Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size

Cell size varies during the cell cycle and in response to external stimuli. This requires the tight coordination, or "scaling," of mRNA and protein quantities with the cell volume in order to maintain biomolecule concentrations and cell density. Evidence in cell populations and single cells indicates that scaling relies on the coordination of mRNA transcription rates with cell size. Here, we use a combination of single-molecule fluorescence in situ hybridization (smFISH), time-lapse microscopy, and mathematical modeling in single fission yeast cells to uncover the precise molecular mechanisms that control transcription rates scaling with cell size. Linear scaling of mRNA quantities is apparent in single fission yeast cells during a normal cell cycle. Transcription of both constitutive and periodic genes is a Poisson process with transcription rates scaling with cell size and without evidence for transcriptional off states. Modeling and experimental data indicate that scaling relies on the coordination of RNA polymerase II (RNAPII) transcription initiation rates with cell size and that RNAPII is a limiting factor. We show using real-time quantitative imaging that size increase is accompanied by a rapid concentration-independent recruitment of RNAPII onto chromatin. Finally, we find that, in multinucleated cells, scaling is set at the level of single nuclei and not the entire cell, making the nucleus a determinant of scaling. Integrating our observations in a mechanistic model of RNAPII-mediated transcription, we propose that scaling of gene expression with cell size is the consequence of competition between genes for limiting RNAPII.