Center for Genomic Information Encoded by RNA Nucleotide Modifications

Post-transcriptional mechanisms control gene expression in virtually every cell. A major mediator of post-transcriptional gene regulation is the translating ribosome, which comprises three different types of RNAs: rRNA, tRNA and mRNA. These RNAs, along with ribosomal and mRNA-binding proteins, form a multi-RNA/multi-protein complex that can markedly influence mRNA stability and translation. Importantly, this complex is not constitutive. Instead, rRNA-tRNA, rRNA-mRNA, and tRNA-mRNA interactions are highly regulated, although the mechanisms of its regulation are poorly understood. A potential mechanism may involve chemical modification of their nucleotides. Indeed, rRNA, tRNA and mRNA are subjected to diverse chemical modifications whose stoichiometry is highly regulated in different tissues or disease states. Our underlying hypothesis is that the regulated nucleotide modifications in rRNA, tRNA, and mRNA act as a “code” that controls these RNAs and their mutual interactions, thus encoding unique patterns of gene expression. Although rRNA, tRNA, and mRNA nucleotide modifications are poised to be critical regulators of gene expression, studying how these modifications influence each other to control gene expression has been difficult to explore. In part this reflects the lack of scalable methods to quantify and profile nucleotide modifications in rRNA, tRNA, and mRNA. Another problem is that understanding the interactions of rRNA, tRNA, and mRNA requires specialized expertise in each of these three major areas of RNA biology. It is therefore critical for experts in rRNA, tRNA, and mRNA to work together to decipher the mutual interactions of these RNAs. The Center will bring together a team of experts in these diverse types of RNAs who will work together to develop novel techniques to probe nucleotide modifications and how they interact to orchestrate unique patterns of gene expression. The Center will develop novel technologies for mapping and quantifying rRNA, tRNA, and mRNA modifications, identify the dynamic modification sites in tissues and disease, and determine the function of these dynamic modifications. The methods and datasets that will be developed in the Center will provide the foundational knowledge needed to accelerate new areas of epitranscriptomics research in rRNA, tRNA, and mRNA biology. The Center has a major outreach and educational mission. The outreach/educational opportunities will include sponsored undergraduate research, breakout project funding, funding for training visiting outside investigators, and funding for an annual symposium. We will also develop a website that curates the epitranscriptomic mapping data generated by the Center to ensure rapid and easy access to the new data we generate. Overall, the Center’s mission is to serve as a hub for training researchers in epitranscriptomics, as well as to develop new enabling technologies, develop foundational datasets, and reveal fundamental principles of modified nucleotide function in rRNA, tRNA, and mRNA that are needed to open up new areas of epitranscriptomics research.