What is ViTa ?
ViTa is a database which collects virus data from miRBase and ICTV, VirGne, VBRC.., etc, including known miRNAs
on virus and supporting predicted host miRNA targets by miRanda and TargetScan. ViTa also provide effective annotations,
including human miRNA expression, virus infected tissues, annotation of virus and comparisons. Additionally, a
multiple functions and graphical web interface are designed and implemented to help users to investigate the microRNA
roles in viral existence. ViTa is developed by Bidlab(2005), and will be maintain and update. More and more disease is
supported in future.
 Data Generation Flow
miRNAs are produced from viruses
Virus can produce miRNAs after infecting. The main function may escape host T cell, and reduce its
expression, but not infective activity, and exist synchronous. For example, HIV is a famous virus
which causes AIDS, can encode nef miRNAs that repress HIV's T antigen, but maintain its' infection.
Relationship between miRNA and virus
MicroRNAs have multiple roles in regulation
of post-transcripts, which are ~ 22 nt long non-coding RNAs
found in all metazoan eukaryotes. Now, miRNAs are also produced
from and viruses in mammalian. The possible role
is to assist in escaping from host immunity mechanism by decreasing
its activity (Omoto, Ito et al. 2004) or regulating host mRNAs.
Under powerful function of microRNAs/siRNAs in mammals, we try to
collect virus data from other databases, and predict putative
miRNAs on viruses to look for potential relationships between
existence of influenza viruses and miRNAs, which are produced
from its own or helper viruses. |
Infection of HIV |
Why to find host miRNA targets on virus ?
Recently, miRNAs are discovered to affect viral existence by targeting to viruses after entering hosts,
such as hepatitis C virus(Jopling, Yi et al. 2005) and HIV(Hariharan, Scaria et al. 2005). Human miR-122a
appears to assist HCV replicate in host by targeting to 3’ UTR on HCV genome. Oppositely, HIV is suppressed
by targeting several genes by human microRNAs. These tell us human microRNAs as regulators for affecting
life cycle of viruses in host. And the relationship between viruses and host miRNAs is worthy to further
research for potential therapy.
Application
The database will be developed as follows. (i) It will be made to support miRNA annotations including miRNA
genes and miRNA targets on viruses for other hosts, not only human, mouse, rat and chicken; (ii) The ViTa data
will be further analyzed to support the miRNAs involved in the combinatorial control of the expression of
infecting viruses. (iii) A complete relationship between viruses and diseases are contained later.
1. Ambros, V., B. Bartel, et al. (2003). "A uniform system for microRNA annotation." Rna 9(3): 277-9.
Bartel, D. P. (2004). "MicroRNAs: genomics, biogenesis, mechanism, and function." Cell 116(2): 281-97.
Buchen-Osmond, C. (2003). "The universal virus database ICTVdB." COMPUTING IN SCIENCE & ENGINEERING
5(3): 16-25.
2. Griffiths-Jones, S. (2004). "The microRNA Registry." Nucleic Acids Res 32(Database issue): D109-11.
3. Griffiths-Jones, S., R. J. Grocock, et al. (2006). "miRBase: microRNA sequences, targets and gene
nomenclature." Nucleic Acids Res 34(Database issue): D140-4.
4. Hariharan, M., V. Scaria, et al. (2005). "Targets for human encoded microRNAs in HIV genes." Biochem
Biophys Res Commun 337(4): 1214-8.
5. Hofacker, I. L. (2003). "Vienna RNA secondary structure server." Nucleic Acids Res 31(13): 3429-31.
6. Hsu, P. W., H. D. Huang, et al. (2006). "miRNAMap: genomic maps of microRNA genes and their target
genes in mammalian genomes." Nucleic Acids Res 34(Database issue): D135-9.
7. John, B., A. J. Enright, et al. (2004). "Human MicroRNA targets." PLoS Biol 2(11): e363.
8. Jopling, C. L., M. Yi, et al. (2005). "Modulation of hepatitis C virus RNA abundance by a liver-
specific MicroRNA." Science 309(5740): 1577-81.
9. Krek, A., D. Grun, et al. (2005). "Combinatorial microRNA target predictions." Nat Genet 37(5): 495-
500.
10. Kulkarni-Kale, U., S. Bhosle, et al. (2004). "VirGen: a comprehensive viral genome resource." Nucleic
Acids Res 32(Database issue): D289-92.
11. Lecellier, C. H., P. Dunoyer, et al. (2005). "A cellular microRNA mediates antiviral defense in human
cells." Science 308(5721): 557-60.
12. Lefkowitz, E. J., C. Upton, et al. (2005). "Poxvirus Bioinformatics Resource Center: a comprehensive
Poxviridae informational and analytical resource." Nucleic Acids Res 33(Database issue): D311-6.
13. Lewis, B. P., C. B. Burge, et al. (2005). "Conserved seed pairing, often flanked by adenosines,
indicates that thousands of human genes are microRNA targets." Cell 120(1): 15-20.
14. Lewis, B. P., I. H. Shih, et al. (2003). "Prediction of mammalian microRNA targets." Cell 115(7): 787-98.
Lu, J., G. Getz, et al. (2005). "MicroRNA expression profiles classify human cancers." Nature 435(7043):
834-8.
15. Neilson, J. R. and P. A. Sharp (2005). "Herpesviruses throw a curve ball: new insights into microRNA
biogenesis and evolution." Nat Methods 2(4): 252-4.
16. Rehmsmeier, M., P. Steffen, et al. (2004). "Fast and effective prediction of microRNA/target duplexes."
Rna 10(10): 1507-17.
17. Thompson, J. D., D. G. Higgins, et al. (1994). "CLUSTAL W: improving the sensitivity of progressive
multiple sequence alignment through sequence weighting, position-specific gap penalties and weight
matrix choice." Nucleic Acids Res 22(22): 4673-80.
18. Washietl, S., I. L. Hofacker, et al. (2005). "Fast and reliable prediction of noncoding RNAs." Proc
Natl Acad Sci U S A 102(7): 2454-9.
19. Zuker, M. (2003). "Mfold web server for nucleic acid folding and hybridization prediction." Nucleic
Acids Res 31(13): 3406-15.
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