1392 Accessibility to chromatin is mainly regulated at the level of post-translational modifications (PTMs) of histone proteins (see examples in Fig. 2) which define the degree of com- paction from loose (euchromatin) to very dense (heterochro- matin). Protein modifications by acetylation, methylation, ubiquitination, and phosphorylation represent the main marks which are “written” onto different amino acids of N-terminal tails and globular domains of histone H2B, H3, and H4. During a regulatory cycle, these marks can be removed again by deacetylases, demethylases, and phospha- tases, or one modification can be replaced by another on the same residue. This is the case in lysine modification, which can either be acetylated or methylated on the same nitrogen atom. Usually, the catalytic enzymes performing the specific addition or removal of the PTM are part of specialized histone-modifying complexes. Several of these complexes, such as the Saga/Ada or NuA4 acetyltransferase complexes, the SET-methyltransferase complexes or the histone deace- tylase complexes are deeply studied, and for many members of these complexes, structural data as well as detailed mech- anistic insights are available. Comparative analyses have shown that the basic mechanisms are conserved in eukaryotes (Aagaard et al. 1999; Allfrey et al. 1964; Allfrey and Mirsky 1964; Bannister et al. 2001; Bannister and Kouzarides 2011; Czermin et al. 2001; Jenuwein and Allis 2001; Richards and Elgin 2002; Vermeulen et al. 2010), with notable exceptions Appl Microbiol Biotechnol (2012) 95:1389–1404 such as a loss of key components of heterochromatin in species of the Saccharomycotina sub-phylum (Hickman et al. 2011; Huang 2002; Rusche et al. 2003). The dynamic activities carried out by “writing and eras- ing” modifications on histones result in a spatially and temporally changing combination of different histone marks at regulatory and coding regions of genes as well as in non- coding DNA stretches. These combinations are believed to generate a “code” that is recognized by “reader” proteins. Their role is to recruit transcriptional activators or repressors to these encoded locations (Bartke and Kouzarides 2011; Gardner et al. 2011; Kouzarides 2007; Li et al. 2007) and to change chromatin structure and compaction by interaction with factors responsible for the formation of heterochroma- tin. Because such histone marks, much like DNA methyla- tion, can be stably transmitted during meiosis and over many mitotic cell cycles to daughter cells, the histone code has become an integrated component of epigenetic regula- tion. However, although epigenetic regulation employs his- tone marks, regulation at the chromatin level does not necessarily trigger an epigenetic event. In filamentous fungi, chromatin histone modifications and structure transitions have been studied mainly in the context of DNA methyla- tion (Foss et al. 1993; Freitag et al. 2004; Kouzminova and Selker 2001; Tamaru and Selker 2001), light regulation (Grimaldi et al. 2006) in Neurospora crassa, in connection Fig. 2 Known post-translational modifications of N-terminal tails in histones H3 and H4 of A. nidulans. AC—acetylation, ME—methyla- tion and PH—phosphorylation have been shown to be present at several residues within histone proteins. The following regulators and enzyme complexes were determined to be involved in modification of residues: Saga/Ada multi-subunit complex containing GcnE as catalyt- ic subunit for histone acetyltransferase activity; EsaA—H4 acetyltrans- ferase putatively part of the NuA4 complex; CclA—a member of the putative Set1 histone H3K4 methyltransferase complex; ClrD—a H3K9 methyltransferase necessary for di- and trimethylation of H3K9; RmtA-C—histone H4R3 methyltransferases involved in oxida- tive stress response (Bauer et al. 2010); HDAC—histone deactylases, e.g., HdaA responsible for the main deacetylase activity in A. nidulans; KDM—histone demethylases: KdmA and KdmB are capable of re- moving the tri-methylation mark of H3K9 (Agnieszka Gacek and Joseph Strauss unpublished) but involvement of H3S10ph and H3K27me in controlling secondary metabolism is tentative