For microarray analysis, the aerial parts of 18-day-old WT, brd2-1, brd1-2 brd2-1, and brd1-2 brd2-1 brd13-4 (brdx3) seedlings were collected in three biological replicates. RNA was extracted using an RNeasy Plant Kit (QIAGEN) and digested with TURBO DNase (Ambion). Microarray hybridization was performed as described previously (Buszewicz et al., 2016) using the Affymetrix Gene Atlas system according to the manufacturer's instructions. Data analysis was performed using Bioconductor packages in the R environment. Raw CEL files were annotated to the associated annotation package pd.aragene 1.1 st built with the pdInfoBuilder package (Falcon et al., 2020). Normalization of the raw intensities was performed using the Robust Multiarray Averaging method from the oligo package (Carvalho and Irizarry, 2010). Differential gene expression analysis was performed with the limma package (Ritchie et al., 2015). Data were fitted to a linear model, and moderated t-statistics were computed by empirical Bayes moderation. A gene was identified as differentially expressed in a selected genotype when the P value was <0.01 and the expression fold change was >1.5 relative to the WT. Overlap between brdx3 and brm-1 transcriptional profiles was analyzed using a published dataset (Buszewicz et al., 2016). Genes were selected as differentially expressed based on the same P value (<0.01) and fold change (>1.5) values. The AgriGO online tool was used for GO analysis (http://systemsbiology.cau.edu.cn/agriGOv2/) (Tian et al., 2017). Venn diagrams were constructed using the DeepVenn tool (Hulsen et al., 2008).

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