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

PLoS Genet. 2020 Apr 24;16(4):e1008764. doi: 10.1371/journal.pgen.1008764. eCollection 2020 Apr.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Assembly and Disassembly
  • Enhancer Elements, Genetic*
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant*
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Promoter Regions, Genetic
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcriptional Activation
  • Zea mays / genetics*
  • Zea mays / growth & development


  • Plant Proteins
  • Transcription Factors

Grants and funding

This work was supported by the National Natural Science Foundation of China (91935305, 31701431) and the National Key Research and Development Program of China (2016YFD0100404). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.