Coordination of modifications across RNA species

Project Summary Ribonucleic acid (RNA) is a dynamic molecule marked by diverse enzyme-mediated chemical modifications that intricately influence its function and destiny within cells. The recognition of enzymes — one kind for installing specific chemical modification of RNAs and another kind for RNA modification removal—hints at a purposeful regulatory role in biological processes. While conventional research tends to scrutinize individual modifications within a single RNA molecule, our investigation has uncovered a broader landscape. This extends beyond modifying one RNA species, weaving connections across distinct categories, such as mRNA, tRNA, and rRNA. Our experimental tests have validated this expansive insight and created a groundbreaking coregulation hypothesis. If substantiated and refined, it will be a further conceptual contribution that promises to reshape our understanding of RNA modifications, exerting influence over the depositions and ramifications of multiple RNA alterations. With a foundation built on our past achievements, our overarching objective is to delve deeper into the collective impacts and regulatory mechanisms orchestrated by multiple enzyme- mediated modifications in distinct RNA species, particularly in gene regulation. In our proposed research, we strategically chose two directions: investigating mRNA and tRNA modifications in one path and exploring mRNA and rRNA modifications in another. This deliberate choice aims to uncover the extent of crosstalk in translation, probing whether the collective impacts of modifications in distinct RNA species exhibit nonlinearity and surpass the simple sum. We employ various methodologies to conduct these fundamental experimental investigations, drawing from biochemistry (including enzymology), molecular biophysics, RNA biology, and structural biology. Whether or not the crosstalk between modification of distinct RNA species is a collective impact or a nonlinear effect of coregulation, our research outcomes will transcend the current focus on isolated RNA species; we seek to offer a holistic view of the intricate impact of enzyme-mediated RNA modifications in gene regulation—a landscape meticulously guided by genetically coded proteins.