Enhancer RNAs are necessary and sufficient for activity-dependent neuronal gene transcription

Abstract

Enhancer elements in DNA regulate gene expression programs important for neuronal fate and function, and are increasingly implicated in brain disease states. Enhancers undergo bidirectional transcription to generate non-coding enhancer RNAs (eRNAs), but the function of eRNAs in neuronal systems remains controversial. Here, we performed genome-wide characterization of transcribed enhancers from rat cortical neurons, revealing elevated sequence conservation, enriched localization near genes involved in neuronal or synaptic function, and correlated activity-dependent regulation of putative eRNA-mRNA pairs. Functional validation using a CRISPR-dCas9 fusion system to drive eRNA synthesis from enhancers produced corresponding increases in mRNA at linked genes. Focusing on eRNAs arising from enhancers at the Fos gene locus, we report that eRNA and mRNA correlate on a single-cell level, that CRISPR-targeted eRNA delivery to an enhancer is sufficient for mRNA induction, and that eRNA knockdown decreases mRNA and alters neuronal physiology. These results suggest that eRNAs regulate gene expression and neuronal function.