The NuRD complex shapes RNA polymerase III activity at highly expressed tRNA gene clusters, tuning the dynamic range of cellular tRNA pools

Abstract

RNA polymerase III (Pol III) produces noncoding RNAs involved in diverse cellular activities, including translation (tRNA, 5S rRNA, 7SL RNA), RNA processing (U6 snRNA, RPPH1, RMRP), and transcription regulation (7SK snRNA). In this way, Pol III activity must be broadly coupled with cellular demands for protein accumulation and growth, increasing in response to nutrient availability and decreasing during differentiation and exit from proliferation. However, the currently established mechanisms of Pol III regulation remain relatively limited, due in part to the few Pol III-centered protein-protein interaction (PPI) studies performed to date. To address this gap, we first investigated PPIs shared by multiple Pol III subunits to understand the macromolecular interactome of Pol III, with special attention directed at potential regulatory candidates. Our proteomic survey uncovers interactions between Pol III and the NuRD (Nucleosome Remodeling and Deacetylase) complex. Taken further, we show that NuRD localizes to active Pol III-transcribed genes and that its recruitment is Pol III-dependent but nonrandom, with peak occupancy and regulatory hallmarks converging on tRNA gene clusters associated with notably high expression levels. Inhibiting NuRD-associated histone deacetylase function reduces Pol III transcription at these sites, suggesting NuRD restricts Pol III and thereby modulates the global dynamic range of Pol III-derived RNA species. These findings are congruent with the transcriptionally repressive nature of NuRD and bring-to-light a new regulatory mechanism that may couple signaling events and changes in metabolic needs with the dynamic availability of specific tRNA pools.