The roles of the RPD3 histone deacetylase in facilitating transcriptional responses to osmotic stress in S. cerevisiae

Abstract

Modification of N-terminal histone tails is one of the major mechanisms by which chromatin state is modified to influence transcription, alongside DNA methylation. The most widely observed of the various histone modifications is acetylation, which is canonically known as a transcriptional up regulator. However, this view has been challenged by observations that RPD3, a widely-conserved histone deacetylase in S. cerevisiae, is required for full transcriptional induction during various stress responses in this organism. RPD3 forms 3 protein complexes in the cell known as Rpd3L, Rpd3S and Rpd3µ and it has not been defined in the literature which of these complexes mediates RPD3 action during the osmotic stress response. Furthermore, the mechanism by which RPD3 mediates transcriptional activation is undefined, with conflicting results in the literature. In this research, northern blotting analysis is carried out to analyse the transcriptional responses of strains carrying deletions in subunits of different RPD3 complexes to induction of osmotic stress via NaCl and sorbitol. Strains carrying deletions in Rpd3L subunits are found to be defective in the transcriptional response to osmotic stress, a result consistent with literature studies of other stress responses. ChIP-qPCR analysis is also carried out to analyse how histone acetylation is affected by osmotic stress, and how this is affected by loss of RPD3 and members of the different RPD3 complexes. Acetylation is found to increase at stress responsive loci after osmostress, alongside a depletion in total nucleosome occupancy. This is found to be decreased in strains carrying deletions in Rpd3L subunits, but not in strains carrying deletions in Rpd3S or Rpd3µ strains. Overall, the data support a conclusion that RPD3 mediates transcription via histone acetylation and nucleosome depletion at stress-responsive loci in response to osmotic stress, and that the Rpd3L complex is required for RPD3 action in this stress response.