The epitranscriptome, which encompasses the full profiles of RNA modifications, plays a pivotal role in finetuning gene expression. By modulating the functions and metabolism of key components of the translation machinery, including tRNA, ribosome, and mRNA, the epitranscriptome contributes to a broad range of biological processes and is linked to human diseases. Thus, uncovering the function of the epitranscriptome is critical for a comprehensive understanding of the gene expression mechanisms and may lay the foundation for therapeutics.

Our overarching research question is how individual organisms evolve their tailored epitranscriptome for optimizing gene expression. Individual organisms have substantial variations in environmental niches and genomic contents. Regardless of such variations, organisms achieve efficient and optimized gene expression. However, how individual organisms establish optimized gene expression is largely unclear. In this proposal, we focus on the epitranscriptome as a mechanism that may contribute to establishing a tailored gene expression system in individual organisms. The epitranscriptome contains ‘universal’ modifications, which are widely conserved in many taxa, and ‘unique’ modifications, which are restricted to a narrow range of species. Our recent studies have discovered novel unique tRNA modifications and their physiological roles, indicating the significance of unique RNA modifications and variations of the epitranscriptome profiles. However, the limited information on RNA modifications in most organisms is a major knowledge gap to understand how individual organisms evolve their epitranscriptome landscape to establish optimal gene expression systems.

We will address this knowledge gap with three research areas. We aim to; 1) uncover the chemical structure, modifying enzymes, and functions of unique tRNA modifications in various organisms, 2) unveil the remodeling of the landscape of RNA modifications upon environmental changes in non-model organism, and 3) reveal the epistatic network of tRNA modifications for robust gene expression and resilience to perturbation on translation system across organisms. We have developed a tRNA modification profiling pipeline where we combined next generation sequencing of tRNA (tRNA-seq) with RNA mass spectrometric analysis. This method successfully discovered multiple novel unique tRNA modifications in our published work and preliminary data. Additionally, tRNA-seq enables rapid profiling of tRNA modifications, which easily captures the remodeling of the modification landscape. Collectively, our innovative methodologies, strong preliminary data, and deep expertise in the epitranscriptome research field enable us to address these knowledge gaps. Our results will significantly expand our understanding of how individual organisms tailor their epitranscriptome to fine-tune their gene expression
systems.