Identification of two small RNAs within the first 1.5-kb of the herpes simplex virus type 1–encoded latency-associated transcript

References

• Ahmed M, Lock M, Miller C G, Fraser N W. Regions of the herpes simplex virus type 1 latency-associated transcript that protect cells from apoptosis in vitro and protect neuronal cells in vivo. J Virol 2002; 76: 717–729
   Google Scholar
• Banerjee D, Slack F. Control of developmental timing by small temporal RNAs: a paradigm for RNA mediated regulation of gene expression. Bioessays 2002; 24: 119–129
   PubMed Web of Science ®Google Scholar
• Bartel D P. MicroRNAs: genomics, biogenesis, mechanism and function. Cell 2004; 116: 281–297
   PubMed Web of Science ®Google Scholar
• Branco F J, Fraser N W. Herpes simplex virus type 1 latency-associated transcript expression protects trigeminal ganglion neurons from apoptosis. J Virol 2005; 79: 9019–9025
   Google Scholar
• Brennecke J, Stark A, Russell R B, Cohen S M. Principles of MicroRNA-target recognition. PLoS Biol 2005; 3: e85
   PubMed Web of Science ®Google Scholar
• Burnside J, Bernberg E, Anderson A, Lu C, Meyers B C, Green P J, Jain N, Isaacs G, Morgan R W. Marek's disease virus encodes microRNAs that map to meq and the latency-associated transcript. J Virol 2006; 80: 8778–8786
   PubMed Web of Science ®Google Scholar
• Cai X, Lu S, Zhang Z, Gonzalez C M, Damania B, Cullen B R. Kaposis sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc Natl Acad Sci U S A 2005; 102: 5570–5575
   PubMed Web of Science ®Google Scholar
• Carpenter D, Henderson G, Hsiang C, Osorio N, Ben Mohamed L, Jones C, Wechsler S L. Introducing point mutations into the ATGs of the putative open reading frames of the HSV-1 gene encoding the latency associtated transcript (LAT) reduces its anti-apoptosis activity. Microbial Pathogenesis 2007; 44: 98–102
   Google Scholar
• Chan J A, Krichevsky A M, Kosik K S. MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 2005; 65: 6029–6033
   PubMed Web of Science ®Google Scholar
• Chen S H, Kramer M F, Schaffer P A, Coen D M. A viral function represses accumulation of transcripts from productive-cycle genes in mouse ganglia latently infected with herpes simplex virus. J Virol 1997; 71: 5878–5884
   PubMedGoogle Scholar
• Croen K D, Ostrove J M, Dragovic L J, Smialek J E, Straus S E. Latent herpes simplex virus in human trigeminal ganglia. Detection of an immediate early gene “anti-sense” transcript by in situ hybridization. N Engl J Med 1987; 317: 1427–1432
   PubMed Web of Science ®Google Scholar
• Cui C, Griffiths A, Li G, Silva L M, Kramer M F, Gaasterland T, Wang X-J, Coen D C. Prediction and identification of herpes simplex virus 1-encoded microRNAs. J Virol 2006; 80: 5499–5508
   PubMed Web of Science ®Google Scholar
• Deatly A M, Spivack J G, Lavi E, Fraser N W. RNA from an immediate early region of the type 1 herpes simplex virus genome is present in the trigeminal ganglia of latently infected mice. Proc Natl Acad Sci U S A 1987; 84: 3204–3208
   PubMed Web of Science ®Google Scholar
• Deatly A M, Spivack J G, Lavi E, O'Boyle D R, Fraser N W. Latent herpes simplex virus type 1 transcripts in peripheral and central nervous system tissues of mice map to similar regions of the viral genome. J Virol 1988; 62: 749–756
   PubMed Web of Science ®Google Scholar
• Denli A M, Tops B B, Plasterk R H, Ketting R F, Hannon G J. Processing of primary microRNAs by the Microprocessor complex. Nature 2004; 432: 231–235
   PubMed Web of Science ®Google Scholar
• Doench J G, Sharp P A. Specificity of microRNA target selection in translational repression. Genes Dev 2004; 18: 504–511
   PubMed Web of Science ®Google Scholar
• Drolet B S, Perng G-C, Cohen J, Slanina S M, Yukht A, Nesburn A B, Wechsler S L. The region of the herpes simplex virus type 1 LAT gene involved in spontaneous reactivation does not encode a functional protein. Virology 1998; 242: 221–232
   Google Scholar
• Dunn W, Trang P, Zhong Q, Yang E, van Belle C, Liu F. Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol. J Virol 2005; 11: 1684–1695
   Google Scholar
• Dykxhoorn D M, Novina C D, Sharp P A. Killing the messenger: short RNAs that silence gene expression. Nat Rev Mol Cell Biol 2003; 4: 457–467
   PubMed Web of Science ®Google Scholar
• Farrell M J, Dobson A T, Feldman L T. Herpes simplex virus latency-associated transcript is a stable intron. Proc Natl Acad Sci U S A 1991; 88: 790–794
   Google Scholar
• Finnegan E J, Matzke M A. The small RNA world. J Cell Sci 2003; 116: 4689–4693
   PubMed Web of Science ®Google Scholar
• Fraser A. Worms in LA. Nat Genet 2003; 35: 3–5
   Google Scholar
• Garber D A, Schaffer P A, Knipe D M. A LAT-associated function reduces productive-cycle gene expression during acute infection of murine sensory neurons with herpes simplex virus type 1. J Virol 1997; 71: 5885–5893
   PubMedGoogle Scholar
• Gesser R M, Koo S C. Latent herpes simplex virus type 1 gene expression in ganglia innervating the human gastrointestinal tract. J Virol 1997; 71: 4103–4106
   Google Scholar
• Grey F, Antoniewicz A, Allen E, Saugstad J, McShea A, Carrington J C, Nelson J. Identification and characterization of human cytomegalovirus-encoded microRNAs. J Virol 2005; 79: 12095–12099
   PubMed Web of Science ®Google Scholar
• Gupta A, Gartner J J, Sethupathy P, Hatzigeorgiou A G, Frazer N W. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency associated transcript. Nature 2006; 442: 82–85
   PubMed Web of Science ®Google Scholar
• Hanon G J. RNA interference. Nature 2002; 418: 244–251
   Google Scholar
• He L, Thompson J M, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe S W, Hannon G J, Hammond S M. A microRNA polycistron as a potential human oncogene. Nature 2005; 435: 828–833
   PubMed Web of Science ®Google Scholar
• Henderson G, Peng W, Jin L, Perng G-C, Nesburn A B, Wechsler S L, Jones C. Regulation of caspase 8- and caspase 9-induced apoptosis by the herpes simplex virus latency-associated transcript. J NeuroVirol 2002; 8: 103–111
   PubMedGoogle Scholar
• Hill J M, Maggioncalda J B, Garza H H, Jr, Su Y-H, Fraser N W, Block T M. In vivo epinephrine reactivation of ocular herpes simplex virus type 1 in the rabbit is correlated to a 370-base-pair region located between the promoter and the 5′ end of the 2.0 kilobase latency-associated transcript. J Virol 1996; 70: 7270–7274
   Google Scholar
• Huttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 2006; 34: 635–646
   PubMed Web of Science ®Google Scholar
• Hutvagner G, Zamore P D. A microRNA in a multiple-turnover RNAi enzyme complex. Science 2002; 297: 2056–2060
   PubMed Web of Science ®Google Scholar
• Inman M, Perng G-C, Henderson G, Ghiasi H, Nesburn A B, Wechsler S L, Jones C. Region of herpes simplex virus type 1 latency-associated transcript sufficient for wild-type spontaneous reactivation promotes cell survival in tissue culture. J Virol 2001; 75: 3636–3646
   Google Scholar
• Iseni F, Garcin D, Nishio M, Kedersha N, Anderson P, Kolakofsky D. Sendai virus trailer RNA binds TIAR, a cellular protein invilved in virus-induced apoptosis. EMBO J 2002; 21: 5141–5150
   PubMedGoogle Scholar
• Jin L, Peng W, Perng G-C, Nesburn A B, Jones C, Wechsler S L. Identification of herpes simplex virus type 1 (HSV-1) latency associated transcript (LAT) sequences that both inhibit apoptosis and enhance the spontaneous reactivation phenotype. J Virol 2003; 77: 6556–6561
   Google Scholar
• Jin L, Perng G-C, Brick D J, Naito J, Nesburn A B, Jones C, Wechsler S L. Methods for detecting the HSV-1 LAT anti-apoptosis activity in virus infected tissue culture cells. J Virol Meth 2004; 118: 9–13
   Google Scholar
• Jin L, Perng G-C, Nesburn A B, Jones C, Wechsler S L. The baculovirus inhibitor of apoptosis gene (cpIAP) can restore reactivation of latency to a herpes simplex virus type 1 that does not express the latency associated transcript (LAT). J Virol 2005; 12286–12295
   Google Scholar
• Jones C. Alphaherpesvirus latency: its role in disease and survival of the virus in nature. Adv Virus Res 1998; 51: 81–133
   PubMed Web of Science ®Google Scholar
• Jones C. Herpes simplex virus type 1 and bovine herpesvirus 1 latency. Clin Micro Rev 2003; 16: 79–95
   PubMed Web of Science ®Google Scholar
• Khvorova A, Kwak Y G, Tamkun M, Majerfeld I, Yarus M. RNAs that bind and change the permeability of phospholipid membranes. Proc Natl Acad Sci U S A 1999; 96: 10649–10654
   PubMed Web of Science ®Google Scholar
• Krause P R, Croen K D, Straus S E, Ostrove J M. Detection and preliminary characterization of herpes simplex virus type 1 transcripts in latently infected human trigeminal ganglia. J Virol 1988; 62: 4819–4823
   PubMed Web of Science ®Google Scholar
• Krummenacher C, Zabolotny J M, Fraser N W. Selection of a nonconsensus branch point is influenced by an RNA stem-loop structure and is important to confer stability to the herpes simplex virus 2-kilobase latency-associated transcript. J Virol 1997; 71: 5849–5860
   Google Scholar
• Kuwabera T, Hsieh J, Nakashima K, Taira K, Gage F H. A small modulatory dsRNA specified the fate of adult neural stem cells. Cell 2004; 116: 779–793
   Google Scholar
• Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 2001; 294: 853–858
   PubMed Web of Science ®Google Scholar
• Lai E C, Tomancak P, Williams R W, Rubin G M. Computational identification of Drosophila microRNA genes. Genome Biol 2003; 7: 123–130
   Google Scholar
• Lee R C, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans. Science 2001; 294: 862–864
   PubMed Web of Science ®Google Scholar
• Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim V N. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425: 415–419
   PubMed Web of Science ®Google Scholar
• Lee Y, Jeon K, Lee J T, Kim S, Kim V N. MicroRNA maturation: stepwise processing and subcellular localization. EMBO J 2002; 21: 4663–4670
   PubMed Web of Science ®Google Scholar
• Lim L P, Lau N C, Garrett-Engele P, Grimson A, Schelter J M, Castle J, Bartel D P, Linsley P S, Johnson J M. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005; 433: 769–773
   PubMed Web of Science ®Google Scholar
• Lim L P, Lau N C, Weinstein E G, Abdelhakim A, Yekta S, Rhoades M W, Burge C B, Bartel D P. The microRNAs of Caenorhabditis elegans. Genes Dev 2003; 17: 991–1008
   PubMed Web of Science ®Google Scholar
• Lohr J M, Nelson J A, Oldstone M B. Is herpes simplex virus associated with peptic ulcer disease?. J Virol 1990; 64: 2168–74
   PubMed Web of Science ®Google Scholar
• Loutsch J M, Perng G-C, Hill J M, Zheng X, Marquart M E, Block T M, Ghiasi H, Nesburn A B, Wechsler S L. Identical 371-base-pair deletion mutations in the LAT genes of herpes simplex virus type 1 McKrae and 17 syn+ result in different in vivo reactivation phenotypes. J Virol 1999; 73: 767–771
   PubMed Web of Science ®Google Scholar
• Mador N, Goldenberg D, Cohen O, Panet A, Steiner I. Herpes simplex virus type 1 latency-associated transcripts suppress viral replication and reduce immediate-early gene mRNA levels in a neuronal cell line. J Virol 1998; 72: 5067–5075
   Google Scholar
• Mador N, Panet A, Latchman D, Steiner I. Expression and splicing of the latency-associated transcripts of herpes simplex virus type 1 in neuronal and non-neuronal cell lines. J Biochem (Tokyo) 1995; 117: 1288–1297
   Google Scholar
• Maggioncalda J, Mehta A, Fraser N W, Block T M. Analysis of a herpes simplex virus type 1 LAT mutant with a deletion between the putative promoter and the 5′ end of the 2.0-kilobase transcript. J Virol 1994; 68: 7816–7824
   PubMedGoogle Scholar
• Mitchell W J, Lirette R P, Fraser N W. Mapping of low abundance latency-associated RNA in the trigeminal ganglia of mice latently infected with herpes simplex virus type 1. J Gen Virol 1990; 71: 125–132
   PubMed Web of Science ®Google Scholar
• Mott K, Osorio N, Jin L, Brick D, Naito J, Cooper J, Henderson G, Inman M, Jones C, Wechsler S L, Perng G-C. The bovine herpesvirus 1 LR ORF2 is crucial for this gene's ability to restore the high reactivation phenotype to a Herpes simplex virus-1 LAT null mutant. J Gen Virol 2003; 84: 2975–2985
   PubMedGoogle Scholar
• Nahmias A J, Roizman B. Infection with herpes-simplex viruses 1 and 2. 3. N Engl J Med 1973; 289: 781–789
   PubMed Web of Science ®Google Scholar
• Nanbo A, Inoue K, Adachi-Takasawa K, Takada K. Epstein-Barr virus RNA confers resistance to interferon-alpha induced apoptosis in Burkitts lymphoma. EMBO J 2002; 21: 954–965
   PubMed Web of Science ®Google Scholar
• A B Nesburn, 1983, Report of the Corneal Disease Panel: vision research: a national plan The CV Mosby Co. 1983–1987, vol. II. part III. St. Louis, MO, pp part III
   Google Scholar
• O'Donnell K A, Wentzel E A, Zeller K I, Dang C V, Mendell J T. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 2005; 435: 839–843
   PubMed Web of Science ®Google Scholar
• Ohler U. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 2004; 10: 1309–1322
   PubMed Web of Science ®Google Scholar
• Peng W, Henderson G, Perng G-C, Nesburn A B, Wechsler S L, Jones C. The gene that encodes the herpes simplex virus type 1 latency-associated transcript influences the accumulation of transcripts (Bcl-xL and Bcl-xS) that encode apoptotic regulatory proteins. J Virol 2003; 77: 10714–10718
   PubMedGoogle Scholar
• Peng W, Jin L, Henderson G, Perng G-C, Brick D J, Nesburn A B, Wechsler S L, Jones C. Mapping herpes simplex virus type 1 (HSV-1) LAT sequences that protect from apoptosis mediated by a plasmid expressing caspase-8. J NeuroVirol 2004; 10: 260–265
   Web of Science ®Google Scholar
• Perng G, Slanina S M, Ghiasi H, Nesburn A B, Wechsler S L. A 371-nucleotide region between the herpes simplex virus type 1 (HSV-1) LAT promoter and the 2-kilobase LAT is not essential for efficient spontaneous reactivation of latent HSV-1. J Virol 1996a; 70: 2014–2018
   PubMedGoogle Scholar
• Perng G, Slanina S M, Yukht A, Ghiasi H, Nesburn A B, Wechsler S L. The latency-associated transcript gene enhances establishment of herpes simplex virus type 1 latency in rabbits. J Virol 2000; 74: 1885–1891
   PubMed Web of Science ®Google Scholar
• Perng G-C, Chokephaibulkit K, Thompson R L, Sawtell N M, Slanina S M, Ghiasi H, Nesburn A B, Wechsler S L. The region of the herpes simplex virus type 1 LAT gene that is colinear with the ICP34.5 gene is not involved in spontaneous reactivation. J Virol 1996b; 70: 282–291
   PubMed Web of Science ®Google Scholar
• Perng G-C, Dunkel E C, Geary P A, Slanina S M, Ghiasi H, Kaiwar R, Nesburn A B, Wechsler S L. The latency-associated transcript gene of herpes simplex virus type 1 (HSV-1) is required for efficient in vivo spontaneous reactivation of HSV-1 from latency. J Virol 1994; 68: 8045–8055
   PubMed Web of Science ®Google Scholar
• Perng G-C, Esmail D, Slanina S, Yukht A, Ghiasi H, Osorio N, Mott K R, Maguen B, Jin L, Nesburn A B, Wechsler S L. Three herpes simplex virus type 1 latency-associated transcipt mutants with distinct and assymetric effects on virulence in mice compared with rabbits. J Virol 2001; 75: 9018–9028
   PubMed Web of Science ®Google Scholar
• Perng G-C, Ghiasi H, Slanina S M, Nesburn A B, Wechsler S L. The spontaneous reactivation function of the herpes simplex virus type 1 LAT gene resides completely within the first 1.5 kilobases of the 8.3-kilobase primary transcript. J Virol 1996c; 70: 976–984
   PubMed Web of Science ®Google Scholar
• Perng G-C, Jones C, Ciacci-Zanella J, Stone M, Henderson G, Yukht A, Slanina S M, Hoffman F M, Ghiasi H, Nesburn A B, Wechsler S L. Virus-induced neuronal apoptosis blocked by the herpes simplex virus latency-associated transcript (LAT). Science 2000; 287: 1500–1503
   PubMed Web of Science ®Google Scholar
• Perng G-C, Maguen B, Jin L, Mott K R, Osorio N, Slanina S M, Yukht A, Ghiasi H, Nesburn A B, Inman M, Henderson G, Jones C, Wechsler S L. A gene capable of blocking apoptosis can substitute for the herpes simplex virus type 1 latency-associated transcript gene and restore wild-type reactivation levels. J Virol 2002; 76: 1224–1235
   PubMed Web of Science ®Google Scholar
• Perng G-C, Slanina S M, Yukht A, Drolet B S, Keleher W, Ghiasi H, Nesburn A B, Wechsler S L. A herpes simplex virus type 1 latency-associated transcript mutant with increased virulence and reduced spontaneous reactivation. J Virol 1999; 73: 920–929
   Google Scholar
• Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sanders C, Grasser F A, van Dyk L F, Kiong Ho C, Sherman S, Chien M, Russo J J, Ju J, Randall G, Lindenbach B D, Rice C M, Simon V, Ho D D, Zavolan M, Tuschi T. Identification of microRNAs of the herpesvirus family. Nat Methods 2005; 2: 269–276
   PubMed Web of Science ®Google Scholar
• Pfeffer S, Zavolan M, Grasser F A, Chien M, Russo J J, Ju J, John B, Enright A J, Marks D, Sander C, Tuschi T. Identification of virus-encoded microRNAs. Science 2004; 304: 734–736
   PubMed Web of Science ®Google Scholar
• Reinhart B J, Bartel D P. Small RNAs correspond to centromere heterochromatic repeats. Science 2002; 397: 1831–1835
   Google Scholar
• Rock D L, Beam S L, Mayfield J E. Mapping bovine herpesvirus type 1 latency-related RNA in trigeminal ganglia of latently infected rabbits. J Virol 1987; 61: 3827–3831
   PubMed Web of Science ®Google Scholar
• Rock D L, Nesburn A B, Ghiasi H, Ong J, Lewis T L, Lokensgard J R, Wechsler S L. Detection of latency-related viral RNAs in trigeminal ganglia of rabbits latently infected with herpes simplex virus type 1. J Virol 1987; 61: 3820–3826
   PubMed Web of Science ®Google Scholar
• Ruby J G, Jan C H, Bartel D P. Intronic microRNA precursors that bypass Drosha processing. Nature 2007; 448: 83–87
   PubMed Web of Science ®Google Scholar
• Samols M A, Hu J, Skalsky R L, Renne R. Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol 2005; 79: 9301–9305
   PubMed Web of Science ®Google Scholar
• Sawtell N M, Thompson R L. Herpes simplex virus type 1 latency-associated transcription unit promotes anatomical site-dependent establishment and reactivation from latency. J Virol 1992; 66: 2157–2169
   Google Scholar
• Schors K, Yehiely F, Kular R K, Kotlo K U, Brewer G, Deiss L P. Cell death inhibiting RNA (CDIR) derived from a 3′-untranslated region binds AUF1 and heat shock protein 27. J Biol Chem 2002; 277: 47061–47072
   Google Scholar
• Stevens J G, Wagner E K, Devi-Rao G B, Cook M L, Feldman L T. RNA complementary to a herpesvirus alpha gene mRNA is prominent in latently infected neurons. Science 1987; 235: 1056–1059
   PubMed Web of Science ®Google Scholar
• Sullivan C S, Grundhoff A T, Tevethia S, Pipas J M, Ganem D. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 2005; 435: 682–686
   PubMed Web of Science ®Google Scholar
• Thompson R L, Sawtell N M. The herpes simplex virus type 1 latency-associated transcript gene regulates the establishment of latency. J Virol 1997; 71: 5432–40
   PubMedGoogle Scholar
• Wagner E K, Bloom D C. Experimental investigation of herpes simplex virus latency. Clin Microbiol Rev 1997; 10: 419–443
   PubMed Web of Science ®Google Scholar
• Wagner E K, Devi-Rao G, Feldman L T, Dobson A T, Zhang Y F, Flanagan W M, Stevens J G. Physical characterization of the herpes simplex virus latency- associated transcript in neurons. J Virol 1988a; 62: 1194–202
   PubMed Web of Science ®Google Scholar
• Wagner E K, Flanagan W M, Devi-Rao G, Zhang Y F, Hill J M, Anderson K P, Stevens J G. The herpes simplex virus latency-associated transcript is spliced during the latent phase of infection. J Virol 1988b; 62: 4577–4585
   PubMed Web of Science ®Google Scholar
• Whitley R. Herpes simplex virus infections of the central nervous system. Encephalitis and neonatal herpes. Drugs 1991; 42: 406–427
   Google Scholar
• Whitley R. Herpes simplex virus. Lippincott-Raven, Philadelphia, New York 1997
   Google Scholar
• Xu P, Guo M, Hay B A. MicroRNAs and the regulation of cell death. Trends Genet 2004; 20: 617–624
   PubMed Web of Science ®Google Scholar
• Yi R, Qin Y, Macara I G, Cullen B R. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 2003; 17: 3011–3016
   PubMed Web of Science ®Google Scholar
• Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003; 31: 3406–3415
   PubMed Web of Science ®Google Scholar
• Zwaagstra J C, Ghiasi H, Slanina S M, Nesburn A B, Wheatley S C, Lillycrop K, Wood J, Latchman D S, Patel K, Wechsler S L. Activity of herpes simplex virus type 1 latency-associated transcript (LAT) promoter in neuron-derived cells: evidence for neuron specificity and for a large LAT transcript. J Virol 1990; 64: 5019–5028
   PubMedGoogle Scholar