Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures

Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we show that warm temperature promotes both callus formation and shoot regeneration efficiency in Arabidopsis thaliana. Our RNA sequencing analysis unveil that this accompanied by the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1), encoding a transcription factor involved in shoot meristem formation, and ISOPENTENYLTRANSFERASE (IPT1) and YUCCA1/4 (YUC1/4), encoding key enzymes for cytokinin and auxin biosynthesis, respectively. Consistently, mutations in CUC1 and IPT1 or chemical inhibition of YUCs reduce the enhancement of shoot regeneration at warm temperature. When combined with ChIP sequencing analyses, our RNA sequencing data further reveal that histone variant H2A.Z is enriched on these differentially expressed loci at 17°C and that its occupancy level decreases when the ambient temperature increases to 27°C. This study thus unveil a new epigenetic mechanism that influences hormone-induced regeneration and brings further insights on how incubation temperature is a crucial parameter in optimizing protocols for in vitro tissue culture. Overall design: RNA sequencing in Arabidopsis thaliana hypocotyl explants exposed to CIM for 4 days then SIM for 4 days, at either 17°C or 27°C