Illuminating Post-Transcriptional Regulation through Proteogenomic Integration

Project Summary The central dogma of molecular biology outlines the information flow from DNA to RNA to protein, positioning proteins as essential executors of most cellular functions. Despite this, most omics research has disproportionately focused on DNA and RNA. Protein abundances are only modestly correlated with mRNA across tissues and organisms, and gene expression profiles provide limited insights into post-translational modifications (PTMs) that modulate protein function. Following transcription, a complex network of regulators— including ribosomes, non-coding RNAs (ncRNAs), ribosome-binding proteins (RBPs), and ubiquitin- proteasome—affect protein abundance and activity. However, systematic characterizations of post- transcriptional regulators (PTRs) remain sparse. Moreover, the impact of genetic variants on proteins and PTMs is poorly understood. There is a critical need to bridge this significant knowledge gap between DNA/RNA information and the proteome, as this missing link impedes the development of diagnostics and treatments targeting proteins. The objective of this proposal is to address this gap by developing proteogenomic toolsets to reveal PTR networks and genetic regulators of protein/PTMs. The central hypothesis is that protein abundance, function, and diversity are modulated by intertwined PTR processes and genetic variants, in addition to mRNA levels. The project will pioneer innovative integrative proteogenomic approaches, leveraging rapidly expanding proteogenomics, functional genomics, 3D structural datasets, and cutting-edge statistical genetics, machine/deep learning, and multi-modal methods. Building on the extensive work by the PI's NIGMS ESI R35 MIRA-funded research, this research program will unravel PTR mechanisms driving protein diversity and function by addressing three fundamental questions: Key Question 1. How do post-transcriptional regulatory networks shape protein abundance? Key Question 2. How do genetic variants influence protein expression and function? Key Question 3. How are post-translation modifications regulated by genomic variants? This research program is significant because it will substantially expand our understanding of PTR networks that govern protein abundance, diversity, and function. The research will immediately deliver computational tools and PTR knowledge base across human tissues, which can be extended to illuminate PTR biology across diverse cells and organisms. Ultimately, this work will provide a missing link in fundamental biology between DNA/RNA and protein functions, laying the foundations for diagnostic and treatment advances targeting proteins.