title: SIREs: searching for iron-responsive elements.
abstract: The iron regulatory protein/iron-responsive element regulatory system plays a crucial role in the post-transcriptional regulation of gene expression and its disruption results in human disease. IREs are cis-acting regulatory motifs present in mRNAs that encode proteins involved in iron metabolism. They function as binding sites for two related trans-acting factors, namely the IRP-1 and -2. Among cis-acting RNA regulatory elements, the IRE is one of the best characterized. It is defined by a combination of RNA sequence and structure. However, currently available programs to predict IREs do not show a satisfactory level of sensitivity and fail to detect some of the functional IREs. Here, we report an improved software for the prediction of IREs implemented as a user-friendly web server tool. The SIREs web server uses a simple data input interface and provides structure analysis, predicted RNA folds, folding energy data and an overall quality flag based on properties of well characterized IREs. Results are reported in a tabular format and as a schematic visual representation that highlights important features of the IRE. The SIREs (Search for iron-responsive elements) web server is freely available on the web at http://ccbg.imppc.org/sires/index.html.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Monica
authors.initials: M
authors.lastname: Campillos
authors.forename: Ildefonso
authors.initials: I
authors.lastname: Cases
authors.forename: Matthias W
authors.initials: MW
authors.lastname: Hentze
authors.forename: Mayka
authors.initials: M
authors.lastname: Sanchez
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D006801:Humans; D020407:Internet; D007501:Iron / Q000378:metabolism; D035925:Iron-Regulatory Proteins / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D012984:Software; D020506:Untranslated Regions
chemical_list: D035925:Iron-Regulatory Proteins; D038621:Regulatory Sequences, Ribonucleic Acid; D020506:Untranslated Regions; D012313:RNA; D007501:Iron
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