Involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to carbon source switch in budding yeast

We applied RNA-Seq analysis to investigate the involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to a carbon source switch from 2% glucose to 3% ethanol. Cells were cultured in synthetic complete medium with 2% glucose and switched to 3% ethanol. Samples were collleted in log phase in glucose, 1 hour after the switch (acute response) or 20 hours after the switch (adaptation). The data show that subtelomeric genes are repressed in sml1 rad53 mutants irrespective of the carbon source, in a histone-dependent manner. The data further show that Rad53 is not involved in the global carbon source switch response, but specifically in the expression of switch-inducible subtelomeric genes. Overall design: The dataset includes 10 samples in experimental duplicates. sml1? = control (glucose, 1 hour ethanol, 20 hours ethanol), sml1?rad53? = deletion of RAD53 (glucose, 1 hour ethanol, 20 hours ethanol), sml1?hht2? = deletion of HHT2 which is one of two genes encoding histone H3 (glucose, 1 hour ethanol), sml1?rad53?hht2? = deletion of RAD53 and HHT2 (glucose, 1 hour ethanol). The control strain is sml1? because deletion of SML1 rescues the lethality of rad53?. The dataset allows the comparison of sml1?rad53? vs. sml1? in glucose and at 1 hour and 20 hours after the carbon sourcce switch. It allows the contribution of HHT2 to transcriptional alterations in sml1?rad53? in glucose and at 1 hour after the carbon source switch (sml1?rad53?hht2? vs. sml1?rad53?).