Exploring the Evolution of RNA Binding and Regulation

RNA-protein interactions are essential to all aspects of gene regulation. And with this essentiality comes a level of complicatedness for their complete understanding. RNA-binding proteins primarily govern RNA regulation. As a family, these proteins largely contain multiple RNA-binding domains which bind and regulate RNA in a variety of ways. How RNA-protein interactions evolve overtime and across species remains largely unstudied. Additionally, how RNA-binding domains contribute to RNA-protein interactions and how multi-domain RNA-binding proteins bind RNA is not well understood. Here, we detail the importance of RNA-protein interactions as can be observed through a multitude of regulatory processes. We then focus on the conserved neuronal RNA-binding protein Unkempt and highlight that protein and even motif conservation are insufficient to define species-specific binding patterns. We find that evolving RNA contextual features such as adjacent sequences and RNA secondary structure play a large role in RNA-guided genomic evolution. Further, we examine three RNA-binding proteins—Musashi-1, Musashi-2, and Unkempt—which have all been shown to have overlapping specificity. We investigate these proteins domain-by-domain to understand how each domain contributes to the overall specificity and affinity of the protein. Finally, we explore two of these proteins in competition—Musashi-1 and Unkempt—and show competitory potential of some RNA sequences as guided by individual protein specificities. This work provides a comprehensive overview and analysis of the evolution of RNA binding and regulation and serves as a foundational study to better understand RNA-protein interactions on a deeper level.