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Transcriptome for: MYB42 inhibits hypocotyl cell elongation by coordinating brassinosteroid homeostasis and signaling in Arabidopsis

Cite this dataset

Zhuang, Yamei (2022). Transcriptome for: MYB42 inhibits hypocotyl cell elongation by coordinating brassinosteroid homeostasis and signaling in Arabidopsis [Dataset]. Dryad.


The precise control of brassinosteroids (BRs) homeostasis and signaling is a prerequisite for hypocotyl cell elongation in plants. Little is known, however, of such regulators of BR homeostasis and signaling. Here, we have demonstrated that MYB42 negatively regulates hypocotyl elongation through partial inhibition of BRASSINAZOLE-RESISTANT 1 (BZR1) signaling and promotion of BR inactivation. Transgenic Arabidopsis plants repressing the expression of MYB42 and its paralog MYB85 (MYB85 RNAi;myb42) exhibited longer hypocotyls than wild-type (WT) plants in darkness, while MYB42 or MYB85 overexpression inhibits hypocotyl elongation. Hypocotyl length of MYB85 RNAi;myb42 plants can be resorted into WT level by MYB42 overexpression. MYB42 inhibits hypocotyl elongation by mediating BR signaling, because MYB42 expression is repressed with BR treatment and in the dominant BR mutant bzr1-1D, and mutation of both MYB42 and MYB85 enhances the dwarf phenotype of the BR receptor mutant bri1-5. BZR1 directly represses MYB42 expression in response to BR, and the hypocotyl length of bzr1-1D is reduced in MYB42 overexpression plants but increased in MYB85 RNAi;myb42 plants. These results show MYB42 is a negative target of BZR1. Transcriptome data revealed that a number of BZR1-induced genes associated with cell elongation are down-regulated by MYB42, suggesting that MYB42 may partially inhibit BZR1 signaling. In addition, MYB42 enlarges its action in BR signaling through feedback activation of the BR-inactivating enzyme DOGT1. The present study shows a MYB42-mediated multilevel system that contributes to fine regulation of BR-induced hypocotyl elongation.


Hypocotyls of 5-day-old dark-grown MYB85RNAi;myb42 and wild-type seedlings with or without 0.02 uM PCZ were sampled for total RNA extraction with the TRIzol reagent (Invitrogen). For each genotype, 3 independent lines including at least 100 plants were selected. After mRNA library construction, sequencing was performed on an Illumina HiSequation 2500 platform (Annoroad Gene). Sequence data with base-pair qualities in the Q>20 were extracted by custom Perl scripts. The filtered reads were mapped to the Arabidopsis genome (TAIR10) using the splice-aware read aligner TopHat2 software with default parameters (Kim et al. 2013). To calculate gene expression intensity, read counts were normalized to the number of fragments per kilobase of transcript per million mapped reads (FPKM) according to the gene length and total mapped reads. The R package DEGseq was used to identify DEGs from RNA-Seq data. Genes with FPKM less than 1 were removed from analyses. DEGs were characterized according to the criterion of fold change (FC) >2.0 and false discovery rate (FDR) < 0.05.