Co-expression of host and viral microRNAs in porcine dendritic cells infected by the pseudorabies virus

PLoS ONE

Volumn 6, Issue 3, 2011, Pages

  Anselmo, Anna ^a   Flori, Laurence ^b   Jaffrezic, Florence ^b   Rutigliano, Teresa ^a   Cecere, Maria ^a   Cortes Perez, Naima ^b   Lefèvre, François ^c   Rogel Gaillard, Claire ^b,d   Giuffra, Elisabetta ^a,b  

^a PARCO TECNOLOGICO PADANO   (Italy)

^b UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^c INRA Institut National de la Recherche Agronomique   (France)

^d DIF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; VIRUS RNA; MESSENGER RNA; MICRORNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DENDRITIC CELL; DOWN REGULATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE INSERTION; GENE MAPPING; GENE REPLICATION; GENE SEQUENCE; GENETIC HETEROGENEITY; LATENT PERIOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PSEUDORABIES HERPETOVIRUS; SEQUENCE ALIGNMENT; TRANSCRIPTION REGULATION; UPREGULATION; VIRUS CELL INTERACTION; ANIMAL; BIOLOGICAL MODEL; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; GENOME; HOST PATHOGEN INTERACTION; METABOLISM; MOLECULAR GENETICS; PSEUDORABIES; SWINE; SWINE DISEASE; VIROLOGY;

ANIMALIA; HERPESVIRIDAE; SUID HERPESVIRUS 1; SUIDAE; SUS;

ANIMALS; BASE SEQUENCE; DENDRITIC CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENOME; HERPESVIRUS 1, SUID; HOST-PATHOGEN INTERACTIONS; MICRORNAS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PSEUDORABIES; RNA, MESSENGER; RNA, VIRAL; SUS SCROFA; SWINE; SWINE DISEASES;

EID: 79952384277     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0017374     Document Type: Article

References (55)

1. Olena AF, Patton JG, (2010) Genomic organization of microRNAs. J Cell Physiol 222: 540-545.
2. Umbach JL, Wang K, Tang S, Krause PR, Mont EK, et al. (2010) Identification of viral microRNAs expressed in human sacral ganglia latently infected with herpes simplex virus 2. J Virol 84: 1189-1192.
3. Umbach JL, Cullen BR, (2009) The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev 23: 1151-1164.
4. Boss IW, Plaisance KB, Renne R, (2009) Role of virus-encoded microRNAs in herpesvirus biology. Trends Microbiol 17: 544-553.
5. Bloom DC, Giordani NV, Kwiatkowski DL, (2010) Epigenetic regulation of latent HSV-1 gene expression. Biochim Biophys Acta 1799: 246-256.
6. 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.
7. 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.
8. Skalsky RL, Cullen BR, (2010) Viruses, microRNAs, and host interactions. Annu Rev Microbiol 64: 123-141.
9. Cullen BR, (2009) Viral and cellular messenger RNA targets of viral microRNAs. Nature 457: 421-425.
10. Umbach JL, Cullen BR, (2009) In-depth analysis of KSHV microRNA expression provides insights into the mammalian microRNA processing machinery. J Virol 84: 695-703.
11. 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.
12. Umbach JL, Kramer MF, Jurak I, Karnowski HW, Coen DM, et al. (2008) MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454: 780-783.
13. Guo X, Su B, Zhou Z, Sha J, (2009) Rapid evolution of mammalian X-linked testis microRNAs. BMC Genomics 10: 97.
14. Umbach JL, Wang K, Tang S, Krause PR, Mont EK, et al. (2010) Identification of viral microRNAs expressed in human sacral ganglia latently infected with herpes simplex virus 2. J Virol 84: 1189-1192.
15. 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.
16. Flori L, Rogel-Gaillard C, Cochet M, Lemonnier G, Hugot K, et al. (2008) Transcriptomic analysis of the dialogue between Pseudorabies virus and porcine epithelial cells during infection. BMC Genomics 9: 123.
17. Flori L, Rogel-Gaillard C, Mariani V, Lemonnier G, Cochet M, et al. (2008) A combined transcriptomic approach to analyse the dialogue between pseudorabies virus and porcine cells. Dev Biol (Basel) 132: 99-104.
18. Brukman A, Enquist LW, (2006) Pseudorabies virus EP0 protein counteracts an interferon-induced antiviral state in a species-specific manner. J Virol 80: 10871-10873.
19. Steinman RM, Hemmi H, (2006) Dendritic cells: translating innate to adaptive immunity. Curr Top Microbiol Immunol 311: 17-58.
20. Takeuchi O, Akira S, (2009) Innate immunity to virus infection. Immunol Rev 227: 75-86.
21. Freer G, Matteucci D, (2009) Influence of dendritic cells on viral pathogenicity. PLoS Pathog 5: e1000384.
22. McCullough KC, Ruggli N, Summerfield A, (2009) Dendritic cells-at the front-line of pathogen attack. Vet Immunol Immunopathol 128: 7-15.
23. Carrasco CP, Rigden RC, Schaffner R, Gerber H, Neuhaus V, et al. (2001) Porcine dendritic cells generated in vitro: morphological, phenotypic and functional properties. Immunology 104: 175-184.
24. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
25. Burnside J, Bernberg E, Anderson A, Lu C, Meyers BC, et al. (2006) Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J Virol 80: 8778-8786.
26. Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, et al. (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
27. Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, et al. (2010) Characterization of the Melanoma miRNAome by Deep Sequencing. PLoS One 5: e9685.
28. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18: 610-621.
29. John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA targets. PLoS Biol 2: e363.
30. Lewis BP, Burge CB, Bartel DP, (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
31. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E, (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284.
32. Kozomara A, Griffiths-Jones S, (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
33. Das S, (2009) Evolutionary origin and genomic organization of micro-RNA genes in immunoglobulin lambda variable region gene family. Mol Biol Evol 26: 1179-1189.
34. Smith CM, Steitz JA, (1998) Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5′-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol Cell Biol 18: 6897-6909.
35. Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, et al. (2010) Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics 11: 288.
36. Szczyrba J, Loprich E, Wach S, Jung V, Unteregger G, et al. (2010) The microRNA profile of prostate carcinoma obtained by deep sequencing. Mol Cancer Res 8: 529-538.
37. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, et al. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
38. Hashimi ST, Fulcher JA, Chang MH, Gov L, Wang S, et al. (2009) MicroRNA profiling identifies miR-34a and miR-21 and their target genes JAG1 and WNT1 in the coordinate regulation of dendritic cell differentiation. Blood 114: 404-414.
39. Cekaite L, Clancy T, Sioud M, (2010) Increased miR-21 expression during human monocyte differentiation into DCs. Front Biosci (Elite Ed) 2: 818-828.
40. Koh W, Sheng CT, Tan B, Lee QY, Kuznetsov V, et al. (2010) Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of hepatic nuclear factor 4 alpha. BMC Genomics 11 (Suppl 1): S6.
41. Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, et al. (2009) Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA 15: 2147-2160.
42. Bai ZQ, Lei XF, Wang LD, Gao SJ, (2008) Identification and Function of MicroRNAs Encoded by Herpesviruses. Virol Sin 23: 459-472.
43. Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, et al. (2004) Identification of virus-encoded microRNAs. Science 304: 734-736.
44. Tang S, Patel A, Krause PR, (2009) Novel less-abundant viral microRNAs encoded by herpes simplex virus 2 latency-associated transcript and their roles in regulating ICP34.5 and ICP0 mRNAs. J Virol 83: 1433-1442.
45. Umbach JL, Nagel MA, Cohrs RJ, Gilden DH, Cullen BR, (2009) Analysis of human alphaherpesvirus microRNA expression in latently infected human trigeminal ganglia. J Virol 83: 10677-10683.
46. Kent JR, Kang W, Miller CG, Fraser NW, (2003) Herpes simplex virus latency-associated transcript gene function. J Neurovirol 9: 285-290.
47. Moens U, (2009) Silencing viral microRNA as a novel antiviral therapy? J Biomed Biotechnol 2009: 419539.
48. Kwiatkowski DL, Thompson HW, Bloom DC, (2009) The polycomb group protein Bmi1 binds to the herpes simplex virus 1 latent genome and maintains repressive histone marks during latency. J Virol 83: 8173-8181.
49. Song W, Tao K, Li H, Jin C, Song Z, et al. (2010) Bmi-1 is related to proliferation, survival and poor prognosis in pancreatic cancer. Cancer Sci 101: 1754-1760.
50. Derfuss T, Meinl E, (2002) Herpesviral proteins regulating apoptosis. Curr Top Microbiol Immunol 269: 257-272.
51. Heidari M, Sarson AJ, Huebner M, Sharif S, Kireev D, et al. (2010) Marek's disease virus-induced immunosuppression: array analysis of chicken immune response gene expression profiling. Viral Immunol 23: 309-319.
52. Ji J, Glaser A, Wernli M, Berke JM, Moradpour D, et al. (2008) Suppression of short interfering RNA-mediated gene silencing by the structural proteins of hepatitis C virus. J Gen Virol 89: 2761-2766.
53. Riteau B, de Vaureix C, Lefevre F, (2006) Trypsin increases pseudorabies virus production through activation of the ERK signalling pathway. J Gen Virol 87: 1109-1112.
54. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, et al. (2003) A uniform system for microRNA annotation. RNA 9: 277-279.
55. Robinson MD, Smyth GK, (2007) Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23: 2881-2887.