The Rpd3/HDAC complex is present at the URS1 cis-element with hyperacetylated histone H3.

In eukaryotes, the hypoacetylated state of histone N-terminal lysines at many gene-promoters, which is created by histone deacetylases (HDACs), is changed to the hyperacetylated state by the function of histone acetyltransferases (HATs) upon transcription activation. Although much insight has been obtained to date as to how modification of the histone tail regulates gene expression, little is known about how the transition between the unmodified and modified states takes place. In Saccharomyces cerevisiae, the HDAC complex containing Rpd3 (Rpd3L) represses the transcription of several sets of genes through the URS1 cis-element. We found that the histone H3 acetylation level at the URS1 of seven genes (INO1, CAT2, ACS1, YAT1, RIM4, CRC1, and SIP4) was elevated in the presence of Rpd3/HDAC in growth in acetate-containing medium (YPA), suggesting that a mechanism that regulates HDAC activity is present in this organism. The biological significance of this phenomenon is discussed below.