Differentially expressed genes between WT and HRE1a OX, WT and HRE1ß OX, and WT and AtRH17 OX
We characterized and compared the biological and molecular functions of HRE1a and HRE1ß, two alternative splicing variants of HRE1, a AP2/ERF transcription factor in Arabidopsis. To compare the downstream regulatory mechanisms of HRE1a and HRE1ß, Quant-Seq analysis was carried out. The experiment was designed to identify and compare differentially expressed genes (DEGs) between WT and HRE1a-overexpressing transgneic plants (OXs) and WT and HRE1ß OXs grown for 14 days under SD conditions. We analyzed the biological process gene ontology (GO) annotation categories of the DEGs in HRE1a OXs and HRE1ß OXs. The genes upregulated in HRE1a OXs, but not in HRE1ß OXs, were enriched in the regulation of biological processes such as flower development, shoot system development, circadian rhythms, gene expression, response to gibberellin, nitrogen compound metabolic process, and aromatic compound biosynthetic processes. However, the genes up-regulated in HRE1ß OXs, but not in HRE1a OXs, were enriched in the regulation of the following processes: response to toxic substances, secondary metabolic processes, response to biotic stimulus, glutathione metabolic process, response to reactive oxygen species, cell wall organization, DNA replication, response to salicylic acid, lipid localization, response to oxidative stress, carbohydrate metabolic process, photosynthesis, mitotic cell cycle process, response to osmotic stress, and response to abscisic acid. The genes upregulated in both HRE1a OXs and HRE1ß OXs were enriched in biological processes involved in response to abiotic stimulus, response to light stimulus, response to endogenous stimulus, response to oxygen-containing compound, and response to lipid. In addition, we investigated the biological function of AtRH17, a DEAD-box RNA helicase gene in Arabidopsis, in salt stress response. To investigate the downstream regulatory mechanisms of AtRH17, Quant-Seq analysis was carried out. The experiment was designed to identify DEGs between WT and AtRH17 OXs grown for 14 days under SD conditions. GO annotation enrichment and KEGG pathway analysis showed that the upregulated and downregulated genes are involved in various biological functions including secretion, signaling, detoxification, metabolic pathways, catabolic pathways, and biosynthesis of secondary metabolites as well as in stress responses. Genevestigator analysis of the upregulated genes showed that nine genes, namely, LEA4-5, GSTF6, DIN2/BGLU30, TSPO, GSTF7, LEA18, HAI1, ABR, and LTI30, were upregulated in Arabidopsis under salt, osmotic, and drought stress conditions. In particular, the expression levels of LEA4-5, TSPO, and ABR were higher in AtRH17 OXs than in WT under salt stress condition. Overall design: Differentially expressed genes between WT and HRE1a OX, WT and HRE1ß OX, and WT and AtRH17 OX at 14 days after germination under SD conditions (8-h-light and 16-h-dark cycle) were explored in whole genome level.