Extended Data Fig. 9: Epigenetic state of genes overlapping Stowaway motifs.
From: Multilayered epigenetic control of persistent and stage-specific imprinted genes in rice endosperm
a–d, Differences in allelic weighted CG methylation (a,c) and Z-scored H3K27me3 levels (b,d) in four regions harbouring Stowaway motifs (a,b) and Stowaway motifs overlapping with hypo-DMRs of maternally inherited regions (c,d) in 5-DAP endosperm. P values were calculated by two-sided Wilcoxon rank-sum test with adjustment by Bonferroni methods. Statistical analyses were performed using 2,000 randomly selected samples from each category. e, Proportion of Stowaway motifs overlapping with hypo-DMRs of maternally inherited alleles in six genomic categories. f, Histograms showing distribution of the Stowaway motif sequence in the three categories of genes shown in the Venn diagram (Fig. 5f). Different colors indicate whether the Stowaway motif overlaps with hypo-DMRs of maternally inherited alleles (red) or not (blue). g, h, Differences in average allelic weighted CG methylation (g) and Z-scored H3K27me3 levels (h) between paternal and maternal alleles in 5-DAP endosperm are indicated according to three categories of genes shown in the Venn diagram (Fig. 5f). Colors of boxes represent different classes of imprinted genes. P values were calculated by two-sided Wilcoxon rank-sum test and adjustment by Bonferroni methods. In a–d, g, h, all data are from eight independent crosses, each consisting of two biological replicates of two combinations of reciprocal crosses between NIP-KAS and NIP-9311. The box plots show the median (line within the box), the lower and upper quartiles (box), margined by the largest and smallest data points that are still within the interval of 1.5 times the interquartile range from the box (whiskers); outliers are not shown.
