Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors

Sumona P Dhara,Paul L Auer,Michael J Flister,Michael D Laiosa,Andrea Rau,Nicole M Recka,Ava J Udvadia

doi:10.1038/s41598-019-50485-6

Abstract

In contrast to mammals, adult fish display a remarkable ability to fully regenerate central nervous system (CNS) axons, enabling functional recovery from CNS injury. Both fish and mammals normally undergo a developmental downregulation of axon growth activity as neurons mature. Fish are able to undergo damage-induced “reprogramming” through re-expression of genes necessary for axon growth and guidance, however, the gene regulatory mechanisms remain unknown. Here we present the first comprehensive analysis of gene regulatory reprogramming in zebrafish retinal ganglion cells at specific time points along the axon regeneration continuum from early growth to target re-innervation. Our analyses reveal a regeneration program characterized by sequential activation of stage-specific pathways, regulated by a temporally changing cast of transcription factors that bind to stably accessible DNA regulatory regions. Strikingly, we also find a discrete set of regulatory regions that change in accessibility, consistent with higher-order changes in chromatin organization that mark (1) the beginning of regenerative axon growth in the optic nerve, and (2) the re-establishment of synaptic connections in the brain. Together, these data provide valuable insight into the regulatory logic driving successful vertebrate CNS axon regeneration, revealing key gene regulatory candidates for therapeutic development.

Highlights

Damage to nerves in the central nervous system (CNS) as a result of disease or injury most often results in a permanent loss of function in humans
Our analysis reveals that successful CNS axon regeneration is regulated by stage-specific gene regulatory modules, and punctuated by regeneration-associated changes in chromatin accessibility at stages corresponding to axonogenesis and synaptogenesis
We hypothesized that regeneration-associated gene expression changes in axotomized retinal ganglion cell (RGC) would follow a temporal pattern corresponding to the changing requirements of axons as they grow through different environments leading from retina to optic tectum

Summary

Introduction

Damage to nerves in the CNS as a result of disease or injury most often results in a permanent loss of function in humans. In adult mammalian retinal ganglion cell (RGC) neurons, genetic and pharmacologic manipulations of neuron-intrinsic pathways have shown promise in activating a regenerative state after optic nerve injury[1,2,3,4,5,6,7,8] Even under these growth-enhanced conditions, regeneration mostly occurs only in a subset of RGCs2, with the majority of axons rarely growing beyond a few millimeters. Our analysis reveals that successful CNS axon regeneration is regulated by stage-specific gene regulatory modules, and punctuated by regeneration-associated changes in chromatin accessibility at stages corresponding to axonogenesis and synaptogenesis. Together, these data suggest candidates for gene regulatory targets for promoting successful vertebrate CNS axon regeneration

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Conclusion