Comparative transcriptomic analysis to identify brassinosteroid response genes.

Brassinosteroids (BRs) are plant growth-promoting steroid hormones. BRs affect plant growth by regulating panels of downstream genes. Much effort has been made to establish BR-regulated gene expression networks, but there is little overlap among published expression networks. In this study, we built an optimal BR-regulated gene expression network using the model plant Arabidopisis (Arabidopisis thaliana). Seven- and 24-day-old seedlings of the constitutive photomorphogenesis and dwarfism (cpd) mutant and bri1-701 (brassinosteroid-insensitive 1-701) brl1 (BRI1-like receptor genes 1) brl3 triple mutant seedlings were treated with brassinolide (BL), and RNA sequencing (RNA-seq) was used to detect differentially expressed genes (DEGs). Using this approach, we generated a transcriptomic database of 4498 DEGs and identified 110 transcription factors that specifically respond to BR at different stages. We also found that, among the identified BR-responsive transcription factors, ABSCISIC ACID-INSENSlTIVE4 (ABI4), an ethylene response factor (ERF) transcription factor, inhibits BR-regulated growth. Compared to wild-type plants, the abi4-102 mutant was less sensitive to brassinazole (BRZ) and more sensitive to BR. Next, we performed a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) assay and established that ABI4 binds directly to the BAK1 (BRI1-associated receptor kinase 1) promoter and inhibits transcription. These results provide insight into BR-responsive gene functions in regulating plant growth at different stages and may serve as a basis for predicting gene function, selecting candidate genes, and improving the understanding of BR regulatory pathways.