Fig. 2

H2Aub is required for gene repression and activation. a, b MA plots showing differential gene expression (Log2 fold change (Log2fc)) in Mph2a;H2AK115R/K116R (a) and Mph2a;H2AK119R (b) mutants compared to wild type (WT). Significant changes are marked in red (log2 fold change ≥ 1 and adjusted p value ≤ 0.05) and blue (log2 fold change ≤ −1 and adjusted p value ≤ 0.05). c Presence of only-H2Aub, H2Aub/H3K27me3, or only-H3K27me3 marks on upregulated (Up) and downregulated (Down) genes in Mph2a;H2AK115R/K116R and Mph2a;H2AK119R mutants. Presence of modifications is based on their distribution in WT. **p < 0.01 (Hypergeometric test). d Expression level distribution of genes marked by only-H2Aub, H2Aub/H3K27me3, and only-H3K27me3 in WT. **p < 0.01 (Hypergeometric test). e, f Boxplots showing the H2Aub level (RPKM, reads per kilobase per million mapped reads) on upregulated genes in Mph2a;H2AK115R/K116R (e) and Mph2a;H2AK119R (f) mutants. g, h Boxplots showing H2Aub levels on downregulated genes in Mph2a;H2AK115R/K116R (g) and Mph2a;H2AK119R (h) mutants. H2Aub levels in e-h were calculated as the average RPKM from 1 kb upstream of the transcriptional start to the transcriptional start of genes. *p < 0.05; **p < 0.01 (Wilcoxon test). i, j MA plots showing differential expression of transposable elements (TEs) (Log2fc) in Mph2a;H2AK115R/K116R (i) and Mph2a;H2AK119R (j) mutants. Significant gene expression changes are marked in red (log2 fold change ≥ 1 and adjusted p value ≤ 0.05) and blue (log2 fold change ≤ −1 and adjusted p value ≤ 0.05). k Presence of only-H2Aub, H2Aub/H3K27me3, or only-H3K27me3 marks on upregulated (Up TE) and downregulated (Down TE) TEs in Mph2a;H2AK115R/K116R and Mph2a;H2AK119R mutants. *p < 0.05; **p < 0.01 (Hypergeometric test). l Expression level distribution of transposable elements (TEs) marked by only-H2Aub, H2Aub/H3K27me3, and only-H3K27me3 in WT. **p < 0.01 (Hypergeometric test). m, n Boxplots showing the H2Aub levels on upregulated TEs in Mph2a;H2AK115R/K116R (m) and Mph2a;H2AK119R (n) mutants. o, p Boxplots showing H2Aub levels on downregulated TEs in Mph2a;H2AK115R/K116R (o) and Mph2a;H2AK119R (p) mutants. H2Aub levels in m-p were calculated as the average RPKM from the start to the end of TEs. Boxes show medians and the interquartile range, and error bars show the full range excluding outliers. *p < 0.05; **p < 0.01 (Wilcoxon test)