The data presented here demonstrate that bidirectional capped RNAs, as measured by CAGE, are robust predictors of enhancer activity in a cell. Transcription is only measured at a fraction of chromatin-defined enhancers and few untranscribed enhancers show potential enhancer activity. This implies that many chromatin-defined enhancers are not regulatory active in that particular cellular state, but may be active in other cells of the same lineage32 or are pre-marked for fast regulatory activity upon stimulation33. Of course, given the relative instability of enhancer RNAs some chromatin-defined sites may be active but fall below the limits of detection of CAGE.
