Muller glia mediated regeneration restores neuronal diversity and retinal circuit organization in the adult zebrafish

Abstract

The ability to regenerate neurons with appropriate identities and circuit connectivity is a fundamental challenge in regenerative biology. Unlike mammals, adult zebrafish robustly regenerate retinal neurons after injury through the reprogramming of Muller glia. However, the extent to which regenerated neurons faithfully reconstruct molecular identity, cellular diversity, and circuit organization remains unclear. Here, we combined inducible lineage tracing, single-cell RNA sequencing and high-resolution morphological analysis to define the molecular identities and structural organization of regenerated neurons following photoreceptor-selective light lesion or NMDA-induced inner retinal injury. Both injury paradigms regenerated all major retinal cell classes, although the relative abundance of regenerated cell types reflected the pattern of neuronal loss. Across major neuronal classes and subtypes, regenerated neurons largely reestablished endogenous molecular identities, with the residual transcriptional differences primarily reflecting ongoing maturation. Regenerated amacrine and bipolar neurons recovered subtype diversity, characteristic dendritic morphologies, and laminar organization. Regenerated retinal ganglion cells likewise restored broad molecular diversity and appropriate retinotectal projections, while a subset underwent microglia-mediated refinement. Together, these findings demonstrate that Muller glia-mediated regeneration largely reconstructs neuronal identity, cellular diversity and key features of retinal circuit organization, providing insights into understanding how complex neuronal tissues are rebuilt after injury.