5hmC and other epigenetic modifications in ESCs. (A) Correlation between 5hmC and various marks. The TFBSs were sorted based on the 5hmC levels in ±2 K regions relative to the center of the binding sites. 5hmC levels at promoter-proximal TFBSs were positively correlated with H327me3 levels and inversely correlated with GROseq and PolII levels. Transcription levels of the genes associated with the promoter were calculated using GROseq . In the sorted list, we averaged the transcription levels of the adjacent 100 genes. (B) Clustering results of 5hmC with other epigenomic data at distal (>2kbp from known TSSs) TFBSs. Cluster 1, 8 and 10 are enriched for H3K4me3 and GROseq, showing the properties of promoters. Cluster 5 and 9 display high levels of H3K27ac, indicative of active enhancers. Cluster 2 is enriched for 5hmC and 5fC, has very low GROseq levels, and lacks all investigated histone marks.