Recent genetic, genomic and biochemical research has established a new feature of plant genomes – the widespread co-localisation of genes for specialised metabolic pathways. The ability to synthesise a diverse cocktail of low-molecular weight molecules is essential for all plants to interact and communicate with the environment and provides humans with a plethora of chemical scaffolds to combat illnesses and develop higher-value molecules. The co-localisation of the functionally related biosynthesis genes contrasts the general gene order in eukaryotes and raises numerous questions about the genetic organisation, evolution and regulation of these so called metabolic gene clusters.

Here, an overview about metabolic gene clustering in plants with an emphasis on their transcriptional regulation will be given. The co-localisation of functionally-related genes enables the formation of fundamentally different mechanisms of gene regulation in comparison to the control of dispersed genes. Our research shows that specific chromatin marks delineate and control the expression of plant metabolic gene clusters. Chromatin analyses in A. thaliana reveal that silenced and activated gene clusters are closely associated with histone H3 lysine 27 trimethylation and incorporation of the histone variant H2A.Z, respectively. In contrast, non-clustered genes of multi-step metabolic pathways are not associated with these modifications. Analyses of H3K27me3 profiles in oat, rice and maize suggest a conserved function of histone methylation in the repression of plant metabolic gene clusters across plant species.

In summary, we show that metabolic gene clusters in plants have localised chromatin signatures that are involved in the tight regulation of these clusters. Our work supports the hypothesis of a chromatin code that is associated with clustered eukaryotic genes and affords new opportunities for pathway discovery and manipulation of plant specialised metabolism.