UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize

Abstract

Enhancers are cis-acting DNA segments with the ability to increase target gene expression. They show high sensitivity to DNase and contain specific DNA elements in an open chromatin state that allows the binding of transcription factors (TFs). While numerous enhancers are annotated in the maize genome, few have been characterized genetically. KERNEL ROW NUMBER4 (KRN4), an intergenic quantitative trait locus for kernel row number, is assumed to be a cis-regulatory element of UNBRANCHED3 (UB3), a key inflorescence gene. However, the mechanism by which KRN4 controls UB3 expression remains unclear. Here, we found that KRN4 exhibits an open chromatin state, harboring sequences that showed high enhancer activity toward the 35S and UB3 promoters. KRN4 is bound by UB2-centered transcription complexes and interacts with the UB3 promoter by three duplex interactions to affect UB3 expression. Sequence variation at KRN4 enhances ub2 and ub3 mutant ear fasciation. Therefore, we suggest that KRN4 functions as a distal enhancer of the UB3 promoter via chromatin interactions and recruitment of UB2-centered transcription complexes for the fine-tuning of UB3 expression in meristems of ear inflorescences. These results provide evidence that an intergenic region helps to finely tune gene expression, providing a new perspective on the genetic control of quantitative traits. Author summary With the completion of increasing numbers of plant genome sequences and continuous accumulation of multiomics data, numerous regulatory elements are annotated in those intergenic regions containing open chromatin. Enhancers are cis-acting DNA elements with the ability to increase target gene expression. They show high sensitivity to DNase and contain specific DNA elements in an open chromatin state that allows the binding of transcription factors. KERNEL ROW NUMBER4 (KRN4) is an intergenic region located downstream of a key inflorescence gene UNBRANCHED3 (UB3). However, the mechanism by which KRN4 regulates UB3 expression remains unknown. Here, we showed the genetic interactions between KRN4 and UB3 as well as UNBRANCHED2 (UB2) in controlling inflorescence architecture, enhancer activity of KRN4 toward UB3 promoters, and KRN4- recruited UB2-centered transcription complex for UB3 transcription. These results provide evidence that an intergenic region helps to finely tune gene expression and quantitative traits.