We have discovered that micoRNAs can modulate RNA-binding protein (RBP) binding sites in a dynamic manner and suggest that miRNAs indirectly or directly modulate RBP-binding sites in a dynamic manner adding complexity and hierarchy to a post-transcriptional regulatory code. This model, which we call sxRNA for structurally interacting RNA, represents an exciting new post-transcriptional regulatory paradigm that may provide fundamental aspects of gene expression regulation. We have informatically identified several trans-acting sxRNAs and our preliminary data suggests that both positive and negative variations are possible. Examples of negative or repressor sxRNA complexes inhibit RBP binding activity, while positive or inducer versions of sxRNA complexes may increase RBP binding and can be captured using RBP immunoprecipatation (RIP) followed by miRNA analysis. This novel regulatory mechanism may explain how complex regulation of gene multi-functionality including alternative splicing could be regulated at the post-transcriptional level. Furthermore, combinations of these interactions could be used in a modular and combinatorial manner adding a hierarchical complexity to the post-transcriptional regulatory code. Similar to the impressive microRNA field, sxRNA has the potential to increase our understanding of gene regulation while simultaneously creating technological opportunities to utilize this regulation as a tissue specific mRNA alternative to gene therapy, anti-viral, RNA-based molecular tool, diagnostic, or even therapeutic that exploits these newly discovered post-transcriptional approaches. The goal of this proposal is to test a new post-transcriptional model in which miRNA and RBPs compete in trans to influence RNA structure. This project is designed to identify dozens (possibly hundreds) of naturally occurring microRNA-mRNA-RBP interactions by exploiting both experimental and informatic approaches, characterize the structural nature of the sxRNA trans-RNA interaction and its effect on RBP binding and validate their existence and role in translation in a cellular system using a specifically designed MS2-sxRNA reporter.
We have discovered that micoRNAs modulate RNA-binding protein (RBP) binding sites, which we call 'sxRNA' for structurally interacting RNA, in a dynamic manner by indirectly or directly binding to RBP binding sites adding complexity and hierarchy to a post-transcriptional regulatory code. Furthering our understanding of the rich world of post-transcriptional regulation will facilitate both our knowledge of how protein production is regulate within the cell and open up opportunities to exploit that regulation. This information could eventually be used to enable new mRNA-based therapeutics and molecular tools that make use of post-transcriptional gene regulation approaches.