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Nucleic Acids Res. 2010 Jul;38(Web Server issue):W360-7. doi: 10.1093/nar/gkq371. Epub 2010 May 11.

SIREs: searching for iron-responsive elements.

Author information

1
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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.

PMID:
20460462
PMCID:
PMC2896125
DOI:
10.1093/nar/gkq371
[Indexed for MEDLINE]
Free PMC Article

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