Deep conservation of cis-element variants regulating plant hormonal responses (Plant Cell)

Promoter regions upstream of transcription start sites contain DNA regulatory elements (RE) crucial for the transcriptional control of gene expression. However, REs are short degenerated sequences with low conservation during evolution. In this paper, Lieverman-Lazarovich et al. studied REs in core hormone response genes. The authors develop an alignment-free computational approach to find cases where degenerated parts of the RE are conserved across the evolution of angiosperms. They found cases of “deep” sequence conservation for different hormone responses RE, including auxin, cytokinins, and abscisic acid. These conserved elements could be physiologically important for the precise regulation of gene expression. The authors shows experimentally in Arabidopsis how conserved variants present optimal expression responses as in vivo fluorescent reporters for hormonal responses. Moreover, single nucleotide changes in promoter regions of responsive genes affect expression under hormonal treatments. These findings are important to improve our understanding of the evolution of promoter regions but also to advance the rational design of promoters for synthetic biology in plants. Based on their findings, the authors also present a novel auxin reporter system that works in both Arabidopsis and tomato.  (Summary by Facundo Romani) Plant Cell  10.1105/tpc.19.00129