Genome-wide RNA-seq analysis indicates that the DAG1 transcription factor promotes hypocotyl elongation acting on ABA, ethylene and auxin signaling

Riccardo Lorrai,Rosalba Lepore,Alessandra Boccaccini,Francesco Gandolfi,Paolo Costantino,Paola Vittorioso,Marco Possenti,Anna Tramontano,Veronica Ruta

doi:10.1038/s41598-018-34256-3

Abstract

Hypocotyl elongation is influenced by light and hormones, but the molecular mechanisms underlying this process are not yet fully elucidated. We had previously suggested that the Arabidopsis DOF transcription factor DAG1 may be a negative component of the mechanism of light-mediated inhibition of hypocotyl elongation, as light-grown dag1 knock-out mutant seedlings show significant shorter hypocotyls than the wild type. By using high-throughput RNA-seq, we compared the transcriptome profile of dag1 and wild type hypocotyls and seedlings. We identified more than 250 genes differentially expressed in dag1 hypocotyls, and their analysis suggests that DAG1 is involved in the promotion of hypocotyl elongation through the control of ABA, ethylene and auxin signaling. Consistently, ChIP-qPCR results show that DAG1 directly binds to the promoters of WRKY18 encoding a transcription factor involved in ABA signaling, of the ethylene- induced gene ETHYLENE RESPONSE FACTOR (ERF2), and of the SMALL AUXIN UP RNA 67 (SAUR67), an auxin-responding gene encoding a protein promoting hypocotyl cell expansion.

Highlights

Once germination is completed, the seedling undergoes photomorphogenesis or skotomorphogenesis, depending on the presence or absence of light[1]
Among the up-regulated genes of the dag1/WT hypocotyl comparison group falling in the “response to abscisic acid” biological process and whose expression we validated by RT-qPCR were RAB GTPASE HOMOLOG B18 (RAB18) and ABA REPRESSOR1 (ABR1), encoding a GTPase and a transcription factor respectively, involved in Abscissic acid (ABA) signaling[21,22,23]
The WRKY transcription factors are known as key components of ABA signaling: WRKY18, and the two closely related WRKY60 and WRKY40 proteins, have been shown to cooperate in plant response to biotic stress with both overlapping and distinct functions[40,41]

Summary

Introduction

The seedling undergoes photomorphogenesis or skotomorphogenesis, depending on the presence or absence of light[1]. Auxin plays a pivotal role in promoting cell elongation, and its effect is mediated by the TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN SIGNALING F-BOX (AFB)-Aux/IAA nuclear auxin receptor and the activation of SMALL AUXIN UP RNA (SAUR) genes[2,3]. Once the seedling perceives the light, ethylene signaling is switched off by phyB-mediated EIN3 degradation[7]. It has been proposed that the stimulatory or inhibitory response to exogenous ABA depend on both doses of, and tissue sensitivity to this hormone[11]. Hayashi and collaborators[12] have shown that in dark-grown Arabidopsis seedlings ABA reduces the phosphorylation levels and the activity of the plasma membrane H+-ATPase that triggers growth of the hypocotyl

Methods

Results

Conclusion