Fig. 2

HD2B and MPK3 regulate the basal expression of a subset of defense genes. a Annotation of hd2b deregulated genes. Twenty-six percent of hd2b deregulated genes are downregulated (green, 452 genes) whereas 74% are upregulated (red, 1263 genes). Generation of a hierarchical tree graph with the Agrigo GO Analysis Toolkit shows that 63% of the upregulated genes code for proteins with significant enrichment in “transcription” and “RNA biosynthetic process.” b Comparisons among the transcriptomes of hd2b and mpk3 mutants. Thirty-two percent of upregulated (414) and 29% of downregulated (126) genes in mpk3 are in common with hd2b mutants. c GO analysis of commonly upregulated genes in hd2b and mpk3 mutants with the Agrigo GO Analysis Toolkit. Histograms of the values highlight the enrichment of genes involving RNA biosynthesis and transcription. P values for each enriched class are indicated (p-v). d Comparisons of the 414 commonly upregulated genes in hd2b and mpk3 mutants with the genes upregulated or downregulated in WT seedlings by flg22 treatment for 30 min. e Validation of transcriptomic data by quantitative reverse transcription polymerase chain reaction (RT-qPCR). The upregulation of four genes (of the 150 commonly upregulated genes in hd2b and mpk3 and flg22-treated WT in Fig. 2d) was confirmed by RT-qPCR. f HD2B protein binding to flg22-inducible genes in mock conditions. Chromatin immunoprecipitation (ChIP)-qPCR assays with anti-GFP antibodies were performed on pHD2B::GFP-HD2B seedlings (Fig. 2e). An IgG antibody was used as a negative control. g MPK3 and HD2B promote H3K9 deacetylation of flg22-inducible genes in mock conditions. Using an anti-H3K9ac antibody, ChIP-qPCR assays were performed in hd2b, mpk3, and WT seedlings. Compared with WT, the four loci (Fig. 3e and f) were hyperacetylated in hd2b and mpk3 mutants