Investigating the biological functions, biosynthesis, and dynamic regulations of RNA chemical modifications - Abstract RNA-based therapeutics hold great promise for treating diseases, yet their full potential relies on a deep understanding of how gene expression is regulated at the RNA level. RNA is a diverse and dynamic molecule that undergoes various post-transcriptional processing. Among these, chemical modifications widely installed on RNA significantly expand its diversity, and have great potential to regulate gene expression through modulating RNA’s structure, stability, localization, and interactions, among others. Several types of RNA modifications have been extensively studied and found to influence multiple stages of the RNA life cycle and impact numerous physiological pathways. Dysregulations of RNA modification landscape or malfunctions of their associated effector proteins have been linked to various human diseases. However, despite this progress, most RNA modifications remain underexplored, and their impact on RNA function is still largely unknown. Our research program aims to advance the fundamental understanding of RNA modifications by addressing three key challenges. The first critical challenge is identifying proteins that specifically interact with the modified nucleotides. Revealing these “reader” proteins is the key to understanding the functions of the modifications and biological processes regulated by them, potentially providing new insights into disease mechanisms. While “reader” proteins have been identified for a few types of modifications, effector proteins for most other modifications remain largely unknown. We will develop a new approach to systematically identify modification- mediated RNA-protein interactions as they occur in cells. Additionally, precise mapping of modification sites raises fundamental questions regarding the rules governing their selective deposition. While sequence motifs can often be acquired from modification mapping data, RNA structures that contribute to modification selectivity is challenging to determine and remains largely unexplored. We will investigate RNA structural features that support the site-specific deposition of the RNA pseudouridine modification during its biosynthesis. Lastly, probing the dynamic nature of RNA modifications has been a significant challenge, as current methods are inefficient for dissecting their spatial and temporal dynamics in living cells. We are developing genetically encoded biosensors to enable real-time probing of RNA modification dynamics in living cells. We will apply this tool to study RNA modifications in physiological contexts, such as neuronal development. By integrating innovative biochemical, multi-omics, and imaging approaches, our work has the potential to transform the field by providing novel tools that can be applied to a wide range of RNA chemical modifications in various biological systems, while also accelerating our understanding about the functions, deposition mechanisms and dynamic regulations of RNA modifications. Moreover, our research may lead to new insights into disease mechanisms, facilitate the development of diagnostic tools, and reveal new drug targets related to RNA-based gene expression regulation mechanisms.
