While capped RNAs of protein-coding gene promoters were strongly biased towards the sense direction, similar levels of capped RNA in both directions were detected at enhancers (Fig. 1b, and Supplementary Fig. 2b, c). Thus, bidirectional capped RNAs is a signature feature of active enhancers. On this basis, we identified 43,011 enhancer candidates across 808 human CAGE libraries (see Supplementary Text and Supplementary Figs 6-8). Interestingly, the candidates were depleted of CpG islands (CGI) and repeats (with the exception of neural stem cells, see ref. 9).
