Cell fate decisions require integrating extracellular signaling cues into tightly regulated transcription programs. Communication between the RNA polymerase II holoenzyme complex and dynamic post-translational histone modifications is central for transcription. The RNA pol II holoenzyme is composed of two evolutionarily conserved yet functionally distinct complexes; the core mediator and the CDK8 submodule. In the budding yeast Saccharomyces cerevisiae, the CDK8 submodule, composed of cyclin C, Cdk8p, Med12p, and Med13p, plays important roles in mediating transcription of stress responsive and developmental genes. Histone Lysine methylation is a key regulator of transcription during cell differentiation. Histone H3Lys4 methylation (H3K4Me), regulated by the opposing activities of the Set1p methyltransferase and the Jhd2p demethylase, is important for all phases of transcription. While much work has been done to investigate how H3K4Me regulates transcription, less is understood about how Set1p and Jhd2p are controlled during cell fate determination.
Work in my lab has uncovered an unexpected genetic interaction between the CDK8 submodule, the H3K4Me regulators, and yeast cell fates. When deprived of nutrition, diploid yeast can enter one of two partially overlapping differentiation pathways, meiosis or pseudohyphal growth (PH). We have recently published that both CNC1/CDK8 and JHD2 are required to inhibit PH while yeast are cultured in rich conditions. This study also revealed that Cnc1p/Cdk8p repress locus-specific H3K43Me independently of JHD2, indicating that Cnc1p/Cdk8p can regulate transcription during differentiation by controlling H3K4Me levels.
To identify loci subject to CNC1-dependent H3K43Me controls, we employed ChIP-seq. These experiments identified significant enrichment for H3K43Me in metabolic promoters, which is consistent with a model in which CNC1/CDK8 control H3K4Me of genes important for cell fate decisions. We further explored how CNC1-mediated H3K4Me controls are integrated into cell fate decisions by measuring H3K41Me, 2Me, 3Me in rich and nutrient deprived growth conditions. These experiments revealed an important role for CNC1/CDK8 inhibiting H3K4Me during nutrient deprivation, supporting a key function during cell fate determination. We determined that these methylation controls had a direct impact on target gene transcription using RT-qPCR. Finally, we queried whether CNC1/CDK8 inhibit Set1p catalysis or recruitment by performing ChIP-qPCR directed towards Set1p or H3K43Me. These experiments found that Set1p recruitment is inhibited by CDK8 as cells are poised to differentiate. These data support a model in which CNC1/CDK8 control cell fate decisions by restricting Set1p recruitment in response to developmental cues.