HumanViCe: Host ceRNA network in virus infected cells in human

Frontiers in Genetics

Volumn 5, Issue JUL, 2014, Pages

  Ghosal, Suman ^a   Das, Shaoli ^a   Sen, Rituparno ^b   Chakrabarti, Jayprokas ^a,b  

^a DEPARTMENT OF MATERIALS SCIENCE   (India)

^b Gyanxet   (India)

Author keywords

aPOBEC; CeRNA; CircRNA; Host virus interaction; Immune response; lncRNA; MicroRNA; Virus

Indexed keywords

MICRORNA; MICRORNA 124; MICRORNA 155; NOTCH RECEPTOR; SMALL INTERFERING RNA;

ARTICLE; BK VIRUS; EPSTEIN BARR VIRUS; GENE EXPRESSION; GENE ONTOLOGY; GENE REGULATORY NETWORK; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HERPES VIRUS; HERPES VIRUS SAIMIRI; HUMAN CYTOMEGALOVIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNE RESPONSE; JC VIRUS; MERKEL CELL POLYOMAVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA INTERFERENCE; SIMIAN VIRUS 40; VIRULENCE; VIRUS CELL INTERACTION; VIRUS ENTRY; VIRUS INFECTION; VIRUS REPLICATION; WNT SIGNALING PATHWAY;

EID: 84906279462     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00249     Document Type: Article

References (48)

1. Bartel, D. P. (2009). MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233. doi: 10.1016/j.cell.2009.01.002
2. Berkhout, B., and Haasnoot, J. (2006). The interplay between virus infection and the cellular RNA interference machinery. FEBS Lett. 580, 2896-2902. doi: 10.1016/j.febslet.2006.02.070
3. Bhartiya, D., Pal, K., Ghosh, S., Kapoor, S., Jalali, S., Panwar, B., et al. (2013). lncRNome: a comprehensive knowledgebase of human long noncoding RNAs. Database (Oxford) 2013:bat034. doi: 10.1093/database/bat034
4. Breuer, K., Foroushani, A. K., Laird, M. R., Chen, C., Sribnaia, A., Lo, R., et al. (2013). InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Res. 41, D1228-D1233. doi: 10.1093/nar/gks1147
5. Cesana, M., Cacchiarelli, D., Legnini, I., Santini, T., Sthandier, O., Chinappi, M., et al. (2011). A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147, 358-369. doi: 10.1016/j.cell.2011.09.028
6. Cheshenko, N., Liu, W., Satlin, L. M., and Herold, B. C. (2005). Focal adhesion kinase plays a pivotal role in herpes simplex virus entry. J. Biol. Chem. 280, 31116-31125. doi: 10.1074/jbc.M503518200
7. Choy, E. Y., Siu, K. L., Kok, K. H., Lung, R. W., Tsang, C. M., To, K. F., et al. (2008). An Epstein-Barr virus-encoded microRNA targets PUMA to promote host cell survival. J. Exp. Med. 205, 2551-2560. doi: 10.1084/jem.20072581
8. Cui, C., Griffiths, A., Li, G., Silva, L. M., Kramer, M. F., Gaasterland, T., et al. (2006). Prediction and identification of herpes simplex virus 1-encoded microRNAs. J. Virol. 80, 5499-5508. doi: 10.1128/JVI.00200-06
9. Cullen, B. R. (2006). Viruses and microRNAs. Nat. Genet. 38, S25-S30. doi: 10.1038/ng1793
10. Dunn, W., Trang, P., Zhong, Q., Yang, E., van Belle, C., and Liu, F. (2005). Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol. 7, 1684-1695. doi: 10.1111/j.1462-5822.2005.00598.x
11. Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., et al. (2012). The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789. doi: 10.1101/gr.132159.111
12. Eden, E., Navon, R., Steinfeld, I., Lipson, D., and Yakhini, Z. (2009). GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10:48. doi: 10.1186/1471-2105-10-48
13. Gottwein, E., and Cullen, B. R. (2008). Viral and cellular microRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe 3, 375-387. doi: 10.1016/j.chom.2008.05.002
14. Gottwein, E., Mukherjee, N., Sachse, C., Frenzel, C., Majoros, W. H., Chi, J. T., et al. (2007). A viral microRNA functions as an orthologue of cellular miR-155. Nature 450, 1096-1099. doi: 10.1038/nature05992
15. Ghosal, S., Das, S., Sen, R., Basak, P., and Chakrabarti, J. (2013). Circ2Traits: a comprehensive database for circularRNApotentially associated with disease and traits. Front. Genet. 4:283. 2013. doi: 10.3389/fgene.2013.00283
16. Ghosh, Z., Mallick, B., and Chakrabarti, J. (2009). Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res. 37, 1035-1048. doi: 10.1093/nar/gkn1004
17. Griffiths-Jones, S. (2004). The microRNA registry. Nucleic Acids Res. 32, 109-111. doi: 10.1093/nar/gkh023
18. Griffiths-Jones, S., Saini, H. K., van Dongen, S., and Enright, A. J. (2008). miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154-D158. doi: 10.1093/nar/gkm952
19. Hansen, T. B., Kjems, J., and Damgaard, C. K. (2013). Circular RNA and miR-7 in Cancer. Cancer Res. 73, 5609-5612. doi: 10.1158/0008-5472.CAN-13-1568
20. Hayward, S. D. (2004). Viral interactions with the Notch pathway. Semin. Cancer Biol. 14, 387-396. doi: 10.1016/j.semcancer.2004.04.018
21. Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., and Schuster, P. (1994). Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125, 167-188. doi: 10.1007/BF00818163
22. Jeggari, A., Marks, D. S., and Larsson, E. (2012). miRcode: a map of putative microRNA target sites in the long non-coding transcriptome. Bioinformatics 28, 2062-2063. doi: 10.1093/bioinformatics/bts344
23. Kallen, A. N., Zhou, X. B., Xu, J., Qiao, C., Ma, J., Yan, L., et al. (2013). The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol. Cell 52, 101-112. doi: 10.1016/j.molcel.2013.08.027
24. Karreth, F. A., Tay, Y., Perna, D., Ala, U., Tan, S. M., Rust, A. G., et al. (2011). In vivo identification of tumor- suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147, 382-395. doi: 10.1016/j.cell.2011.09.032
25. Kim, H., Park, S., Min, H., and Yoon, S. (2012). vHoT: a database for predicting interspecies interactions between viral microRNA and host genomes. Arch. Virol. 157, 497-501. doi: 10.1007/s00705-011-1181-y
26. Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001). An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294, 858-862. doi: 10.1126/science.1065062
27. Lee, R. C., Feinbaum, R. L., and Ambros, V. (1993). The C. Elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854. doi: 10.1016/0092-8674(93)90529-Y
28. Lewis, B. P., Burge, C. B., and Bartel, D. P. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20. doi: 10.1016/j.cell.2004.12.035
29. Li, J. H., Liu, S., Zhou, H., Qu, L. H., and Yang, J. H. (2014). starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 42, D92-D97. doi: 10.1093/nar/gkt1248
30. German, M. A., Pillay, M., Jeong, D. H., Hetawal, A., Luo, S., Janardhanan, P., et al. (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol. 8, 941-946. doi: 10.1038/nbt1417
31. Memczak, S., Jens, M., Elefsinioti, A., Torti, A., Krueger, J., Rybak, A., et al. (2013). Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333-338. doi: 10.1038/nature11928
32. Nair, V., and Zavolan, M. (2006). Virus-encoded microRNAs: novel regulators of gene expression. Trends Microbiol. 14, 169-175. doi: 10.1016/j.tim.2006.02.007
33. Nam, J. W., Rissland, O. S., Koppstein, D., Abreu-Goodger, C., Jan, C. H., Agarwal, V., et al. (2014). Global analyses of the effect of different cellular contexts on microRNA targeting. Mol. Cell 53, 1031-1043. doi: 10.1016/j.molcel.2014.02.013
34. Paraskevopoulou, M. D., Georgakilas, G., Kostoulas, N., Reczko, M., Maragkakis, M., Dalamagas, T. M., et al. (2013). DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 41, D239-D245. doi: 10.1093/nar/gks1246
35. Pfeffer, S., Zavolan, M., Grasser, F. A., Chien, M., Russo, J. J., Ju, J., et al. (2004). Identification of virus-encoded microRNAs. Science 304, 734-736. doi: 10.1126/science.1096781
36. Samols, M. A., Skalsky, R. L., Maldonado, A. M., Riva, A., Lopez, M. C., Baker, H. V., et al. (2007). Identification o cellular genes targeted by KSHV-encoded microRNAs. PLoS Pathog. 3:e65. doi: 10.1371/journal.ppat.0030065
37. Sarver, A. L., and Subramanian, S. (2012). Competing endogenous RNA database. Bioinformation 8, 731-733. doi: 10.6026/97320630008731
38. Shackelford, J., and Pagano, J. S. (2004). Tumor viruses and cell signaling pathways: deubiquitination versus ubiquitination. Mol. Cell. Biol. 24, 5089-5093. doi: 10.1128/MCB.24.12.5089-5093.2004
39. Skalsky, R. L., Samols, M. A., Plaisance, K. B., Boss, I. W., Riva, A., Lopez, M. C., et al. (2007). Kaposi's sarcomaassociated herpesvirus encodes an ortholog of miR-155. J. Virol. 81, 12836-12845. doi: 10.1128/JVI.01804-07
40. Sumazin, P., Yang, X., Chiu, H. S., Chung, W. J., Iyer, A., Llobet-Navas, D., et al. (2011). An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147, 370-381. doi: 10.1016/j.cell.2011.09.041
41. Tay, Y., Kats, L., Salmena, L., Weiss, D., Tan, S. M., Ala, U., et al. (2011). Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147, 344-357. doi: 10.1016/j.cell.2011.09.029
42. Tokarev, A., and Guatelli, J. (2011). Misdirection of membrane trafficking by HIV-1 Vpu and Nef: keys to viral virulence and persistence. Cell Logist. 1, 90-102. doi: 10.4161/cl.1.3.16708
43. Umbach, J. L., Kramer, M. F., Jurak, I., Karnowski, H. W., Coen, D. M., and Cullen, B. R. (2008). MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature 454, 780-783. doi: 10.1038/nature07103
44. Wang, J., Liu, X., Wu, H., Ni, P., Gu, Z., Qiao, Y., et al. (2010). CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res. 38, 5366-5383. doi: 10.1093/nar/gkq285
45. Xia, T., O'Hara, A., Araujo, I., Barreto, J., Carvalho, E., Sapucaia, J. B., et al. (2008). EBV microRNAs in primary lymphomas and targeting of CXCL-11 by ebv-mir-BHRF1-3. Cancer Res. 68, 1436-1442. doi: 10.1158/0008-5472.CAN-07-5126
46. Xiao, C., and Rajewsky, K. (2009). MicroRNA control in the immune system: basic principles. Cell 136, 26-36. doi: 10.1016/j.cell.2008.12.027
47. Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., et al. (2011). KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39, W316-W322. doi: 10.1093/nar/gkr483
48. Zhang, R., and Su, B. (2008). MicroRNA regulation and the variability of human cortical gene expression. Nucleic Acids Res. 36, 4621-4628. doi: 10.1093/nar/gkn431