Revealing enhancer-derived RNA (eRNA) transcriptome: eRNA processing and biogenesis during neuronal stimuli-activated transcription

Enhancers are short distal cis-regulatory DNA regions that drive expression of a gene. However, enhancers do not function exclusively as DNA entities. Activated enhancers are transcribed by RNA polymerase II (RNAPII), which produces enhancer-derived RNAs (eRNAs). Production of eRNA creates additional trans-regulatory mechanisms facilitated by DNA-RNA, RNA-RNA, or protein-RNA interactions. Due to eRNAs’ fast degradation rates, and lack of robust and standardized sequencing methods, reports about the molecular nature of eRNA molecules and their processing are conflicting, making mechanisms of gene regulation by eRNA controversial. Even less is known about co- and post-transcriptional processing of eRNA. This project aims to overcome the controversy and fill the knowledge gap by studying a well-defined experimental system, cultured rat cortical neurons, and activation of immediate-early gene (IEG) response, perturbing the core eRNA endonuclease and combining this with eRNA-tailored sequencing, computational and biochemical methods. The developed integrative approach will reveal molecular features of eRNA molecules and their precursors genome-wide, opening the opportunity to study eRNA biogenesis to further understand molecular mechanisms behind the eRNA-mediated gene regulation.