Cells display a remarkable ability to adapt to changes in their environment. Many external stimuli evoke cellular responses that result in reprogramming of transcription profiles. These changes in gene transcription may in turn affect important cellular decisions, such as e.g. proliferation, senescence, or apoptosis. Exactly how cells relay signals from their environment to induce activation or repression of genes is not well understood, especially in terms of cell cycle control. My lab is interested in unraveling the molecular mechanisms of transcriptional responses to environmental stimuli, and how these changes affect cell cycle progression.
Cdk1, transcription, and basic cell cycle regulation
A major funtion of Cdk1 is to control transcriptional programs. Cell cycle entry is well conserved among eukaryotes, and involves the activation of genes involved in cell cycle progression. In higher eukaryotes, the transcription factor E2F induces transcription of a variety of genes that facilitate the G1-S transition. During G1 phase, E2F forms a complex with the Retinoblastoma (Rb) tumor suppressor, which prevents binding of E2F to its target sites in promoters of cell cycle genes. Rb also recruits histone deacetylases (HDACs) to repress transcription. However, when Rb is phosphorylated by the CyclinD-Cdk4/6 and CyclinE-Cdk2 complexes, it no longer recruits HDACs and it dissociates from E2F, resulting in activation of E2F-controlled genes.
A similar mechanism operates in budding yeast. While Rb does not exist in yeast, another protein, Whi5, serves a similar function. Whi5 binds the transcription factor SBF (consisting of Swi4 and Swi6), thus keeping it inactive. Whi5, like Rb, also recruits HDACs that repress transcription. Phosphorylation of Whi5 by Cdk1 leads to dissociation of the complex, allowing SBF to activate a transcriptional program that induces the G1-S transition. Cdk1 also directly phosphorylates transcription factors involved in cell cycle progression. For example, it phosphorylates and activates the forkhead transcription factor Fkh2 as well as its binding partner, the transcriptional co-activator Ndd1.
In addition to phosphorylating transcription factors to induce transcription, Cdk1 may also facilitate transcription by recruiting the proteasome to ORFs, which appears to be independent of its kinase activity.
Transcriptional responses to external stimuli and cell cycle regulation
The cellular response to carbon sources
We make use of several well-defined models to unravel the molecular mechanism of transcription regulation upon environmental stimuli. In particular, we study the cellular responses to changes in external carbon sources, such as glucose and galactose. While the response to these carbon sources has been studied extensively, the interplay between the cell cycle and the genes involved in carbon metabolism remains poorly understood. We make use of a variety of techniques to unravel the role of Cdk1 in regulation of transcription of these genes, including chromatin immunoprecipitation (ChIP), RT-PCR, and ChIP followed by sequencing (ChIP-seq). Together with the genetic network of CDK1, this provides insight in the cellular response to carbon metabolism and feedback to cell cycle control.
The cellular response to DNA damaging agents
We recently identified a genetic interaction between CDK1 and RAD6 (Enserink JM et al, 2009). Rad6 is an E2 ubiquitin conjugase that interacts with several E3 ubiquitin ligases: Ubr1, involved in N-end rule protein degradation; Rad18, involved in post-replication DNA repair; and Bre1. The Rad6-Bre1 complex monoubiquitinates histone H2B and Swd2, leading to methylation oh histone H3, which affects transcription and which has a role in activation of the DNA damage checkpoint that induces cell cycle arrest. Especially the BRE1 branch of the RAD6 pathway strongly genetically interacts with CDK1, indicating an involvement of Cdk1 in Rad6-mediated transcriptional control. We are currently unraveling the role of Cdk1 in regulation of transcription, especially in during DNA damage.