Neuronal plasticity, the ability of the nervous system to adapt to internal or external stimuli, is a fundamental property that underlies brain development, learning, memory, and resilience to neurodegenerative disorders. At the molecular level, neuronal plasticity depends on the activation of neuronal activity-regulated genes (nARGs), a process tightly controlled by enhancer regions—short regulatory DNA sequences. Recent findings reveal that active enhancers produce enhancer-derived RNAs (eRNAs), which may play crucial roles in gene regulation through complex interactions with DNA, RNA, and proteins.
Despite their potential significance, the function of eRNAs in neuronal activity remains poorly understood due to their transient nature and technical challenges in studying them. This project aims to develop innovative experimental approaches to unravel the role of eRNAs in nARG activation. Using rodent primary neuronal culture —a well-established model for studying neuronal plasticity—the project will systematically analyze eRNA responses to external stimuli with high temporal resolution. Comprehensive sequencing technologies will be combined to characterize the molecular features of eRNAs. These data will be complemented by epigenomic profiling to correlate enhancer activity with transcriptional dynamics.
The project will also investigate potential links between eRNA features and neurodegenerative disease-associated mutations, providing insights into how brief stimuli-related gene activation may contribute to disease phenotypes. Together, these studies will create a framework for understanding the regulatory roles of eRNAs in neuronal plasticity and their broader implications for brain development and disorders.
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.
Formation of new synapses, and alteration of the strength and stability of existing synapses are regarded as the main cellular basis for memory and long-term behavioral adaptations. Neuronal activity-regulated gene expression plays a crucial role in synaptic development and function, and its deregulation gives rise to various nervous system disorders. Knowledge about the regulatory mechanisms of activity-dependent gene expression is important both for understanding of nervous system function and for finding new drug targets. The aim of this project is to study the molecular mechanisms of neuronal activity-regulated gene expression, including transcription, translation and posttranslational modifications, in the nervous system health and disease. The studies are focused on two genes, the neurotrophin BDNF and the basic helix-loop-helix transcription factor TCF4.
