Brassinosteroid receptors reveal conserved features of exon-embedded gene regulation

Precise quantitative and spatial control of plant gene expression is typically attributed to cis-regulatory elements in promoters and other non-coding sequences. The extent to which exon-encoded regulatory information shapes plant gene expression and how remains unclear. Here we used BRASSINOSTEROID INSENSITIVE 1 (BRI1) as a model locus and found that it contains an exonic enhancer (EE), which is essential to establish the spatial BRI1 expression pattern. Its disruption restricts BRI1 expression and impairs BRI1-dependent root growth, linking exon-encoded regulatory information and development. The BRI1 EE acts in concert with its promoter, and related receptor kinase genes likewise harbor regulatory information within their coding sequences. Genome-wide surveys show that candidate EEs are associated with highly connected chromatin interaction networks and transcriptionally active loci. Moreover, species comparisons suggest that common features of exon-encoded regulatory information extend across diverse plant lineages. Thus, exon-encoded regulatory information is a vital component of plant gene regulation.