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...

The organization of chromatin affects all aspects of nuclear DNA metabolism in eukaryotes. H3.3 is an evolutionarily conserved histone variant and a key substrate for replication-independent chromatin assembly. Elimination of chromatin remodeling factor CHD1 in Drosophila embryos abolishes incorporation of H3.3 into the male pronucleus, renders the paternal genome unable to participate in zygotic mitoses, and leads to the development of haploid embryos. Furthermore, CHD1, but not ISWI, interacts with HIRA in cytoplasmic extracts. Our findings establish CHD1 as a major factor in replacement histone metabolism in the nucleus and reveal a critical role for CHD1 in the earliest developmental instances of genome-scale, replication-independent nucleosome assembly. Furthermore, our results point to the general requirement of adenosine triphosphate (ATP)-utilizing motor proteins for histone deposition in vivo.H istone-DNA interactions constantly change during various processes of DNA metabolism. Recent studies have highlighted the importance of histone variants, such as H3.3, CENP-A (centromere protein A), or H2A.Z, in chromatin dynamics (1, 2). Incorporation of replacement histones into chromatin occurs throughout the cell cycle, whereas nucleosomes containing canonical histones are assembled exclusively during DNA replication. A thorough understanding of the replication-independent mechanisms of chromatin assembly, however, is lacking.In vitro, chromatin assembly requires the action of histone chaperones and adenosine triphosphate (ATP)-utilizing factors (3). Histone chaperones may specialize for certain histone variants. For example, H3.3 associates with a complex containing HIRA, whereas canonical H3 is in a complex with CAF-1 (chromatin assembly factor 1) (4). The molecular motors known to assemble nucleosomes are ACF (ATP-utilizing chromatin assembly and remodeling factor), CHRAC (chromatin accessibility complex), and RSF (nucleosome-remodeling and spacing factor), which contain the Snf2 family member ISWI as the catalytic subunit (5-7), and CHD1, which belongs to the CHD subfamily of Snf2-like adenosine triphosphatases (ATPases) (8). These factors have not been shown to mediate deposition of histones in vivo. We previously demonstrated that CHD1, together with the chaperone NAP-1, assembles nucleosome arrays from DNA and histones in vitro (9). Here, we investigated the role of CHD1 in chromatin assembly in vivo in Drosophila.We generated Chd1 alleles by P elementmediated mutagenesis (Fig. 1A) (10). Two exci- 2] with Df(2L)Exel7014 affect both copies of the Chd1 gene only (Fig. 1B). We also identified a single point mutation that results in premature translation termination of Chd1 (Q1394*) in a previously described lethal allele, l(2)23Cd[A7-4] (11). Hence, l(2)23Cd[A7-4] was renamed Chd1 [3].sions, Df(2L)Chd1[1] and Df(2L)Chd1[2], deleted fragments of the Chd1 gene and fragments of unrelated adjacent genes. Heterozygous combinations, however, of Chd1[1] or Chd1[Analysis of Western blots of embryos from heterozyg...

Acetylation is the most prominent modification on core histones that strongly affects nuclear processes such as DNA replication, DNA repair and transcription. Enzymes responsible for the dynamic equilibrium of histone acetylation are histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this paper we describe the identification of novel HDACs from the filamentous fungi Aspergillus nidulans and the maize pathogen Cochliobolus carbonum. Two of the enzymes are homologs of Saccharomyces cerevisiae HOS3, an enzyme that has not been identified outside of the established yeast systems until now. One of these homologs, HosB, showed intrinsic HDAC activity and remarkable resistance against HDAC inhibitors like trichostatin A (TSA) when recombinant expressed in an Escherichia coli host system. Phylo genetic analysis revealed that HosB, together with other fungal HOS3 orthologs, is a member of a separate group within the classical HDACs. Immunological investigations with partially purified HDAC activities of Aspergillus showed that all classical enzymes are part of high molecular weight complexes and that a TSA sensitive class 2 HDAC constitutes the major part of total HDAC activity of the fungus. However, further biochemical analysis also revealed an NAD(+)-dependent activity that could be separated from the other activities by different types of chromatography and obviously represents an enzyme of the sirtuin class.