Long non-coding RNAs in infection biology

Frontiers in Genetics

Volumn 3, Issue JAN, 2013, Pages

  Scaria, Vinod ^a   Pasha, Ayesha ^b  

^a CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

^b NATIONAL CHEMICAL LABORATORY   (India)

Author keywords

Host pathogen interactions; Immune; Infection; Long non coding RNA; Pathogen

Indexed keywords

EID: 84876175729     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00308     Document Type: Short Survey

References (57)

1. Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., et al. (2009). Unbiased reconstruction of a mammalian transcriptional network mediating the differential response to pathogens. Science 326, 257-263.
2. Andersson, M. G., Haasnoot, P. C., Xu, N., Berenjian, S., Berkhout, B., and Akusjärvi, G. (2005). Suppression of RNA interference by adenovirus virus-associated RNA. J. Virol. 79, 9556-9565.
3. Ascano, M., Hafner, M., Cekan, P., Gerstberger, S., and Tuschl, T. (2012). Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip. Rev. RNA 3, 159-177.
4. Avrova, A. O., Whisson, S. C., Pritchard, L., Venter, E., De Luca, S., Hein, I., et al. (2007). A novel non-protein-coding infection-specific gene family is clustered throughout the genome of Phytophthora infestans. Microbiology 153(Pt 3), 747-759.
5. Bari, L., Bacsa, S., Sonkoly, E., Bata-Csörgo, Z., Kemény, L., Dobozy, A., et al. (2011). Comparison of stress-induced PRINS gene expression in normal human keratinocytes and HaCaT cells. Arch. Dermatol. Res. 303,745-752.
6. Biffi, G., Tannahill, D., and Balasubramanian, S. (2012). An intramolecular G-quadruplex structure is required for binding of telom-eric repeat-containing RNA to the telomeric protein TRF2. J. Am. Chem. Soc. 134, 11974-11976.
7. Broadbent, K. M., Park, D., Wolf, A. R., Van Tyne, D., Sims, J. S., Ribacke, U., et al. (2011). A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 12, R56.
8. Brunner, A. L., Beck, A. H., Edris, B., Sweeney, R. T., Zhu, S. X., Li, R., et al. (2012). Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol. 13,R75.
9. Buck, A. H., Perot, J., Chisholm, M. A., Kumar, D. S., Tuddenham, L., Cognat, V., et al. (2010). Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection. RNA 16, 307-315.
10. Cazalla, D., Yario, T., and Steitz, J. A. (2010). Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA. Science 328, 1563-1566.
11. Chan, K. Y., Wong, C. M., Kwan, J. S., Lee, J. M., Cheung, K. W., Yuen, M. F., et al. (2011). Genome-wide association study of hepatocellular carcinoma in Southern Chinese patients with chronic hepatitis B virus infection. PLoS ONE 6:e28798. doi:10.1371/journal.pone.0028798
12. Chaudhary, G., and Ratner, L. (2011). The HTLV-1 hbz antisense gene indirectly promotes tax expression via down-regulation of p30(II) mRNA. Virology 410, 307-315.
13. Cook, H. L., Lytle, J. R., Mischo, H. E., Li, M. J., Rossi, J. J., Silva, D. P., et al. (2005). Small nuclear RNAs encoded by Herpesvirus saimiri upregulate the expression of genes linked to T cell activation in virally transformed T cells. Curr. Biol. 15,974-979.
14. Dalmasso, C., Carpentier, W., Meyer, L., Rouzioux, C., Goujard, C., Chaix, M. L., et al. (2008). Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. PLoS ONE 3:e3907. doi:10.1371/journal.pone.0003907
15. Farbrother, P., Wagner, C., Na, J., Tunggal, B., Morio, T., Urushihara, H., et al. (2006). Dictyostelium transcriptional host cell response upon infection with Legionella. Cell. Microbiol. 8,438-456.
16. Franko-Zorilla, J. M., Valli, A., Todesco, M., Mateos, I., Puga, M. I., Rubio-Somoza, I., et al. (2007). Target mimicry provides a new mechanism for the regulation of microRNA activity. Nat. Genet. 39, 1033-1037.
17. Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P.,et al. (2010).PAR-CliP-amethod to identify transcriptome-wide the binding sites of RNA binding proteins. J. Vis. Exp. 41, pii 2034. doi:10.3791/2034
18. Hung,T., and Chang, H. Y. (2010). Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol. 7, 582-585.
19. Iwakiri, D., and Takada, K. (2010). Role of EBERs in the pathogenesis of EBV infection. Adv. Cancer Res. 107, 119-136.
20. Iwakiri, D., Zhou, L., Samanta, M., Matsumoto, M., Ebihara, T., Seya, T., et al. (2009). Epstein-Barr virus (EBV)-encoded small RNA is released from EBV-infected cells and activates signaling from Toll-like receptor 3. J. Exp. Med. 206, 2091-2099.
21. Jalali, S., Gunanathan, G., and Scaria, V. (2012). Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs. Biol. Direct 7, 25.
22. Kapranov, P., Sementchenko, V. I., and Gingeras, T. R. (2003). Beyond expression profiling: next generation uses of high density oligonucleotide arrays. Brief. Funct. Genomic. Pro-teomic. 2,47-56.
23. Kapranov, P., and St Laurent, G. (2012). Dark matter RNA: existence, function, and controversy. Front. Genet. 3:60. doi:10.3389/fgene.2012.00060
24. Keene, J. D. (1985). Interactions between small viral RNAs of vesicular stomatitis virus and components of cellular gene expression. Microbiol. Sci. 2,152-156.
25. Lee, H., and Schatz, M. C. (2012). Genomic dark matter: the reliability of short read mapping illustrated by the genome map-pability score. Bioinformatics 28, 2097-2105.
26. Limou, S., Le Clerc, S., Coulonges, C., Carpentier, W., Dina, C., Delaneau, O., et al. (2009). Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS genomewide association study 02).J. Infect. Dis. 199,419-426.
27. Lipovich, L., Johnson, R., and Lin, C. Y. (2010). MacroRNA underdogs in a microRNA world: evolutionary, regulatory, and biomedical significance of mammalian long non-protein-coding RNA. Biochim. Biophys. Acta 1799,597-615.
28. Liu, Y., Pan, S., Liu, L., Zhai, X., Liu, J., Wen, J., et al. (2012). A genetic variant in long non-coding RNA HULC contributes to risk of HBV-related hepatocellular carcinoma in a Chinese population. PLoS ONE 7:e35145. doi:10.1371/ journal.pone.0035145
29. McGinnis, J. L., Dunkle, J. A., Cate, J. H., and Weeks, K. M. (2012). The mechanisms of RNA SHAPE chemistry. J. Am. Chem. Soc. 134, 6617-6624.
30. McKenna, S. A., Kim, I., Liu, C. W., and Puglisi, J. D. (2006). Uncoupling of RNA binding and PKR kinase activation by viral inhibitor RNAs. J. Mol. Biol. 358, 1270-1285.
31. Moran, V. A., Perera, R. J., and Khalil,A. M. (2012). Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res. 40, 6391-6400.
32. Nakano, K., and Watanabe, T. (2012). HTLV-1 Rex: the courier of viral messages making use of the host vehicles. Front. Microbiol. 3:330. doi:10.3389/fmicb.2012.00330
33. Nanbo, A., Yoshiyama, H., and Takada, K. (2005). Epstein-Barr virus-encoded poly(A)- RNA confers resistance to apoptosis mediated through Fas by blocking the PKR pathway in human epithelial intestine 407 cells. J. Virol. 79, 12280-12285.
34. Pang, K. C., Dinger, M. E., Mercer, T. R., Malquori, L., Grimmond, S. M., Chen, W., et al. (2009). Genomewide identification of long non-coding RNAs in CD8+ T cells. J. Immunol. 182, 7738-7748.
35. Peng, X., Gralinski, L., Armour, C. D., Ferris, M. T., Thomas, M. J., Proll, S., et al. (2010). Unique signatures of long noncoding RNA expression in response to virus infection and altered innate immune signaling. MBio 1,e00206-e00210.
36. Ravasi, T., Suzuki, H., Cannistraci, C.V., Katayama, S., Bajic, V. B., Tan, K., et al. (2010). An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140, 744-752.
37. Rederstorff, M., and Hüttenhofer, A. (2010). Small non-coding RNAs in disease development and host-pathogen interactions. Curr. Opin. Mol. Ther. 12, 684-694.
38. Reeves, M. B., Davies, A. A., McSharry, B. P., Wilkinson, G. W., and Sinclair, J.H. (2007). Complex I binding by a virally encoded RNA regulates mitochondria-induced cell death. Science 316, 1345-1348.
39. Rende, F., Cavallari, I., Corradin, A., Silic-Benussi, M., Toulza, F., Toffolo, G. M., et al. (2011). Kinetics and intracellular compartmentalization of HTLV-1 gene expression: nuclear retention of HBZ mRNAs. Blood 117,4855-4859.
40. Saha, S., Murthy, S., and Rangarajan, P. N. (2006). Identification and characterization of avirus-inducible non-coding RNA in mouse brain. J. Gen. Virol. 87(Pt 7), 1991-1995.
41. Sano, M., Kato, Y., and Taira, K. (2006). Sequence-specific interference by small RNAs derived from adenovirus VAI RNA. FEBSLett. 580, 1553-1564.
42. Sati, S., Ghosh, S., Jain, V., Scaria, V., and Sengupta, S. (2012). Genomewide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci. Nucleic Acids Res. 40, 10018-10031.
43. Scaria, V., Hariharan, M., Maiti, S., Pillai, B., and Brahmachari, S. K. (2006). Host-virus interaction: a new role for microRNAs. Retrovirology 3:68. doi:10.1186/1742-4690-3-68
44. Scheibe, M., Butter, F., Hafner, M., Tuschl, T., and Mann, M. (2012). Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions. Nucleic Acids Res. 40, 1-6.
45. Shapira, S. D., Gat-Viks, I., Shum, B.O.V., Dricot, A., de Grace, M. M., Wu, L. (2009). A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 139,1255-1267.
46. Sierra-Miranda, M., Delgadillo, D. M., Mancio-Silva, L., Vargas, M., Villegas-Sepulveda, N., Martínez-Calvillo, S., et al. (2012). Two long non-coding RNAs generated from subtelomeric regions accumulate in a novel perinuclear compartment in Plasmodium falciparum. Mol. Biochem. Parasitol. 185, 36-47.
47. Sonkoly, E., Bata-Csorgo,Z., Pivarcsi, A., Polyanka, H., Kenderessy-Szabo, A., Molnar, G., et al. (2005). Identification and characterization of a novel, psoriasis susceptibility-related non-coding RNA gene, PRINS. J. Biol. Chem. 280,24159-24167.
48. Vigneau, S., Rohrlich, P. S., Brahic, M., and Bureau, J. E (2003). Tmevpg1, a candidate gene for the control of Theiler's virus persistence, could be implicated in the regulation of gamma interferon. J. Virol. 77, 5632-5638.
49. Wang, K. C., and Chang, H. Y. (2011). Molecular mechanisms of long noncoding RNAs. Mol. Cell 43, 904-914.
50. Wen, J., Parker, B. J., Jacobsen, A., and Krogh, A. (2011). MicroRNA trans-fection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA 17, 820-834.
51. Weng, H. Y., Huang, H. L., Zhao, P. P., Zhou, H., and Qu, L. H. (2012). Translational repression of cyclin D3 by a stable G-quadruplex in its 5′ UTR: implications for cell cycle regulation. RNA Biol. 9, 1099-1109.
52. Xu, N., Segerman, B., Zhou, X., and Akusjärvi, G. (2007). Ade-novirus virus-associated RNAII-derived small RNAs are efficiently incorporated into the RNA-induced silencing complex and associate with polyribosomes. J. Virol. 81, 10540-10549.
53. Yamasaki, C., Murakami, K., and Takeda, J. (2010). H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res. 38, D626-D632.
54. Yan, B., and Wang, Z. (2012). Long non-coding RNA: its physiological and pathological roles. DNA Cell Biol. 31(Suppl. 1),S34-S41.
55. Yeo, G. W., Coufal, N. G., Liang, T. Y., Peng, G. E., Fu, X. D., and Gage, E H. (2009). An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat. Struct. Mol. Biol. 16, 130-137.
56. Yu, E. Z., Burba, A. E., and Gerstein, M. (2007). PARE: a tool for comparing protein abundance and mRNA expression data. BMCBioinformatics 8:309. doi:10.1186/1471-2105-8-309
57. Zhao, J., Sinclair, J., Houghton, J., Bolton, E., Bradley, A., and Lever, A. (2010). Cytomegalovirus beta2.7 RNA transcript protects endothe-lial cells against apoptosis during ischemia/reperfusion injury. J. Heart Lung Transplant. 29, 342-345.