Rpd3p relocation mediates a transcriptional response to rapamycin in yeast

Treating yeast cells with rapamycin, a small molecule that inhibits the TOR proteins, leads to the repression of many genes. Consistent with prior studies, we find that RPD3, which encodes a histone deacetylase (HDAC), is required for repression upon rapamycin treatment. To elucidate the mechanism underlying RPD3-mediated repression, we screened all promoters in yeast for occupancy by Rpd3p before and after treatment with rapamycin. We find that Rpd3p binds to the promoters of rapamycin-repressible genes only following treatment. These data conflict with a previously proposed model suggesting that Rpd3p is constitutively bound to rapamycin-repressible genes and becomes active only after a stimulus such as treatment with rapamycin. Rather, the comprehensive analysis presented here strongly supports a model in which recruitment of Rpd3p to gene promoters is a regulated step in the control of gene repression.