References
- Liesegang TJ. Herpes simplex virus epidemiology and ocular importance. Cornea. 2001;20:1–13. doi:https://doi.org/10.1097/00003226-200101000-00001.
- Pepose JS, Keadle TL, Morrison LA. Ocular herpes simplex: changing epidemiology, emerging disease patterns, and the potential of vaccine prevention and therapy. Am J Ophthalmol. 2006;141:547–57. doi:https://doi.org/10.1016/j.ajo.2005.10.008.
- Rowe AM, St Leger AJ, Jeon S, Dhaliwal DK, Knickelbein JE, Hendricks RL. Herpes keratitis. Prog Retin Eye Res. 2013;32:88–101. doi:https://doi.org/10.1016/j.preteyeres.2012.08.002.
- Tuck AC, Tollervey DA. Transcriptome-wide Atlas of RNP composition Reveals Diverse Classes of mRNAs and lncRNAs. Cell 2013;154:996–1009. doi:https://doi.org/10.1016/j.cell.2013.07.047.
- Bergmann JH, Spector DL. Long non-coding RNAs: modulators of nuclear structure and function. Curr Opin Cell Biol. 2014;26:10–18. doi:https://doi.org/10.1016/j.ceb.2013.08.005.
- Guttman M, Rinn JL. Modular regulatory principles of large non-coding RNAs. Nature. 2012;482:339–46. doi:https://doi.org/10.1038/nature10887.
- Lee JT. Epigenetic regulation by long noncoding RNAs. Science. 2012;338:1435–39. doi:https://doi.org/10.1126/science.1231776.
- Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet. 2009;10:155–59. doi:https://doi.org/10.1038/nrg2521.
- Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang QH, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010;143:46–58. doi:https://doi.org/10.1016/j.cell.2010.09.001.
- Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010;329:689–93. doi:https://doi.org/10.1126/science.1192002.
- Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011;43:904–14. doi:https://doi.org/10.1016/j.molcel.2011.08.018.
- Batista PJ, Chang HY. Long noncoding RNAs: cellular address codes in development and disease. Cell. 2013;152:1298–307. doi:https://doi.org/10.1016/j.cell.2013.02.012.
- Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464:1071–U1148. doi:https://doi.org/10.1038/nature08975.
- Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet. 2010;42:1113-+. doi:https://doi.org/10.1038/ng.710.
- Qureshi IA, Mehler MF. Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci. 2012;13:528–41. doi:https://doi.org/10.1038/nrn3234.
- Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I, Long Noncoding A. RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011;147:358–69. doi:https://doi.org/10.1016/j.cell.2011.09.028.
- Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, et al. A long noncoding RNA mediates both activation and repression of immune response genes. Science. 2013;341:789–92. doi:https://doi.org/10.1126/science.1240925.
- Gao ZX, Song XL, Li SS, Lai XR, Yang YL, Yang G, Li ZJ, Cui YH, Pan HW. Assessment of DNA damage and cell senescence in corneal epithelial cells exposed to airborne particulate matter (PM2.5) collected in Guangzhou, China. Invest Ophthalmol Vis Sci. 2016;57:3093–102. doi:https://doi.org/10.1167/iovs.15-18839.
- Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45. doi:https://doi.org/10.1101/gr.092759.109.
- Jin X, Qin Q, Chen W, Qu J. Expression of toll-like receptors in the healthy and herpes simplex virus-infected cornea. Cornea. 2007;26:847–52. doi:https://doi.org/10.1097/ICO.0b013e318093de1f.
- Sarangi PP, Kim B, Kurt-Jones E, Rouse BT. Innate recognition network driving herpes simplex virus-induced corneal immunopathology: role of the toll pathway in early inflammatory events in stromal keratitis. J Virol. 2007;81:11128–38. doi:https://doi.org/10.1128/jvi.01008-07.
- Bryant-Hudson KM, Gurung HR, Zheng M, Carr DJ. Tumor necrosis factor alpha and interleukin-6 facilitate corneal lymphangiogenesis in response to herpes simplex virus 1 infection. J Virol. 2014;88:14451–57. doi:https://doi.org/10.1128/JVI.01841-14.
- Li H, Zhang J, Kumar A, Zheng M, Atherton SS, Yu FS. Herpes simplex virus 1 infection induces the expression of proinflammatory cytokines, interferons and TLR7 in human corneal epithelial cells. Immunology. 2006;117:167–76. doi:https://doi.org/10.1111/j.1365-2567.2005.02275.x.
- Wuest TR, Carr DJ. VEGF-A expression by HSV-1-infected cells drives corneal lymphangiogenesis. J Exp Med. 2010;207:101–15. doi:https://doi.org/10.1084/jem.20091385.
- Miles D, Athmanathan S, Thakur A, Willcox M. A novel apoptotic interaction between HSV-1 and human corneal epithelial cells. Curr Eye Res. 2003;26:165–74.
- Miles DH, Thakur A, Cole N, Willcox MD. The induction and suppression of the apoptotic response of HSV-1 in human corneal epithelial cells. Invest Ophthalmol Vis Sci. 2007;48:789–96. doi:https://doi.org/10.1167/iovs.06-0609.
- Goodkin ML, Epstein S, Asbell PA, Blaho JA. Nuclear translocation of NF-kappaB precedes apoptotic poly(ADP-ribose) polymerase cleavage during productive HSV-1 replication in corneal epithelial cells. Invest Ophthalmol Vis Sci. 2007;48:4980–88. doi:https://doi.org/10.1167/iovs.07-0489.
- Peng XX, Gralinski L, Armour CD, Ferris MT, Thomas MJ, Proll S, Bradel-Tretheway BG, Korth MJ, Castle JC, Biery MC, et al. Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. mBio. 2010;1:9. doi:https://doi.org/10.1128/mBio.00206-10.
- Josset L, Tchitchek N, Gralinski LE, Ferris MT, Eisfeld AJ, Green RR, Thomas MJ, Tisoncik-Go J, Schroth GP, Kawaoka Y, et al. Annotation of long non-coding RNAs expressed in Collaborative Cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts. RNA Biol. 2014;11:875–90. doi:https://doi.org/10.4161/rna.29442.
- Yin Z, Guan D, Fan Q, Su J, Zheng W, Ma W, Ke C. lncRNA expression signatures in response to enterovirus 71 infection. Biochem Biophys Res Commun. 2013;430:629–33. doi:https://doi.org/10.1016/j.bbrc.2012.11.101.
- Ouyang J, Zhu XM, Chen YH, Wei HT, Chen QH, Chi XJ, Qi BM, Zhang LF, Zhao Y, Gao GF, et al. NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription. Cell Host Microbe. 2014;16:616–26. doi:https://doi.org/10.1016/j.chom.2014.10.001.
- Carnero E, Barriocanal M, Prior C, Unfried JP, Segura V, Guruceaga E, Enguita M, Smerdou C, Gastaminza P, Fortes P. Long noncoding RNA EGOT negatively affects the antiviral response and favors HCV replication. EMBO Rep. 2016;17:1013–28. doi:https://doi.org/10.15252/embr.201541763.
- Zhang Q, Chen CY, Yedavalli VS, Jeang KT. NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. mBio. 2013;4:e00596–00512. doi:https://doi.org/10.1128/mBio.00596-12.
- Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, Kato A, Kawaguchi Y, Sato H, Yoneda M, et al. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Mol Cell. 2014;53:393–406. doi:https://doi.org/10.1016/j.molcel.2014.01.009.
- Li J, Chen CC, Ma XC, Geng GN, Liu BF, Zhang YJ, Zhang SY, Zhong FD, Liu C, Yin Y, et al. Long noncoding RNA NRON contributes to HIV-1 latency by specifically inducing tat protein degradation. Nat Commun. 2016;7. doi:https://doi.org/10.1038/ncomms11730.
- Kambara H, Niazi F, Kostadinova L, Moonka DK, Siegel CT, Post AB, Carnero E, Barriocanal M, Fortes P, Anthony DD, et al. Negative regulation of the interferon response by an interferon-induced long non-coding RNA. Nucleic Acids Res. 2014;42:10668–U10805. doi:https://doi.org/10.1093/nar/gku713.
- Nishitsuji H, Ujino S, Yoshio S, Sugiyama M, Mizokami M, Kanto T, Shimotohno K. Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc Natl Acad Sci U S A. 2016;113:10388–93. doi:https://doi.org/10.1073/pnas.1525022113.
- Smith JS, Robinson NJ. Age-specific prevalence of infection with herpes simplex virus types 2 and 1: A global review. J Infect Dis. 2002;186:S3–S28. doi:https://doi.org/10.1086/343739.
- Kaye S, Choudhary A. Herpes simplex keratitis. Prog Retin Eye Res. 2006;25:355–80. doi:https://doi.org/10.1016/j.preteyeres.2006.05.001.
- Arduino PG, Porter SR. Herpes Simplex Virus Type I infection: overview on relevant clinico-pathological features. J Oral Pathol Med. 2008;37:107–21. doi:https://doi.org/10.1111/j.1600-0714.2007.00586.x.
- Granerod J, Ambrose HE, Davies NWS, Clewley JP, Walsh AL, Morgan D, Cunningham R, Zuckerman M, Mutton KJ, Solomon T, et al. Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study. Lancet Infect Dis. 2010;10:835–44. doi:https://doi.org/10.1016/s1473-3099(10)70222-x.
- Whitley RJ. Herpes simplex encephalitis: adolescents and adults. Antiviral Res. 2006;71:141–48. doi:https://doi.org/10.1016/j.antiviral.2006.04.002.
- Galvan V, Roizman B. Herpes simplex virus 1 induces and blocks apoptosis at multiple steps during infection and protects cells from exogenous inducers in a cell-type-dependent manner. Proc Natl Acad Sci U S A. 1998;95:3931–36.
- Terasaka Y, Miyazaki D, Yakura K, Haruki T, Inoue Y. Induction of IL-6 in transcriptional networks in corneal epithelial cells after herpes simplex virus type 1 infection. Invest Ophthalmol Vis Sci. 2010;51:2441–49. doi:https://doi.org/10.1167/iovs.09-4624.
- Rutkowski AJ, Erhard F, L’Hernault A, Bonfert T, Schilhabel M, Crump C, Rosenstiel P, Efstathiou S, Zimmer R, Friedel CC, et al. Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun. 2015;6:7126. doi:https://doi.org/10.1038/ncomms8126.
- Hu BX, Huo YX, Chen GJ, Yang LP, Wu DD, Zhou JM. Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts. Virol J. 2016:13. doi:https://doi.org/10.1186/s12985-016-0592-5.
- Duan F, Liao J, Huang Q, Nie Y, Wu K. HSV-1 miR-H6 inhibits HSV-1 replication and IL-6 expression in human corneal epithelial cells in vitro. Clin Dev Immunol. 2012;2012:192791. doi:https://doi.org/10.1155/2012/192791.
- Nie Y, Cui D, Pan Z, Deng J, Huang Q, Wu K. HSV-1 infection suppresses TGF-beta1 and SMAD3 expression in human corneal epithelial cells. Mol Vis. 2008;14:1631–38.
- Shah A, Farooq AV, Tiwari V, Kim MJ, Shukla D. HSV-1 infection of human corneal epithelial cells: receptor-mediated entry and trends of re-infection. Mol Vis. 2010;16:2476–86.