Global analysis of RNA-protein interactions and RNA secondary structure in eukaryotes

At the heart of post-transcriptional regulatory pathways in eukaryotes are cis- and trans-acting features and factors including RNA secondary structure as well as RNA-binding proteins (RBPs) and their binding sites on target RNAs. However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus of most eukaryotic organisms is still lacking. Here, I will describe the use our novel protein interaction profile sequencing (PIP-seq) approach on nuclei from eukaryotic cells to globally profile both RNA secondary structure and RNA-protein interaction sites in this cellular compartment. From our analysis, we find that these patterns underlie the regulation of alternative splicing and polyadenylation in eukaryotic organisms. Thus, our simultaneous, transcriptome-wide view of RNA secondary structure and RNA-protein interaction sites in eukaryotic nuclei provides important insights into the regulatory effects of these features and factors on transcript maturation processes.