Enhancer- and promoter-like repeat elements (ELRs and PLRs) in human tissues and cell lines. (A) TE families enriched for ELR and PLR in different ENCODE cell lines based on histone modification ChIP-seq data using a unique mapping strategy. Bubble size indicates corrected enrichment P-value and color marks enrichment score. The enrichment test was performed with a combination of the binomial test and hypergeometric test (Methods). (B) TE families enriched for ELRs and PLRs in NIH Roadmap Epigenomics cell lines based on the consolidated histone modification ChIP-seq data. Tissue-specifically enriched TE families such as ERV1 and ERVL in ESCs and iPSCs are marked by lavender ellipses. (C) Cumulative ratio of ELRs and PLRs among MIR, L2, and all TEs in human tissues in NIH Roadmap data. (D) Saturation estimation of active TEs bound by EP300. Upper panel is the heat map of detected active TEs bound by EP300 in human cell lines or tissues collected from GEO; each column is a sample, and each row is a TE; values in the heat map are binary, and 1 (red) means the TE is bound by EP300; lower panel is the cumulative ratio of the active TEs among MIR, L2, and all TEs; 55.51% of the EP300-bound TEs are restricted to predominately one tissue or cell. (E) Distance distribution of centers of ELRs to nearest eQTLs from GRASP database; 74.35% of the ELR centers have eQTLs in vicinity of 10 kb. The permutated background was the mean value by sampling the same number and same length sequences to the all ELRs 100 times. (F,G) Hi-C (GSM1551552) PETs and H3K27ac ChIA-PET (GSE59395) PET frequencies linking ELRs and TSSs, compared to the same number of nearest non-ELR and non-PLR TEs in the same families (background).
