Widespread Transcription at Neuronal Activity-Regulated Enhancers

We used genome-wide sequencing methods to study stimulus-dependent enhancer function in mouse cortical neurons. We identified ∼12,000 neuronal activity-regulated enhancers that are bound by the general transcriptional co-activator CBP in an activity-dependent manner. A function of CBP at enhancers may be to recruit RNA polymerase II (RNAPII), as we also observed activity-regulated RNAPII binding to thousands of enhancers. Notably, RNAPII at enhancers transcribes bi-directionally a novel class of enhancer RNAs (eRNAs) within enhancer domains defined by the presence of histone H3 monomethylated at lysine 4. The level of eRNA expression at neuronal enhancers positively correlates with the level of messenger RNA synthesis at nearby genes, suggesting that eRNA synthesis occurs specifically at enhancers that are actively engaged in promoting mRNA synthesis. These findings reveal that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis. Regulatory proteins bind non-coding DNA either close to a gene's mRNA transcription start site at a promoter, or further away on the genome at an enhancer. Enhancers act by helping to recruit the RNA polymerase to the promoter. Now a genome-wide sequencing study of more than 10,000 enhancers that respond to electrical activity in neurons shows that the regulatory process also brings the polymerase to the enhancers themselves, where it transcribes non-coding RNAs. This 'enhancer RNA' (eRNA) synthesis occurs only at enhancers actively engaged in promoting mRNA synthesis from a promoter. The results suggest that at least in the brain, enhancers play a more active 'promoter-like' role in regulating gene expression than previously appreciated. Regulatory proteins bind non-coding DNA either at promoters (near to a gene's transcription start site) or at enhancers (far away). Binding at enhancers helps to bring the transcription enzyme RNA polymerase to promoters. Here, studies of some 12,000 enhancers that respond to electrical activity in neurons show that binding to enhancers also brings the polymerase to the enhancers themselves, where it transcribes a novel class of non-coding RNAs. Enhancers may thus be more similar to promoters than hitherto appreciated.