Super-enhancer-mediated transcriptional regulation of gene clusters in plants

Functionally related genes are frequently organized into clusters in plant genomes, including homologous gene clusters (HGCs) derived from duplicated genes and biosynthetic gene clusters (BGCs) composed of genes involved in the same metabolic pathway. Genes within a BGC are often co-expressed in a tissue- and time-specific manner, enabling the controlled production of specialized metabolites in specific plant tissues or in response to specific environmental cues. A few recent studies have revealed that transcriptional super-enhancers (SEs) play a central role in coordinating the co-expression of genes within BGCs. In Arabidopsis thaliana, SEs have been identified for a substantial proportion of BGCs. In addition, these clusters, together with their cognate SEs, are embedded within the same topologically associating domains. Disruption of these SEs through T-DNA insertions or clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-induced deletions can alter the expression of entire gene clusters. Notably, SEs linked to gene clusters can be readily predicted and mapped using tissue-specific chromatin accessibility datasets. Molecular dissection of SE-mediated regulation of BGCs holds great promise for advancing synthetic biology, metabolic engineering, and crop improvement.