STARR-Seq Identifies Enhancers in the Arabidopsis thaliana Genome

Plants respond to environmental stimuli by tightly controlled changes in gene expression. Key features of gene regulation, long-range activation and topological domains, appear to be missing in chromatin interaction data of the plant Arabidopsis thaliana. This lack of distal physical interactions among chromosomes has been interpreted to mean that plants do not utilize typical enhancers, though enhancers are frequent among other higher eukaryotes. We challenge this interpretation with an alternative method to characterize enhancers, STARR-seq. We optimized STARR-seq for transient expression in plants and demonstrate the method’s ability to scale to large plant genomes. We applied STARR-seq to Arabidopsis, which has a well-defined chromatin accessibility landscape but few known enhancers. We seek to addresses fundamental questions of plant gene regulation as well as offers new avenues for crop design in a changing climate.