Extended Data Fig. 7: CK2 modulates genome-wide H3K27 trimethylation and gene expression in Arabidopsis.

a, Principle component (PC) analysis of WT and ck2b-quad transcriptomes at a seedling stage. Data are plotted using two PCs. Three biological replicates for each genotype were performed. b, Gene Ontology (biological processes) enrichment analysis of DEGs in ck2b (relative to WT). The abscissa represents the proportion of enriched genes in each GO term, and the size of the circle indicates the number of enriched genes. P values are adjusted using the Benjamini-Hochberg procedure. c, Heatmaps showing H3K27me3 distribution at individual loci in WT and ck2b-quad seedlings. TSS for transcription start site, TES for transcription end site, and scales on the right represent RPM values. d,e, Correlation analysis of biological replicates of H3K27me3 ChIP-seq experiments using WT (d) and ck2b-quad (e) seedlings. Three biological replicates were performed for each genotype. Values on both x and y axes are read coverages. f, Venn diagram showing overlapping of the protein-coding genes upregulated in ck2b-quad, list of genes upregulated in clf-29 swn-4, and the protein-coding loci bearing H3K27me3. Notably, the list of genes upregulated in clf swn is from the published study⁴⁹. g, Levels of H3K27me3 across the FLC locus in the seedlings of WT and clf-29. Levels of the FLC fragments immunoprecipitated by anti-H3K27me3 were quantified by qPCR and normalized to input DNA. Data are presented as mean values ± s.d. of three biological replicates.