RBPSponge: genome-wide identification of lncRNAs that sponge RBPs

Abstract

Summary Long non-coding RNAs (lncRNAs) can act as molecular sponge or decoys for an RNA-binding protein (RBP) through their RBP-binding sites, thereby modulating the expression of all target genes of the corresponding RBP of interest. Here, we present a web tool named RBPSponge to explore lncRNAs based on their potential to act as a sponge for an RBP of interest. RBPSponge identifies the occurrences of RBP-binding sites and CLIP peaks on lncRNAs, and enables users to run statistical analyses to investigate the regulatory network between lncRNAs, RBPs and targets of RBPs. Availability and implementation The web server is available at https://www.RBPSponge.com. Supplementary information Supplementary data are available at Bioinformatics online.

Disease-Associated Circular RNAs: From Biology to Computational Identification

“…We will revisit this topic in a later section of this review. In addition to regulating miRNA, circRNAs also serve as the sponge of RNAbinding proteins (RBPs) to regulate intracellular transport (Figure 1(a)), thereby modulating gene expression of relevant RBPs of interest [53]. Readers with interests in this topic could find more details in several recent reviews [54][55][56].…”

A novel long noncoding RNA, TMEM92‐AS1, promotes gastric cancer progression by binding to YBX1 to mediate CCL5

“…Considering that TMEM92‐AS1 is mainly located in the nucleus rather than the cytoplasm, suggesting that TMEM92‐AS1 acts primarily at the transcriptional level, it may interact with molecules or proteins in the nucleus. Numerous studies have shown that most lncRNA function by interacting with RNA‐binding proteins (RBP) [12–14]. To explore the precise functional mechanism of TMEM92‐AS1, we tried to identify the RBP that bind to it.…”

An alternative D. melanogaster 7SK snRNP

“…This raises the question of the possible role of those pseudogenes as molecular sponge, similarly to PTENP1 which is the pseudogene of PTEN protein [ 50 ]. Moreover, many lncRNAs function as molecular sponges for miRNA or RNA Binding Protein (RBP) to limit the abundance of their functional binding sites [ 51 , 52 ]. In previous study, two 7SK gene copies were found in C. elegans genome, but the expression of only one could be detected by Northern blot, probably due to the very low expression level of the other.…”