Fig. 1

UBP12/13 directly repress PRC2 target genes. a Fold enrichment of the overlap of lists of genes upregulated in ubp12/13 (1150 genes, yellow circle) and genes upregulated in PRC1 (bmi1a/b, 387 genes, blue circle) [19], PRC2 (clf swn, 2824 genes, red circle) [19], and EMF1c (emf1, 2140 genes, purple circle) [9] mutants. The dashed line indicates the expected overlap based on chance. p values are based on a hypergeometric test for significant over-enrichment. b Waffle plot showing the presence of the H2Aub1 and H3K27me3 marks in wild type on UBP12/13 target genes. The black border indicates those UBP12/13 targets that are marked with H3K27me3 (and hence PRC2 targets). Each square corresponds to about 10 genes. c Boxplots showing differential expression of all expressed UBP12/13 targets (green) and all other protein-coding genes (grey). Test for significance was done by the Mann-Whitney U test; ns p ≥ 0.05, *p < 0.05, **p < 0.01,***p < 0.001. d Metagene profiles showing the median of H2Aub1 and H3K27me3 enrichment for gene categories defined by the presence of significant H2Aub1 and H3K27me3 peaks. The darker grey box indicates the first 1 kb of the gene body, and both grey boxes together indicate the mean gene body size within that category. e Pie charts indicating the percentage of genes in the indicated category corresponding to UBP12/13 targets. Note that above “UBP12/13 targets” refers to genes gaining H2Aub1 in ubp12/13 mutants. The biological material underlying the RNA-seq data in this figure is 2-week-old whole plants (bmi1a/b, clf swn, and ubp12/13) and 3-week-old whole plants (emf1). ChIP-seq data was obtained from 33 DAG rosettes