Global Control of Cell-Cycle Transcription: Interplay Between CDK-APC/C and the Transcription Factor Network

Abstract

A periodic transcriptional program is a conserved feature of the eukaryotic cell cycle, yet there have been contrasting views on whether it is predominantly controlled by a CDK-APC/C network or a transcription factor (TF) network. I have sought to determine how the components in the CDK-APC/C network regulate the systems-level behaviors of the TF network. In this dissertation, I will establish these feedback regulations and propose an integrated model for the control of the cell-cycle transcriptional program in budding yeast Saccharomyces cerevisiae.First, by re-examining the transcriptomic dynamics in cyclin mutants from previous reports drawing conflicting conclusions, I show that these data are fully compatible with an integrated model in which both CDK activities and the TF network contribute to the cell-cycle transcriptional program in wild-type cells. Using a quantitative model, I validate that network TFs can still retain their function even when transcript levels are substantially reduced in cyclin mutant cells. These results highlight the critical roles of both the TF network and the CDK feedbacks in generating the cell-cycle transcriptional program.I have further dissected the precise roles of CDK-APC/C in regulating the TF network. Using an integrated genetic-genomic approach, I establish that G1 cyclin-CDKs stimulate network TFs both directly by inhibiting transcriptional corepressors Whi5/Stb1 and indirectly by inhibiting APC/C. Significantly, the dynamics of the cell-cycle transcriptional program can be greatly restored in a cdk1 apc whi5Δ stb1Δ quadruple mutant. These results suggest a model in which the TF network is inhibited by multiple mechanisms in early G1, which are relieved by CDKs to initiate global cell-cycle transcription after cell cycle commitment.Next, I have sought to determine how multiple cycles of transcription persist in cells arrested with constitutively high CDK activity. I show that the transcriptional repressors for G1/S transcription are down-regulated by mitotic cyclin-CDKs, leading to prompt re-initiation of cell-cycle transcription when mitotic progression is genetically perturbed. Finally, I tested the hypothesis that timely mitotic exit prevents uncoupled dynamics of the cell-cycle transcriptional program. I characterized the transcriptomic dynamics in cells arrested at mitotic exit and showed that substantial transcript dynamics persist during the anaphase/telophase arrests. By comparing the transcriptome datasets from various mutants, I establish the physiological roles of APC/CCdc20 and mitotic exit pathways in regulating the activities of the TF network.Taken together, this dissertation establishes the first mechanistic model for an integrated network that controls the robust cell-cycle transcriptional program in budding yeast.