Role of 3D chromatin architecture in axonal regeneration following peripheral nerve injury

PROJECT SUMMARY/ABSTRACT Nerve injuries are highly prevalent worldwide and are associated with sensory and motor impairment, neuropathic pain, and permanent disability, resulting in significant health burden and costs for the healthcare system. While axons in the peripheral nerves can regenerate following an injury, their growth rate is too slow for successful functional recovery. The study of the molecular mechanisms regulating the regenerative capacity of the peripheral axons is paramount to provide insights for strategies aimed at boosting their regenerative potential. One key factor for long-distance regeneration of peripheral axons is the transcriptional reprogramming of neurons into a growing state, involving activation of regenerative gene networks. For this reason, epigenetic mechanisms that broadly open the chromatin, affecting the expression of multiple genes, are preferred therapeutical targets to enhance nerve regeneration. The folding of the genome into three-dimensional topologically associating domains (TADs) allows coordinated changes in gene expression in response to specific inputs, by facilitating the interaction between gene promoters and regulatory enhancers. Our unpublished data in mouse dorsal root ganglia sensory neurons show that the full activation of regenerative genes after nerve injury depends on regulated chromatin interactions within TADs. Thus, we hypothesize that TADs and the enhancer–promoter interactions formed in response to nerve injury regulate the regenerative program. Furthermore, we hypothesize that modulating TADs and enhancer–promoter interactions can represent a novel therapeutical approach to enhance nerve regeneration. In Aim 1, we will use high-throughput transcriptomics and genome-wide mapping methodologies in isolated mouse dorsal root ganglia neurons following sciatic nerve crush injury or sham control to investigate the molecular mechanisms by which enhancer–promoter interactions generated in response to injury can promote regenerative gene transcription. We will identify novel molecular modulators of these genomic interactions, and we will perform functional studies to investigate their role in axon regeneration. In Aim 2, we will use super-resolution imaging, biochemical, and genome-wide mapping approaches to identify regulators of the transcription machinery at these chromatin contacts. We will perform functional studies to investigate their role in axon growth. In Aim 3, we will characterize known regulators of TADs and address the extent to which these regulators can be manipulated to enhance nerve regeneration. Findings from this project will add critical knowledge about how regenerative gene expression is regulated by genome conformation, providing key insights into how to activate the regenerative program in a specific and sustained way to promote axonal regeneration and relieve the burden of nerve injury.