Cell Size Modulates SBF and Whi5 Chromatin Binding to Regulate the Start of the Budding Yeast Cell Cycle

Cell growth and division are tightly coordinated to cell size. In budding yeast, increasing cell size promotes the G1/S transition, called Start, by activating the transcription factor SBF, which drives a large fraction of cell-cycle-dependent gene expression. Part of this regulation arises because the concentration of the SBF inhibitor Whi5 decreases as cells grow. However, cells lacking Whi5 can still maintain a relatively accurate size when the SBF activator Cln3 is also removed, indicating that there are additional size control mechanisms. To understand how cell size is mechanistically translated into the activity of SBF-regulated promoters, we quantified the binding kinetics of Whi5 and SBF in live cells using single-molecule fluorescence microscopy. We found that increasing cell size is associated with both a decreased chromatin affinity of Whi5 and an increased chromatin affinity of SBF, accompanied by a higher SBF:Whi5 cell copy-number ratio. Chromatin-binding trends under basal and Whi5 overexpression conditions indicate that Whi5 restricts SBF association with chromatin. The transition point at which SBF binding overtakes Whi5 binding coincides with the onset of the expression of the G1 cyclins CLN1 and CLN2, two SBF targets that are important for committing cells to division. Reduced Whi5 binding reflects changes in its chromatin-association rate, as Whi5 and SBF dwell times on chromatin remain ~10 s and are largely independent of cell size. Together, these results show how changes in SBF and Whi5 abundance and chromatin association transmit cell size information to the genome to regulate the size-dependent Start transition in budding yeast.