Bioactive small molecules are critical in Aspergillus species during their development and interaction with other organisms. Genes dedicated to their production are encoded in clusters that can be located throughout the genome. We show that deletion of hdaA, encoding an Aspergillus nidulans histone deacetylase (HDAC), causes transcriptional activation of two telomere-proximal gene clusters-and subsequent increased levels of the corresponding molecules (toxin and antibiotic)-but not of a telomere-distal cluster. Introduction of two additional HDAC mutant alleles in a ⌬hdaA background had minimal effects on expression of the two HdaA-regulated clusters. Treatment of other fungal genera with HDAC inhibitors resulted in overproduction of several metabolites, suggesting a conserved mechanism of HDAC repression of some secondary-metabolite gene clusters. Chromatin regulation of small-molecule gene clusters may enable filamentous fungi to successfully exploit environmental resources by modifying chemical diversity.A distinguishing characteristic of filamentous fungi is their ability to produce a wide variety of small molecules that aid in their survival and pathogenicity. These include compounds, such as pigments, that play a role in virulence and protect the fungus from environmental damage, as well as toxins that kill host tissues or hinder competition from other organisms. These secondary metabolites (SM) (27) can also impact humans in both beneficial and detrimental ways. Many widely used pharmaceuticals are natural products of fungi, as are some of the most potent carcinogens yet identified. Genetic studies, augmented by analysis of whole genome sequences, have revealed that most fungal SM biosynthetic genes are found in compact clusters functioning as individual genetic loci (27). The genus Aspergillus, whose members include toxinproducing pathogens (Aspergillus flavus and A. fumigatus) and pharmaceutical-producing species (A. nidulans and A. terreus), is renowned for prodigious metabolite production and serves as the model for natural-product exploration. Detailed comparison of the genomes of several aspergilli indicates a genomic landscape in which the greatest diversity between species is represented in these SM clusters (28).There has been considerable debate as to the role that gene clustering plays in the secondary metabolism of fungi. Such gene arrangement must be advantageous to the fungus; if natural selection did not favor clustering, one would assume that processes such as gene translocation and unequal crossing over would have caused dispersal over evolutionary history. Support for horizontal transfer from prokaryotes, in which genes are often arranged into operons, exists for the penicillin biosynthetic cluster (9) but not for other fungal clusters. A prokaryotic gene transfer hypothesis is weakened by the fact that fungal SM genes often contain introns and employ codon usage typical of other fungal genes. Another hypothesis holds that clustering provides a selective advantage to the cluster itself i...