Comparisons of DDM1, H3K27me1, H4K16Ac, and H3.3(HTR5) chromatin association by ChIP-seq in WT andddm1leaves, as well as MGH3 in pollen from WT andddm1/+ plants. Stable and revertant differentially methylated regions (DMRs) lost DNA methylation inddm1mutants, and stable DMRs never regained methylation when DDM1 was reintroduced.74Thus, DMRs represent epigenetic targets of DDM1. Heatmaps and metaplots were generated using DeepTools,75where each region was scaled to 2 kb with 5 kb upstream and 5 kb downstream with a bin size of 10 bp and sorted based on DDM1 levels in WT. Metaplots above each heatmap show the mean value for each region. Random regions are revertant DMRs reshuffled randomly in the genome, whereas random genes correspond to the same number of protein coding genes selected at random (seeTable S1). DDM1 and H3.1 (H3K27me1) are specifically enriched at DDM1 targets (DMRs), while H4K16Ac, H3.3, and MGH3 are specifically depleted, except inddm1mutants. Similar analyses were performed on all transposable elements for comparison (Figure S5). See alsoFigure S5.
