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 UB2centered 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.

Gene duplication at the Fascicled ear1 locus controls the fate of inflorescence meristem cells in maize

“…We hypothesize that in Fas1 alleles, promoters or enhancers formed as a result of the duplication events. Distal regulation of gene expression has been described for teosinte branched1 ( 53 ) and unbranched3 ( 54 ). The unknown regulatory sequences at Fas1 , whether they are enhancer–promoter or promoter–promoter chromatin interactions, cause ectopic expression of zmm8 and drl2 at an earlier stage than in wild type.…”

“…Agrobacterium tumefaciens GV3101 cells were used for transformation, and the Nicotiana benthamiana was used for transient expression with three replicates. After 48 h of growth under a 16 h light/8 h dark cycle, 1 mM luciferin (Promega) was applied to the abaxial epidermis of each leaf, and the luciferin signal were detected and captured as described in ( 54 ).…”

Unraveling the 3D Genome Architecture in Plants: Present and Future

“…Maize KRN4 is a distal enhancer that interacts with the promoter of UB3, a key inflorescence gene. This enhancerpromoter interacting loop fine-tunes UB3 expression and controls inflorescence development and kernel row number (Du et al, 2020). However, only a few similar cases of chromatin loops controlling phenotypes have been elucidated in plants.…”

Plant 3D genomics: the exploration and application of chromatin organization

“…Likewise, the intergenic quantitative trait locus (QTL) KRN4 associated with kernel row number was mapped to a c. 60 kb region downstream of UNBRANCHED3 (UB3) in maize. KRN4 has been shown to act as an enhancer of the UB3 promoter to fine-tune the expression of UB3 in the meristem of the ear inflorescence by interacting with the UB3 promoter and recruiting the UB2centered transcriptional complex (Du et al, 2020).…”