Abstract: Using the fitness-based interferential genetics (FIG) approach in yeast, potential in vivo gene targets of the Rpd3 histone deacetylase were selected. In agreement with previous studies using different methods, three genes were found to be involved in the translational machinery (MRPL27, FHL1 and RDN1). Moreover, other selected genes are linked to cell-cycle control (CSE4, AMN1, VAC17 and GRR1). In addition to playing a crucial role in cell cycle progression to the S phase and participating in the G(2)-M transition, GRR1 has important functions related to nutrient import to the cell via the the derepression of hexose transporters and the induction of amino acid permeases. Consistent with this, FIG selection also retrieved: the PMA1 gene, encoding the plasma H(+)-membrane ATPase; FOL2 and FOL3, involved in folic acid biosynthesis; and UBR2, which indirectly downregulates the proteasome genes. Finally, the other selected genes, ISU1, involved in the biosynthesis of the iron-sulphur cluster in mitochondria, and the less well functionally defined BSC5 and YBR270c, may participate in the cell's antioxidant and stress defence. The genes emerging from this FIG selection thus appear to be part of the downstream molecular mechanisms of the TOR signalling pathway, accounting for its effects on cell proliferation and longevity. From our results on gene expression under conditions of RPD3 overexpression, and by comparison with the available pharmacogenomics studies, it is proposed that FIG could be an invaluable approach for contributing to our understanding of complex cell regulatory systems. Copyright (c) 2007 John Wiley & Sons, Ltd.