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Fig. 4 | Genome Biology

Fig. 4

From: BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes

Fig. 4

The BIND&MODIFY showed the heterogeneity of H3K27me3 regulation. A The read counts of H3K27me3 in ChIP-seq (Chr20:52,317,726–52,320,951) was shown in upper panel. The single-molecular resolution of Chr20:52,317,726–52,320,951visualize each molecular methylation statues of H3K27me3. The rows in heatmap represented the different DNA molecules. The color indicated the methylation ratio (non-sliding 50-bp bins), which represented the possible H3K27me3 signal. The DNA molecules could be classified into three states: heavy state (methyl) (We used the m.6A methylation probability cut-off 0.80 in the single-molecular analysis; the methylated bins were defined as the methylation ratio > 0.5 in bins and at least 2 methylation sites; heavy states were defined as the methylation bin density > 75%), medium state (defined as the methylation bin density 25 ~ 75%), and light state (defined as the methylation bin density < 25%). The right heatmap showed the CpG methylation distribution on the corresponding DNA molecules in the left H3K27me3 heatmap (one-to-one matching). The H3K27me3 signal decreased with the decreasing CpG methylation (scatter plot). B H3K27me3 heterogeneity pattern of genetic promoters in Chr20 (method in Fig. S13). Each pixel on each row corresponds to methylation bin density of each individual DNA molecule, and each row corresponds to each genetic promoter (2 kb upstream of the transcription start site included most of the promoter regions). The methylation bin density was ranked from low to high (left to right). The blue, white-yellow, red corresponded matched the heavy, medium, light state. The left green bar (expr) showed the average expression value (expected count) of the corresponding gene clusters. Cluster 3, Cluster 4 with high RNA expression level were highlighted by green box. Cluster 1, Cluster 5 with low RNA expression level were highlighted by purple box. C The bar plot showed the GO enrichment analysis of the Cluster 1. Details of H3K27me3 heterogeneity calculation methods can be found in Fig. S18

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