Principles of Speckle-Based Gene Regulation

The cell nucleus houses different types of non-DNA substructures, called nuclear bodies. Among these, nuclear speckles predominate. Speckles occupy ~15-30% of the nuclear volume and are present in cells throughout our bodies. Proteins involved in different stages of RNA production are highly concentrated within speckles, and speckles are the key nuclear body that associates with active euchromatin. How speckles regulate gene expression has historically been murky due to lack of mechanistic insight. My past and current research centers on the view that nuclear speckles regulate gene expression in unique and diverse ways, and that understanding how this works will illuminate disease mechanisms and new therapeutic paths. My previous work finds two major ways that gene regulation can be impacted by speckles. First, transcription factors help specific genomic regions localize at speckles, boosting expression of modestly-sized gene neighborhoods. In the proposed research, we seek to identify new transcription factors that drive DNA-speckle association, determine the importance of this novel transcription factor function for cancer biology, and develop ways to inhibit it using covalent ligands. We apply these objectives to clear cell renal cell carcinoma, neuroblastoma, and macrophage inflammatory signaling, but hope that the principles uncovered will be applicable across disease states and model systems. Second, speckles themselves can adopt two major states, altering expression of large gene neighborhoods. We propose here that this is controlled at the molecular level by factors that link two structural sub-compartments of the speckle. We also propose that speckle states are highly dynamic and responsive to extracellular cues via key well-known signaling pathways. We will examine this in cell culture models and in living animals, testing the hypothesis that the signals secreted after a meal dynamically regulate speckle form and gene-activating function to coordinate expression of hundreds of genes within large speckle-associating genomic neighborhoods. In the long term, we anticipate that understanding how speckles are dynamically regulated will provide new tools that could sensitize tumors to existing treatments. Over the course of the proposed research, we will integrate imaging, genomic, bioinformatic, proteomic, and functional approaches to understanding the principles of 1) regulated DNA positioning at speckles and 2) regulated speckle states. Ultimately, we strive to create textbook models for speckle-based gene regulation that can then be applied across disease conditions to improve patient outcomes and quality-of-life.