Fig. 8

Investigation of methylation repatterning within candidate RdDM target genes that discriminate msh1-derived states. a Two of the putative cluster motifs identified based on differential gene methylation across four msh1-derived states. Hierarchical clustering on a set of 14-bp regions encompassing DMPs from seven (TOR, SYD, NRPB1, NRPD1, UBP26, SUVR5, UPF1) of the 67 core hub loci followed by DNA multiple sequence alignment of each cluster permitted the identification of methylation motifs (see “Methods” for more detail). b Difference of methylation levels on gene body DMPs within motif cluster 11 in the putative RdDM target gene UBP26. Variations on motif methylation repatterning at DMPs are shown with chromosome and position. Individual detected methylation changes are shown as color-coded dots for each plant assayed in each msh1 state, with positive (orange) indicating DMP and negative (blue) for no detected methylation change. Each line represents a single plant dataset. c Sample DMPs within motif cluster 11 in UBP26 and UPF1 that show dcl2/dcl3/dcl4-sensitivity in graft rootstock (state 1) and graft progeny (state 3) from contrasted mutant rootstock experiments. Note that dcl2/dcl3/dcl4 effects can only be assayed for msh1 and graft progeny data. All data associated with the seven genes in this figure are shown in Extended data 7. d Sample putative cluster motifs identified based on differential gene methylation across four msh1-derived states in analyses of the 67 core hub loci followed by DNA multiple sequence alignment of each cluster for methylation motifs. A complete data report for motifs identified based on all 67 genes is shown in Additional file 8