Transcriptomic and ChIP-Seq analyses reveal an important role for the ABI4 during BR response in Arabidopsis
Brassinosteroids (BRs) are growth-promoting steroid hormones in plants. BRs affect plant growth by regulating panels of downstream genes. Much effort has been made to establish BR-regulated gene expression networks, but these published expression networks poorly overlap. To address this, here we build an optimal BR-regulated gene expression network. 7- and 24-day-old seedlings of constitutive photomorphogenesis and dwarfism (cpd) mutant and bri1-701 (brassinosteroid-insensitive 1) brl1 (BRI1-like receptor genes 1) brl3 (BRI1-like receptor genes 3) triple mutant seedlings were treated with brassinolide (BL), and RNA sequencing (RNA-seq) was used to detect differentially expressed genes (DEGs). By this approach, we generated a transcriptomic database of 4498 DEGs and identified 110 transcription factors specifically respond to BR at different stage. Moreover, we 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 found that ABI4 directly binds to the BAK1 (BRI1 Associated receptor Kinase 1) promoter and inhibits transcription. These results provide new insights 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. Overall design: mRNA profiles of 7-and 24-day old cpd  and bri1-701 brl1 brl3 arabidopsis seedlings treated with or without brassinolide (BL) were generated by deep sequencing, in triplicate.