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Background  Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and functional consequences of disrupting those key BR genes still require detailed investigation.    Results  Here we performed phenotypic and transcriptomic comparisons of  A. thaliana  lines carrying a loss-of-function mutation in  BRI1  gene,  bri1– 5, that exhibits a dwarf phenotype and its three activation-tag suppressor lines that were able to partially revert the  bri1–5  mutant phenotype to a WS2 phenotype, namely  bri1–5/bri1–1D ,  bri1–5/brs1–1D,  and  bri1–5/bak1–1D.  From the three investigated  bri1–5  suppressors,  bri1–5/bak1–1D  was the most effective suppressor at the transcriptional level. All three  bri1–5  suppressors showed altered expression of the genes in the abscisic acid (ABA signaling) pathway, indicating that ABA likely contributes to the partial recovery of the wild-type phenotype in these  bri1–5  suppressors. Network analysis revealed crosstalk between BR and other phytohormone signaling pathways, suggesting that interference with one hormone signaling pathway affects other hormone signaling pathways. In addition, differential expression analysis suggested the existence of a strong negative feedback from BR signaling on BR biosynthesis and also predicted that  BRS1 , rather than being directly involved in signaling, might be responsible for providing an optimal environment for the interaction between BRI1 and its ligand.    Conclusions  Our study provides insights into the molecular mechanisms and functions of key brassinosteroid (BR) signaling genes, especially  BRS1 .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07778-w.

Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes