While the central dogma of biology shows a straightforward linear relationship from DNA to RNA to proteins, RNA is, in reality, more than just a messenger between DNA and protein. To date, it has been shown that eukaryotic RNA molecules undergo a variety of post-transcriptional regulatory events before being translated into proteins and these events help determine what types of proteins are produced and also affect cellular processes from development to responding to stress. While it is known that RNA secondary structure and RNA-binding protein (RBP) interaction with target RNAs are two major components of determining the outcomes of post-transcriptional regulatory mechanisms, global overviews of these two features remain lacking in our current literature. Here, I have used a combination of Protein-Interaction Profile Sequencing (PIP-seq), mRNA-sequencing, and RNA affinity pulldown to investigate the dynamics of RBP-RNA interaction and RNA secondary structure in a model of plant response to abscisic acid and a model of mammalian erythropoiesis. The studies survey the relationship between RBP-RNA interactions, their effect on RNA secondary structure and ultimately aims to identify important sites of interaction as well as potential novel regulators of plant ABA response and mammalian red blood cell development. By studying the same types of relationships in two distinct eukaryotic models, I demonstrate how PIP-seq is a method suited for studying RBP-RNA interaction without prior knowledge of the system, as it is both able to recapitulate known dynamics and identify novel interactions. At the same time, PIP-seq analysis allows users to attain a global overview of the dynamics of RBP-RNA interactions and of RNA secondary structure, while also providing a detailed look at specific interactions.