Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L.

Abstract

Auxin is the major regulator of plant growth and development. It regulates gene expression via a family of transcription factors (ARFs) that bind to auxin responsive elements (AuxREs) in the gene promoters. The canonical AuxREs found in regulatory regions of many auxin responsive genes contain the TGTCTC core motif, whereas ARF binding site is a degenerate TGTCNN with TGTCGG strongly preferred. Thereby two questions arise: which TGTCNN variants are functional AuxRE cores and whether different TGTCNN variants have distinct functional roles? In this study, we performed meta-analysis of microarray data to reveal TGTCNN variants essential for auxin response and to characterize their functional features. Our results indicate that four TGTCNN motifs (TGTCTC, TGTCCC, TGTCGG, and TGTCTG) are associated with auxin up-regulation and two (TGTCGG, TGTCAT) with auxin down-regulation, but to a lesser extent. The genes having some of these motifs in their regulatory regions showed time-specific auxin response. Functional annotation of auxin up- and down-regulated genes also revealed GO terms specific for the auxin-regulated genes with certain TGTCNN variants in their promoters. Our results provide an idea that various TGTCNN motifs may play distinct roles in the auxin regulation of gene expression.

Auxin 2016: a burst of auxin in the warm south of China

“…This work shows that ARFs dimerize through their DNA-binding domain and suggests that the distance between target sites in promoters determines the specificity of ARF binding on everted site repeats (Boer et al, 2014). A new preferred motif, TGTCGG, was also found in this study, a result supported by a bioinformatic analysis of promoters of auxin-induced genes (Zemlyanskaya et al, 2016) presented by Victoria Mironova (Novosibirsk State University, Novosibirsk, Russia). Moreover, Andrea Gallavotti (Waksman Institute, Rutgers University, Piscataway, NJ, USA) discussed a DNA affinity purification sequencing (DAP-seq) approach that has identified binding sites on naked genomic DNA for several ARFs from both Arabidopsis and maize (O'Malley et al, 2016).…”

Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots

“…The fast primary auxin response is mediated through the ARF family of transcriptional factors, which binds TGTC-containing cis-regulatory elements 13 . While several TGTCNN hexamers are associated with auxin-responsive gene expression in general 14 , we investigate here if there are motifs associated with fold-change-specific auxin response.…”

Deep conservation of response element variants regulating plant hormonal responses

“…The sequence preference of each TF is commonly portrayed as a Position Weight Matrix (PWM), or a DNA motif, which presents the contribution of each nucleotide position to the TF binding. Motifs for the main hormone response regulating TF were derived based on biochemical affinity methods and on enriched sequences in the promoters of genes induced by hormone application 4,5 . These motifs represent a consensus of many sequences and are composed of a short core of invariant nucleotides and several variant nucleotides which identity has little effect on TF binding.…”