SIREs (searching for IREs) is an improved bioinformatic program that detect iron-responsive elements-like motifs based on present and previous iron-responsive elements binding studies [1,2,3 and Sanchez et al. manuscript in preparation]. SIREs program is a Perl-based program that screens for a 19 or 20 nucleotide sequence corresponding to the core sequence of an iron-responsive elements (nucleotides n07 to n25 squared in the below figure).

SIREs Home

Previous SELEX (systematic evolution of ligands by exponential enrichment) experiments have reported that the 6 nucleotide apical loop of an iron-responsive element can differ from the canonical CAG(U/A)GN sequence [1,2,3]. Our programme takes into consideration this variability and allows a total of 18 motifs (2 canonical and 16 SELEX motifs) proven to bind Iron Regulatory Protein 1 and/or Iron Regulatory Protein 2 in vitro with a relative binding efficiency bigger than 20%. The new 16 SELEX motifs differ from the canonical sequence in the sequence of the 6 nucleotide apical loop of an IRE (positions n14 to n19) or at the C bulge (n8 is a G in motif 18) (See table below). Some of these motifs have been reported to be specific for the binding of IRP1 or IRP2 (see specificity column in the table).

Table%2018%20IRE%20Motifsv2

Because the IREs of Dmt1 and Hif2aplha have one bulge nucleotide at the right side of the upper stem (position n21b, U, see red arrow in figure below), we design the SIREs program in order to be able to detect similar type of IREs allowing one single bulge nucleotide at positions n20b, n21b, n22b or n23b. In addition, SIREs program allow the detection of IRE-like motif with a mistmach in the upper stem (positions n13-n20, n12-n21, n11-n22, n10-n23, n09-n24 or n07-n25), similarly as the one present in the Gox mRNA (see red arrow in figure below) [4]. The detection of one bulge nucleotide at the right side of the upper stem or a mismatch in the upper stem or at position n07-n25 is mutually exclusive.

Hif2a DMT1 And Gox

Predicted IRE motifs are reported as SIREs Predictions that include the 19 or 20 nucleotide sequence corresponding to positions n07 to n25. Additional 6 nucleotides from the lower stem are also reported. The RNA Folding predicted by the RNAfold Program of the Vienna Package is also reported for the predicted IRE.

The following information is provided for each predicted IRE:

Sensitivity, specificity and precision of the SIREs program for the three different stringent levels have been calculated using a data set of 32 novel IRP-target genes recently identified enriched on IRE-containing mRNA (Sanchez et al., manuscript in preparation) and 150 random sequences that are not expected to harbor IRE elements. Values are reported in the below table.

High Medium Low
Sensitivity 0.28 0.44 0.56
Specificity 0.99 0.95 0.91
Precision 0.90 0.67 0.58
Recall 0.87 0.88 0.91

In summary, our SIREs program represents an improved software of the currently available programs that can predict IRE sequences [7,8] since it is able to detect IRE-like sequences with a combination of 18 motifs in the 6 nucleotide apical loop, one single mismatch in the upper stem or at position n07-n25 or one single bulge nucleotide at the right side of the upper stem.