IRESite is an exhaustive, manually annotated non-redundant relational database focused on the IRES elements (Internal Ribosome Entry Site) and containing information not available in the primary public databases. IRES elements were originally found in eukaryotic viruses hijacking initiation of translation of their host. Later on, they were also discovered in 5'-untranslated regions of some eukaryotic mRNA molecules. Currently, IRESite presents up to 92 biologically relevant aspects of every experiment, e.g. the nature of an IRES element, its functionality/defectivity, origin, size, sequence, structure, its relative position with respect to surrounding protein coding regions, positive/negative controls used in the experiment, the reporter genes used to monitor IRES activity, the measured reporter protein yields/activities, and references to original publications as well as cross-references to other databases, and also comments from submitters and our curators. Furthermore, the site presents the known similarities to rRNA sequences as well as RNA-protein interactions. Special care is given to the annotation of promoter-like regions. The annotated data in IRESite are bound to mostly complete, full-length mRNA, and whenever possible, accompanied by original plasmid vector sequences. New data can be submitted through the publicly available web-based interface at http://www.iresite.org and are curated by a team of lab-experienced biologists.

Charles University Faculty of Science Department of Genetics and Microbiology Vinicna 5 Prague 2 128 44 Czech Republic

Zobrazit více v PubMed

Cevallos R.C., Sarnow P. Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J. Virol. 2005;79:677–683. PubMed PMC

Pisarev A.V., Shirokikh N.E., Hellen C.U. Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites. C. R. Biol. 2005;328:589–605. PubMed

Pelletier J., Sonenberg N. Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA. Nature. 1988;334:320–325. PubMed

Han B., Zhang J.T. Regulation of gene expression by internal ribosome entry sites or cryptic promoters: the eIF4G story. Mol. Cell. Biol. 2002;22:7372–7384. PubMed PMC

Verge V., Vonlanthen M., Masson J.M., Trachsel H., Altmann M. Localization of a promoter in the putative internal ribosome entry site of the Saccharomyces cerevisiae TIF4631 gene. RNA. 2004;10:277–286. PubMed PMC

Mauro V.P., Edelman G.M., Zhou W. Reevaluation of the conclusion that IRES-activity reported within the 5′ leader of the TIF4631 gene is due to promoter activity. RNA. 2004;10:895–897. discussion 898. PubMed PMC

Liu Z., Dong Z., Han B., Yang Y., Liu Y., Zhang J.T. Regulation of expression by promoters versus internal ribosome entry site in the 5′-untranslated sequence of the human cyclin-dependent kinase inhibitor p27kip1. Nucleic Acids Res. 2005;33:3763–3771. PubMed PMC

Hecht K., Bailey J.E., Minas W. Polycistronic gene expression in yeast versus cryptic promoter elements. FEMS Yeast Res. 2002;2:215–224. PubMed

Holcik M., Sonenberg N. Translational control in stress and apoptosis. Nature Rev. Mol. Cell Biol. 2005;6:318–327. PubMed

Komar A.A., Hatzoglou M. Internal ribosome entry sites in cellular mRNAs: mystery of their existence. J. Biol. Chem. 2005;280:23425–23428. PubMed

Johannes G., Carter M.S., Eisen M.B., Brown P.O., Sarnow P. Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray. Proc. Natl Acad. Sci. USA. 1999;96:13118–13123. PubMed PMC

Stoneley M., Willis A.E. Cellular internal ribosome entry segments: structures, trans-acting factors and regulation of gene expression. Oncogene. 2004;23:3200–3207. PubMed

Pickering B.M., Willis A.E. The implications of structured 5′ untranslated regions on translation and disease. Semin. Cell Dev. Biol. 2005;16:39–47. PubMed

Marash L., Kimchi A. DAP5 and IRES-mediated translation during programmed cell death. Cell Death Differ. 2005;12:554–562. PubMed

Spriggs K.A., Bushell M., Mitchell S.A., Willis A.E. Internal ribosome entry segment-mediated translation during apoptosis: the role of IRES-trans-acting factors. Cell Death Differ. 2005;12:585–591. PubMed

Holcik M. Targeting translation for treatment of cancer—a novel role for IRES? Curr. Cancer Drug Targets. 2004;4:299–311. PubMed

Blumenthal T. Operons in eukaryotes. Brief Funct. Genomic Proteomic. 2004;3:199–211. PubMed

Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer S., Tacker M., Schuster P. Fast folding and comparison of RNA secondary structures. Monatsheft für Chemie. 1994;125:167–188.

Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Res. 2005;33:D34–D38. PubMed PMC

Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Church D.M., DiCuccio M., Edgar R., Federhen S., Helmberg W., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2005;33:D39–D45. PubMed PMC

Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. PubMed PMC

Andreeva A., Howorth D., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 2004;32:D226–D229. PubMed PMC

Bonnal S., Boutonnet C., Prado-Lourenco L., Vagner S. IRESdb: the Internal Ribosome Entry Site database. Nucleic Acids Res. 2003;31:427–428. PubMed PMC

Mignone F., Grillo G., Licciulli F., Iacono M., Liuni S., Kersey P.J., Duarte J., Saccone C., Pesole G. UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2005;33:D141–D146. PubMed PMC

IRESite--a tool for the examination of viral and cellular internal ribosome entry sites

Firefly luciferase gene contains a cryptic promoter