spongeScan – a graphical web tool for detecting microRNA binding elements in lncRNA sequences

Non-coding RNA transcripts such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are important genetic regulators. However, the functions of many of these transcripts are still not clearly understood. Recently, it has become apparent that there is significant crosstalk between miRNAs and lncRNAs and that this creates competition for binding between the miRNA, a lncRNA and other regulatory targets. Indeed, various competitive endogenous RNAs (ceRNAs) have already been identified where a lncRNA acts by sequestering miRNAs. This implies the down-regulation in the interaction of the miRNAs with their mRNA targets, what has been called a sponge effect. Multiple approaches exist for the prediction of miRNA targets in mRNAs. However, few methods exist for the prediction of miRNA response elements (MREs) in lncRNAs acting as ceRNAs (sponges).

Researchers from the Prince Felipe Research Center, Spain have developed spongeScan , a graphical web tool to compute and visualize putative MREs in lncRNAs, along with different measures to assess their likely behavior as ceRNAs.

Flowchart showing the main strategy behind the spongeScan application


K-mers of 6, 7 and 8 nucleotides are searched for by using sliding windows of different sizes. Different k-mer frequencies are obtained for each pair k-mer – lncRNA. Highly enriched k-mers are reported and checked for correspondence with a miRNA canonical seed. Pair-wise predictions are then represented in spongeScan.


Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A. (2016) spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res [Epub ahead of print]. [article]

Leave a Reply

Your email address will not be published. Required fields are marked *