets, 10.1517/14728222.2013.830712

Wu, Y.Q., D.J. Chen, H.B. He, D.S. Chen, L.L. Chen, H.C. Chen and Z.F. Liu, 2012. Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs. PLoS ONE, Vol. 7. 10.1371/journal.pone.0030988

Xiang, J., A. Cheng, M. Wang, S. Zhang and D. Zhu et al., 2012. Computational identification of microRNAs in Anatid herpesvirus 1 genome. Virol. J., Vol. 9. 10.1186/1743-422X-9-93

Yao, Y., L.P. Smith, L. Petherbridge, M. Watson and V. Nair, 2012. Novel microRNAs encoded by duck enteritis virus. J. Gen. Virol., 93: 1530-1536.
CrossRef  |  PubMed  |  

Yao, Y., Y. Zhao, H. Xu, L.P. Smith, C.H. Lawrie, M. Watson and V. Nair, 2008. MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1: Predominance of virus-encoded microRNAs. J. Virol., 82: 4007-4015.
CrossRef  |  Direct Link  |  

Zhang, T., T. Cheng, L. Wei, Y. Cai and A.E. Yeo et al., 2012. Efficient inhibition of HIV-1 replication by an artificial polycistronic miRNA construct. Virol. J., Vol. 9. 10.1186/1743-422X-9-118

Zhang, X.D., Y.H. Zhang, Y.H. Ling, Y. Liu and H.G. Cao et al., 2013. Characterization and differential expression of microRNAs in the ovaries of pregnant and non-pregnant goats (Capra hircus). BMC Genomics, Vol. 14. 10.1186/1471-2164-14-157

Zhao, P., L. Zhao, K. Zhang, H. Feng and H. Wang et al., 2012. Infection with street strain rabies virus induces modulation of the microRNA profile of the mouse brain. Virol. J., Vol. 9. 10.1186/1743-422X-9-159

Zhou, L., G.M. Pupo, P. Gupta, B. Liu and S.L. Tran et al., 2012. A parallel genome-wide mRNA and microRNA profiling of the frontal cortex of HIV patients with and without HIV-associated dementia shows the role of axon guidance and downstream pathways in HIV-mediated neurodegeneration. BMC Genomics, Vol. 13. 10.1186/1471-2164-13-677

Zhu, J.Y., M. Strehle, A. Frohn, E. Kremmer, K.P. Hofig, G. Meister and H. Adler, 2010. Identification and analysis of expression of novel microRNAs of murine gammaherpesvirus 68. J. Virol., 84: 10266-10275.
CrossRef  |  PubMed  |