Highly accessible AU-rich regions in 3′ untranslated regions are hotspots for binding of proteins and miRNAs
BackgroundMicroRNAs (miRNAs) are endogenous short non-coding RNAs involved in the regulation of gene expression at the post-transcriptional level typically by promoting destabilization or translational repression of target RNAs. Sometimes this regulation is absent or different, which likely is the result of interactions with other post-transcriptional factors, particularly RNA-binding proteins (RBPs). Despite the importance of the interactions between RBPs and miRNAs, little is known about how they affect post-transcriptional regulation in a global scale.\n\nResultsIn this study, we have analyzed CLIP datasets of 49 RBPs in HEK293 cells with the aim of understanding the interplay between RBPs and miRNAs in post-transcriptional regulation. Our results show that RBPs bind preferentially in conserved regulatory hotspots that frequently contain miRNA target sites. This organization facilitates the competition and cooperation among RBPs and the regulation of miRNA target site accessibility. In some cases RBP enrichment on target sites correlates with miRNA expression, suggesting coordination between the regulatory factors. However, in most cases, competition among factors is the most plausible interpretation of our data. Upon AGO2 knockdown, transcripts that contain such hotspots that overlap target sites of expressed miRNAs in 3UTRs are significantly less up-regulated than transcripts without them, suggesting that RBP binding limits miRNA accessibility.\n\nConclusionsWe show that RBP binding is concentrated in regulatory hotspots in 3UTRs. The presence of these hotspots facilitates the interaction among post-transcriptional regulators, that interact or compete with each other under different conditions. These hotspots are enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are important regulatory regions that define an extra layer of auto-regulatory control of post-transcriptional regulation.