Appl Microbiol Biotechnol (2012) 95:1389–1404 A (TR) (Bok et al. 2006). Another fruitful approach used trans-overexpression of a putative regulator that was found by bioinformatics analysis to reside inside a predicted, but silent, SM gene cluster (Bergmann et al. 2007). This strategy resulted in the characterization of aspyridone and its biosyn- thetic genes in A. nidulans. Similarly, overexpression of a regulator residing next to two NRPS genes induced not only expression of these genes on chromosome II, but also led to induction of genes responsible for the synthesis of asperfur- anone on chromosome VIII of A. nidulans (Bergmann et al. 2010). These results suggest that, in addition to metabolite- specific regulation, a regulatory cross-talk between different SM pathways also exists. Genes involved in the biosynthesis of a certain metabolite are usually physically linked on the chromosome (clustered) and transcriptionally co-regulated. Although this clustering has already been observed before for some well-studied SM genes in Aspergillus and Fusarium species (Keller and Hohn 1997), large scale sequencing data revealed that clustering is the rule rather than the exception for SM biosynthetic path- ways. Many examples are known for clustering of bacterial SM genes in large operons that transcribe poly-cistronic mes- sages from a single or from multiple promoters (Malpartida and Hopwood 1984). The linkage of SM genes in fungi underpins the hypothesis that SM genes have been transferred from bacteria to ancestors of fungal lineages or between fungi. Horizontal gene transfer (HGT) events are well documented for β-lactam antibiotics (Brakhage et al. 2009) and have recently been found to be responsible for the presence of the sterigmatocystin gene cluster in Podospora anserina (Slot and Rokas 2011). Strikingly, the A. nidulans and P. anserina ST clusters are highly synthenic providing a strong argument for HGT of a complete cluster. Also, a certain bias for fungal SM cluster position near telomeres is an indication that these genes have been integrated into the fungal genomes as large units. It is known that subtelomeric regions and adjacent euchromatic DNA are highly recombigenic in many organisms and fre- quently contain repetitive elements (Barton et al. 2008; Linardopoulou et al. 2005). Tilburn et al. 1990 found repeti- tive elements in the region adjusted to ωA locus encoding for polyketide synthase involved in biosynthesis of the dark green pigment in the conidium wall. Also recently, repetitive DNA has been discovered flanking the A. nidulans PEN gene cluster which is located at the very end of the right arm of chromo- some VI (Fig. 1). Deletion of the repetitive DNA reduced transcription of PEN genes and antibiotic production (Shaa- ban et al. 2010). Hence, it can be speculated that repetitive elements not only facilitated acquisition but also activation of large genomic segments coding for SMs. In addition, when a selectable marker is inserted into the region instead of the PEN cluster, this transgene is not correctly expressed. This was shown by Palmer and colleagues who found that repression of the marker gene is dependent on heterochromatin formation 1391 Fig. 1 Subtelomeric localization of some well-studied SM gene clus- ters in A. nidulans marked in yellow. The orsellinic acid/F9775 cluster (ORS) is positioned on the left arm of chromosome II, ST—sterigma- tocystin on the right arm of chromosome IV, PEN—penicillin cluster close to the end of chromosome VI's right arm, and MDP—monodic- typhenon on the right arm of chromosome VIII (Palmer et al. 2010; Palmer and Keller 2011). The authors proposed that repression is a consequence of telomere position effects. But as other SM clusters, which are not located near chromosome ends (see examples in Fig. 1), are also regulated by heterochromatin-dependent mechanisms (see below), it remains to be shown if sub-telomeric positioning exerts a considerable regulatory effect on other SM clusters as well. Following the acquisition of these clusters by fungal ancestor lineages, cluster arrangement may have been main- tained because the close proximity of the genes would allow a coordinated transcriptional control by chromatin-based mechanisms. We previously summarized the factors so far identified to play a role in heterochromatin formation and SM gene silencing in A. nidulans (Strauss and Reyes- Dominguez 2011). In this review, we update the picture of chromatin-based fungal SM cluster regulation and highlight similarities and differences between individual clusters within the same organism and between species. Regulation of gene activity by chromatin structure and histone modifications The natural substrate for the transcriptional machinery and regulatory proteins involved in chromosome segregation, DNA replication and repair in the eukaryotic nucleus is not DNA itself, but chromatin. It is composed of structural nuclear proteins such as histones and non-histone chromatin-associated proteins which are tightly associated with DNA and which condense the long DNA molecule into a small volume (Brown 1966; Kornberg 1974; Kornberg and Thomas 1974; Luger et al. 1997). Although packaging is essential and deletion of some chromatin-modifying fac- tors is lethal, chromatin also represents a significant obstacle for DNA-binding factors to access their cognate sequences.