Fig. 2

Features of H3K27me3 long LOCKs. A–C DNA methylation (A), gene expression (B), and gene density (C) in long LOCKs and the background within common PMDs or HMDs. D Relative loop density in the long LOCKs and the background within the whole genome, common PMDs, or common HMDs. Line colors represent the relative loop density within long LOCKs compared to the background in each sample. The Winsorize method was used to remove outliers, excluding samples with values beyond mean ± 3 SDs for long LOCKs or the background. E The enrichment of long LOCKs in S/I/L-PMDs and common HMDs. F Gene density in long LOCKs and in the background within S/I/L-PMDs. G The top 20 pathways most enriched in genes within long LOCKs in S/I/L-PMDs. Each column represents a Roadmap sample. H The beeswarm plot shows the proportion of OGs or TSGs in long LOCKs among all genes in long LOCKs, separately for common PMDs/HMDs and S/I/L-PMDs. The purple dots represent the proportion of OGs or TSGs among all genes in common PMDs/HMDs or S/I/L-PMDs. OGs oncogenes, TSGs tumor suppressor genes. I The density plot shows the proportion of OGs among all genes in long LOCKs, separately for S/I/L-PMDs. J Comparison of the expression of OGs or TSGs within long LOCKs to those outside long or short LOCKs, separately for common PMDs or HMDs. K Consistent with the content depicted in J, but for OGs in S/I/L-PMDs. The two-tailed paired t-test was used (***p < 0.001, **p < 0.01, *p < 0.05, NS = not significant) in (B-D, H, J and K). L H3K27me3 modification near the IGF2BP1 gene in different Roadmap samples. IGF2BP1 is an OG, with more than half of its length located in S-PMDs