Overview



Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression in several physiological and pathological processes. However, the functions of most of lncRNAs remain largely unknown.

A novel regulatory mechanism employed by lncRNAs is what is called the “sponge effect”. By competing with target mRNAs for common miRNA response elements, lncRNAs can adjust miRNA activity levels. There are now tools and databases to search for lncRNAs that sponge a miRNA of interest [1-3]

Sponge-mediated regulatory networks are also discovered between lncRNAs and RBPs. For instance, NORAD is a highly conserved lncRNA that contains several function response elements for PUM1/PUM2 proteins. Multiple studies have showed that the concentration of NORAD within the cell affects the regulatory activities of PUM1/PUM2 [4-5]

We believe that this kind of cross-talk exists between many other RBPs and lncRNAs. However, to the best of our knowledge, there is no tool to explore potential lncRNAs that can act as sponges for RBPs. RBPSponge aims to fill this gap by ranking lncRNAs based on their potential to act as a sponge for an RBP of interest. In addition to identifying the occurrences of RBP binding sites and CLIP peaks on lncRNAs, RBPsponge enables users to run several types of analyses to understand the regulatory network between lncRNAs, RBPs and their targets.



[1] Furio-Tari, P., Tarazona, S., Gabaldon, T., Enright, A., and Conesa, A. (2016). spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res, 44(W1), W176–80.

[2] Li, J., Liu, S., Zhou, H., Qu, L., and Yang, J. (2014). starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res, 42(D1), D92-D97

[3] Wang, P., Zhi, H., Zhang, Y., Liu, Y., Zhang, J., Gao, Y., Guo, M., Ning, S., and Li, X. (2015). miRSponge:a manually curated database for experimentally supported miRNA sponges and ceRNAs. Database, 10.1093/database/bav098

[4] Tichon, A., Gil, N., Lubelsky, Y., Solomon, T. H., Lemze, D., Itzkovitz, S., Stern- Ginossar, N., and Ulitsky, I. (2016). A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells. Nat Comms, 7(12209).

[5] Lee, S., Kopp, F., Chang, T., Sataluri, A., Chen, B., Sivakumar, S., Yu, H., and Xie, Y. (2016). Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins. Cell, 164(1), 69–80.