It was observed previously that the deletion of the open reading frame YNL107w (YAF9) was highly pleiotropic in yeast and caused defective growth phenotypes in the presence of several unrelated inhibitors, including caesium chloride. We have selected multicopy extragenic suppressor genes, revealing that this phenotype can be suppressed by overdosing the transcription factors BDF1 and GAT1 in the yaf9Delta strain. We focused our analysis on suppression by BDF1 and performed a genome-wide transcript analysis on a yaf9Delta strain, compared with the wild-type and BDF1-suppressed strains. YAF9 deletion has a clear effect on transcription and leads to modulation of the level of expression of several genes. Transcription of a considerable portion of the underexpressed genes is restored to wild-type levels in the BDF1-suppressed strain. We show by chromatin immunoprecipitation that both Yaf9p and Bdf1p bind to promoters of some of these genes and that the level of H3 and H4 acetylation at one of these promoters is significantly lowered in the yaf9 deleted strain, compared with the wild-type and the BDF1-suppressed strains.