Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Wu, Yi Quan ^a   Chen, Di Jun ^a   He, Hua Bin ^a   Chen, Dong Sheng ^a   Chen, Ling Ling ^a   Chen, Huan Chun ^a   Liu, Zheng Fei ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA PRECURSOR; VIRUS RNA;

ARTICLE; CELL DEATH; CONTROLLED STUDY; DNA POLYMORPHISM; EPITHELIUM CELL; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INTERACTION; GENE SEQUENCE; GENE TARGETING; GENETIC HETEROGENEITY; GENETIC VARIABILITY; INTRON; NONHUMAN; NORTHERN BLOTTING; PSEUDORABIES HERPETOVIRUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA GENE; VIRUS CELL INTERACTION; VIRUS GENOME; VIRUS LATENCY; VIRUS REPLICATION; ANIMAL; CELL LINE; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; HOST PATHOGEN INTERACTION; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PATHOLOGY; PHYSIOLOGY; PSEUDORABIES; SWINE; SWINE DISEASE; THEORETICAL MODEL; VIROLOGY;

ALPHAHERPESVIRINAE; SUID HERPESVIRUS 1; SUIDAE; SUS;

ANIMALS; BASE SEQUENCE; CELL LINE; EPITHELIAL CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, VIRAL; HERPESVIRUS 1, SUID; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOST-PATHOGEN INTERACTIONS; MICRORNAS; MODELS, THEORETICAL; MOLECULAR SEQUENCE DATA; PSEUDORABIES; RNA, VIRAL; SWINE; SWINE DISEASES;

EID: 84856082789     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030988     Document Type: Article

References (55)

1. Pomeranz LE, Reynolds AE, Hengartner CJ, (2005) Molecular biology of pseudorabies virus: impact on neurovirology and veterinary medicine. Microbiol Mol Biol Rev 69: 462-500.
2. Granzow H, Klupp BG, Mettenleiter TC, (2005) Entry of pseudorabies virus: an immunogold-labeling study. J Virol 79: 3200-3205.
3. Klupp BG, Hengartner CJ, Mettenleiter TC, Enquist LW, (2004) Complete, annotated sequence of the pseudorabies virus genome. J Virol 78: 424-440.
4. Cheung AK, (1991) Cloning of the latency gene and the early protein 0 gene of pseudorabies virus. J Virol 65: 5260-5271.
5. Cheung AK, (1989) Detection of pseudorabies virus transcripts in trigeminal ganglia of latently infected swine. J Virol 63: 2908-2913.
6. Mukerjee R, Kang W, Suri V, Fraser NW, (2004) A non-consensus branch point plays an important role in determining the stability of the 2-kb LAT intron during acute and latent infections of herpes simplex virus type-1. Virology 324: 340-349.
7. Perng GC, Jones C, (2010) Towards an understanding of the herpes simplex virus type 1 latency-reactivation cycle. Interdiscip Perspect Infect Dis 2010: 262415.
8. Bartel DP, (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
9. Krol J, Loedige I, Filipowicz W, (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11: 597-610.
10. Boss IW, Plaisance KB, Renne R, (2009) Role of virus-encoded microRNAs in herpesvirus biology. Trends Microbiol 17: 544-553.
11. Cullen BR, (2009) Viral and cellular messenger RNA targets of viral microRNAs. Nature 457: 421-425.
12. Ouellet DL, Plante I, Landry P, Barat C, Janelle ME, et al. (2008) Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res 36: 2353-2365.
13. Besecker MI, Harden ME, Li G, Wang XJ, Griffiths A, (2009) Discovery of herpes B virus-encoded microRNAs. J Virol 83: 3413-3416.
14. Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, et al. (2004) Identification of virus-encoded microRNAs. Science 304: 734-736.
15. Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, et al. (2005) Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proc Natl Acad Sci U S A 102: 5570-5575.
16. Grey F, Antoniewicz A, Allen E, Saugstad J, McShea A, et al. (2005) Identification and characterization of human cytomegalovirus-encoded microRNAs. J Virol 79: 12095-12099.
17. Cui C, Griffiths A, Li G, Silva LM, Kramer MF, et al. (2006) Prediction and identification of herpes simplex virus 1-encoded microRNAs. J Virol 80: 5499-5508.
18. Glazov EA, Horwood PF, Assavalapsakul W, Kongsuwan K, Mitchell RW, et al. (2010) Characterization of microRNAs encoded by the bovine herpesvirus 1 genome. J Gen Virol 91: 32-41.
19. Anselmo A, Flori L, Jaffrezic F, Rutigliano T, Cecere M, et al. (2011) Co-expression of host and viral microRNAs in porcine dendritic cells infected by the pseudorabies virus. PloS ONE 6: e17374.
20. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
21. Varkonyi-Gasic E, Hellens RP, (2011) Quantitative stem-loop RT-PCR for detection of microRNAs. Methods Mol Biol 744: 145-157.
22. Grundhoff A, Sullivan CS, (2011) Virus-encoded microRNAs. Virology 411: 325-343.
23. Umbach JL, Cullen BR, (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.
24. Riley KJ, Rabinowitz GS, Steitz JA, (2010) Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression. J Virol 84: 5148-5157.
25. Babic N, Mettenleiter TC, Ugolini G, Flamand A, Coulon P, (1994) Propagation of pseudorabies virus in the nervous system of the mouse after intranasal inoculation. Virology 204: 616-625.
26. Shi W, Hendrix D, Levine M, Haley B, (2009) A distinct class of small RNAs arises from pre-miRNA-proximal regions in a simple chordate. Nat Struct Mol Biol 16: 183-189.
27. Chen SJ, Chen GH, Chen YH, Liu CY, Chang KP, et al. (2010) Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing. PloS ONE 5: e12745.
28. Ghosh Z, Mallick B, Chakrabarti J, (2009) Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res 37: 1035-1048.
29. Betel D, Koppal A, Agius P, Sander C, Leslie C, (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 11: R90.
30. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105.
31. Taharaguchi S, Kobayashi T, Yoshino S, Ono E, (2002) Analysis of regulatory functions for the region located upstream from the latency-associated transcript (LAT) promoter of pseudorabies virus in cultured cells. Vet Microbiol 85: 197-208.
32. Cheung AK, (1991) Cloning of the latency gene and the early protein 0 gene of pseudorabies virus. J Virol 65: 5260-5271.
33. Enquist LW, (1999) Life beyond eradication: veterinary viruses in basic science. Arch Virol Suppl 15: 87-109.
34. Triboulet R, Mari B, Lin YL, Chable-Bessia C, Bennasser Y, et al. (2007) Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science 315: 1579-1582.
35. Wang FZ, Weber F, Croce C, Liu CG, Liao X, et al. (2008) Human cytomegalovirus infection alters the expression of cellular microRNA species that affect its replication. J Virol 82: 9065-9074.
36. Bartel DP, (2009) MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
37. Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, et al. (2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res 21: 203-215.
38. Jurak I, Kramer MF, Mellor JC, van Lint AL, Roth FP, et al. (2010) Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2. J Virol 84: 4659-4672.
39. Umbach JL, Strelow LI, Wong SW, Cullen BR, (2010) Analysis of rhesus rhadinovirus microRNAs expressed in virus-induced tumors from infected rhesus macaques. Virology 405: 592-599.
40. Volk N, Shomron N, (2011) Versatility of MicroRNA Biogenesis. PloS ONE 6: e19391.
41. Gottwein E, Cullen BR, (2008) Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell host & microbe 3: 375-387.
42. Chen D, Meng Y, Yuan C, Bai L, Huang D, et al. (2011) Plant siRNAs from introns mediate DNA methylation of host genes. RNA 17: 1012-1024.
43. Guo H, Zhou R, Xi Y, Xiao S, Chen H, (2009) Transcriptional suppression of IE180 and TK promoters by the EP0 of pseudorabies virus strains Ea and Fa. Virus Genes 38: 269-275.
44. Ou CJ, Wong ML, Huang C, Chang TJ, (2002) Suppression of promoter activity of the LAT gene by IE180 of pseudorabies virus. Virus genes 25: 227-239.
45. Jin L, Schnitzlein WM, Scherba G, (2000) Identification of the pseudorabies virus promoter required for latency-associated transcript gene expression in the natural host. J Virol 74: 6333-6338.
46. Stevens JG, Wagner EK, Devi-Rao GB, Cook ML, Feldman LT, (1987) RNA complementary to a herpesvirus alpha gene mRNA is prominent in latently infected neurons. Science 235: 1056-1059.
47. Farrell MJ, Dobson AT, Feldman LT, (1991) Herpes simplex virus latency-associated transcript is a stable intron. Proc Natl Acad Sci U S A 88: 790-794.
48. Steiner I, Mador N, Reibstein I, Spivack JG, Fraser NW, (1994) Herpes simplex virus type 1 gene expression and reactivation of latent infection in the central nervous system. Neuropathol Appl Neurobiol 20: 253-260.
49. Geenen K, Favoreel HW, Nauwynck HJ, (2005) Higher resistance of porcine trigeminal ganglion neurons towards pseudorabies virus-induced cell death compared with other porcine cell types in vitro. J Gen Virol 86: 1251-1260.
50. Chen HC, Fang LR, He QG, Jin ML, Suo XF, et al. (1998) Study on the isolation and identification of the Ea strain of pseudorabies virus. Act Vet Zootech Sinica 29: 156-161.
51. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, et al. (2005) Identification of microRNAs of the herpesvirus family. Nat Methods 2: 269-276.
52. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
53. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1.
54. Ye J, Fang L, Zheng H, Zhang Y, Chen J, et al. (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34: W293-297.
55. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, et al. (2004) GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715.