Protein spatiotemporal dynamics in gene regulation and disease pathology

Abstract

A cell orchestrates billions of proteins to the right place at the right time to perform diverse cellular processes. Over the decades, this field has been evolving by integrating advances in microscopy, biochemistry, and molecular biology to unravel the intricate mechanisms governing protein spatiotemporal dynamics as well as the functional consequences. This thesis focuses on the physical motions of proteins at a length scale of tens of nanometers to several microns, where the apparent diffusion and the condensate dynamics of assembly and disassembly are specifically studied. In the studies presented in this thesis, the functional relevance of protein motion is exemplified in the context of gene regulation and disease pathology. We find that the apparent diffusion of transcription factors (TFs) is preferentially partitioned into slowly diffusing states by interacting with RNA, leading to enhanced chromatin occupancy and gene expression (Oksuz et al., 2023). The assembly and disassembly dynamics of transcriptional condensates are coupled to the active RNA synthesis, linking gene expression and the spatiotemporal organization of transcriptional proteins in a feedback loop (Henninger et al., 2021). In addition to transcriptional proteins, we find insulin receptors (IRs) are incorporated in dynamic condensates in normal cells to perform metabolic signaling transduction. In insulin-resistant cells which could occur in chronic diseases such as type 2 diabetes (T2D), IR signaling is dysregulated, associated with diminished IR condensate dynamics of assembly and disassembly (Dall’Agnese et al., 2022). Furthermore, pathogenic signaling reduces the mobility of key proteins–both inside and outside of condensates—that act in many cellular functions. Such reduced protein mobility under diverse pathogenic stimuli, termed proteolethargy, may account for diverse cellular dysregulation seen in chronic disease (Dall’Agnese, Zheng, Moreno et al., 2024).