Appl Microbiol Biotechnol (2012) 95:1389–1404 1399 Fig. 6 Regulation of SM gene expression by chromatin structure in F. graminearum. I. During primary metabolism, deoxynivalenol (DON) and the aurofusarin (AUR) clusters are silent and marked by HEP1 (ortholog of A. nidulans HepA) bound to H3K9me3. II. Deletion of Hep1 leads to decreased H3K9me3 levels (equal to all tested SM metabolite in liquid cultures (overview presented in Fig. 6). The interpretation of these results remains speculative but one possibility would be chromatin-based up-regulation of the repressor for DON production (Kimura et al. 2003; Kimura et al. 2007) in the hep1 mutant. In any case, the finding that hep1 deletion strongly affects secondary metabolism in F. graminearum supports a more general role for facultative heterochromatin in fungal sec- ondary metabolism. Also for this fungus sequencing infor- mation predicts a vastly higher number of biosynthetic clusters than the number of known metabolites. Efforts to de-repress these clusters of unknown function by modulat- ing culture conditions have been only partially successful (Cuomo et al. 2007; Li et al. 2012; Seong et al. 2009) and mutants involved in heterochromatin formation might be helpful for the identification of novel metabolites from this agronomically important fungus. Concluding remarks and perspectives: similarities, differences, and current limitations Although information on chromatin-level regulation of fungal secondary metabolite gene clusters is still scattered, some general conclusions from the published work can be drawn with confidence. From the actual evidence, it is safe to pre- sume that histone H3 acetylation in promoter regions of SM cluster genes by GcnE-containing complexes is essential for transcriptional activation of SM clusters in A. nidulans. In addition, histone H4 acetylation has been shown to convoy transcriptional activation of several clusters in A. nidulans and A. parasiticus and thus seems to play a role during the acti- vation process. However, the putative H4 acetyltransferase esaA is essential in A. nidulans and thus the quantitative clusters in A. nidulans) on promoters of DON and AUR biosynthetic genes. III. Absence of heterochromatic marks results, on one hand, in the activation of aurofusarin and repression of deoxynovalenol bio- synthetic genes contribution of this protein to SM gene activation is difficult to assess. But based on over-expression studies, which demon- strated a roughly two to three-fold higher transcript abundance of SM cluster genes, we can assume that the contribution of H4K12ac is probably less important than H3 acetylation. The main difference between H3 and H4 acetylation is their dependence on LaeA: whereas H4 acetylation, at least in A. nidulans, is strictly dependent on LaeA, GcnE-mediated H3 acetylation seems to be largely independent of this general regulator. This means that GcnE-containing complexes (such as the putative Saga/Ada complex) are recruited to SM gene promoters by an alternative mechanism to acetylate at least H3K9 and K14 (these two modifications were tested with H3 K9 and K14 acetyl-lysine specific antibodies). Based on the available evidence the GATA-factor AreA, known to recruit acetylation activities to the nitrate promoters, might be a suitable candidate for GcnE/Saga recruitment to ST and other nitrogen-responsive biosynthesis pathways. For the pH- regulated PEN cluster, the general regulator PacC might take over this recruitment role. LaeA not only acts as general SM activator, but to some extent also functions to detain specific chromatin modifica- tions within the borders of active SM clusters. In recent studies high levels of H3acetylation at K9 and K14 were found to be confined to regions inside the transcriptionally active SM clusters. Conversely, adjacent genes not belong- ing to the clusters displayed only elevated H3K14 acetyla- tion under these conditions (Nützmann et al. 2011). On the other hand, H3K9 was found to be highly trimethylated in primary metabolism and reduction of this mark during SM gene expression occurred again only within clusters and in laeA+ strains, but not in genes lying immediately outside the cluster or in laeA mutants (Bok et al. 2009; Reyes- Dominguez et al. 2010). Thus, competing types of H3K9