Transcriptomic reprogramming driven by nuclear and cell size perturbations via compartment-specific protein accumulation and G1 arrest in yeast and human cells

While nuclear and cell sizes are critical determinants of cellular function, their specific impacts on gene expression remain poorly understood. To dissect the direct transcriptomic consequences of nuclear size alterations, we engineered inducible systems in budding yeast (Saccharomyces cerevisiae) that accumulate massive proteins specifically within the nucleus (3xFP-NLS) or the cytosol (3xFP-NES), alongside corresponding control systems (empty vector, 3xFP, and 1xFP-NLS). Using these systems, we profiled global transcript abundance and RNA polymerase II (Pol II) occupancy via high-throughput mRNA-seq and ChIP-seq. Furthermore, to uncouple the transcriptomic effects of general cell volume expansion from nuclear size changes, we performed mRNA-seq on a temperature-sensitive G1-arrest yeast mutant (cdc28-13) expressing the cytosolic accumulation system (3xFP-NES) under restricted temperature (37°C). Finally, to examine the evolutionarily conserved impact of excessive cell expansion in mammalian systems, we performed mRNA-seq on human retinal pigment epithelial (RPE1) cells undergoing palbociclib-induced G1 arrest over an extended time course. Collectively, our integrated cross-species multi-omics analyses uncover a fundamental, nuclear size-dependent transcriptome reprogramming mechanism.