We next studied the relative frequency with which different chromatin states switch to other states across different tissues and cell types (Fig. 5c), relative to switching across samples of the same tissue or cell type (Fig. S7a,b). This revealed a relative switching enrichment between active states and repressed states, consistent with activation and repression of regulatory regions. The only exception was significant switching between transcribed states and active promoter and enhancer states, possibly due to alternative usage of promoters22 and enhancers59 embedded within transcribed elements. These chromatin state switching properties were also found in the 18-state model incorporating H3K27ac marks (Extended Data 5c) and in the subset of 16 ENCODE reference epigenomes using both models (Fig. S7c,d). We found that enhancers and promoters maintained their identity, except for a small subset of regions switching between enhancer signatures and promoter signatures60. Luciferase assays showed that these regions indeed possess both enhancer and promoter activity60, consistent with their epigenomic marks.
