TSS-associated, uncapped small RNAs (TSSa-RNAs), attributed to RNAPII protection and found immediately downstream of mRNA TSSs15,16, were detectable in the same positions downstream of enhancer TSSs (Supplementary Fig. 12), indicating that RNAPII initiation at enhancer and mRNA TSSs is similar. Indeed, CAGE-defined enhancer TSSs resembled the proximal position-specific sequence patterns of non-CGI RefSeq TSSs (Fig. 2c, and Supplementary Fig. 13a). Furthermore, de novo motif analysis revealed sequence signatures in CAGE-defined enhancers closely resembling non-CGI promoters (Fig. 2d, and Supplementary Fig. 13b).
