SIREs: searching for iron-responsive elements
Open Access
- 11 May 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 38 (Web Server), W360-W367
- https://doi.org/10.1093/nar/gkq371
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.htmlKeywords
This publication has 34 references indexed in Scilit:
- Multiple determinants within iron-responsive elements dictate iron regulatory protein binding and regulatory hierarchyRNA, 2009
- Systemic Iron Homeostasis and the Iron-Responsive Element/Iron-Regulatory Protein (IRE/IRP) Regulatory NetworkAnnual Review of Nutrition, 2008
- The Vienna RNA WebsuiteNucleic Acids Research, 2008
- Iron Regulatory Proteins Are Essential for Intestinal Function and Control Key Iron Absorption Molecules in the DuodenumCell Metabolism, 2008
- Iron-regulatory proteins limit hypoxia-inducible factor-2α expression in iron deficiencyNature Structural & Molecular Biology, 2007
- A novel iron responsive element in the 3′UTR of human MRCKαBiochemical and Biophysical Research Communications, 2006
- An Iron-responsive Element Type II in the 5′-Untranslated Region of the Alzheimer's Amyloid Precursor Protein TranscriptJournal of Biological Chemistry, 2002
- A Mutation, in the Iron-Responsive Element of H Ferritin mRNA, Causing Autosomal Dominant Iron OverloadAmerican Journal of Human Genetics, 2001
- Iron Regulatory Proteins 1 and 2 Bind Distinct Sets of RNA Target SequencesJournal of Biological Chemistry, 1996
- Mutation in the iron responsive element of the L ferritin mRNA in a family with dominant hyperferritinaemia and cataractNature Genetics, 1995