Fig. 3

MpBMI1/1L affect morphological development of Marchantia and regulate gene silencing and activation. a–e Morphological phenotypes of 35-day-old wild type (WT), Mpbmi1/1l #1, Mpbmi1/1l #2, Mpbmi1/1l #3, and Mpbmi1l-4 lines. Scale bars: 1 cm. f–h Gemma cups of 35-day-old WT, Mpbmi1/1l #1, and Mpbmi1/1l #2 lines. Scale bars: 0.1 cm. i Western blot showing the bulk H2Aub levels in WT, Mpbmi1/1l #1, Mpbmi1/1l #2, Mpbmi1/1l #3, and Mpbmi1l-4 mutants. j MA plot showing differential gene expression (Log2 fold change (Log2fc)) in Mpbmi1/1l #1 mutants compared to WT. 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, l Boxplot showing the H2Aub (k) and H3K27me3 (l) levels (RPKM, reads per kilobase per million mapped reads) of upregulated and downregulated genes in Mpbmi1/1l #1 mutants. H2Aub and H3K27me3 levels were calculated as the average RPKM from 1 kb upstream of the transcriptional start to the transcriptional end of genes. Boxes show medians and the interquartile range, and error bars show the full range excluding outliers. **p < 0.01 (Wilcoxon test). m Percent of upregulated (Up) and downregulated (Down) genes marked by only-H2Aub, H2Aub/H3K27me3, and only-H3K27me3 in Mpbmi1/1l #1 mutants. **p < 0.01 (Hypergeometric test). n MA plot showing differential transposable element (TE) expression (Log2fc) in Mpbmi1/1l #1 mutants compared to WT. Significant TE 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). o Percent of upregulated (Up_TE) and downregulated (Down_TE) TEs marked by only-H2Aub, H2Aub/H3K27me3, and only-H3K27me3 in Mpbmi1/1l #1 mutants. *p < 0.05; **p < 0.01 (Hypergeometric test)