Detection and quantification of the histone code in the fungal genusAspergillus

In eukaryotes, the combination of different histone post-translational modifications (PTMs) – the histone code – impacts the chromatin organization as compact and transcriptionally silent heterochromatin or accessible and transcriptionally active euchromatin. Although specific histone PTMs have been studied in fungi, an overview of histone PTMs and their relative abundance is still lacking. Here, we used mass spectrometry to detect and quantify histone PTMs in germinating spores of three fungal species belonging to three distinct taxonomic sections of the genusAspergillus(Aspergillus niger, Aspergillus nidulans(two strains), andAspergillus fumigatus). We overall detected 23 different histone PTMs, including a majority of lysine methylations and acetylations, and 23 co-occurrence patterns of multiple histone PTMs. Among those, we report for the first time the detection of H3K79me1/2 and H4K5/8/12ac in Aspergilli. Although all three species harbour the same PTMs, we found significant differences in the relative abundance of H3K9me1/2/3, H3K14ac, H3K36me1 and H3K79me1, as well as the co-occurrence of acetylation on both K18 and K23 of histone H3 in a strain-specific manner. Our results provide novel insights about the underexplored complexity of the histone code in filamentous fungi, and its functional implications on genome architecture and gene regulation.HighlightsQuantitative mass spectrometry allows uncovering major histone PTMs.H3K79me1/2 and H4K5/8/12ac are new histone PTMs detected in Aspergilli.The relative abundance of histone PTMs varies in a strain-specific manner.Variation in histone PTM abundance reflects different chromatin status.