Dynamic balance of H3K9me2 heterochromatin by CoREST-2 and RE-1 in growing neurons

Abstract

A well-balanced chromatin dynamic is vital for the survival and physiology of all cells, including brain neurons. Heterochromatin, commonly associated with transcriptional silencing, also plays significant roles in maintaining genomic stability and facilitating DNA-repair processes. Notably, the bimethylation of histone H3 at lysine 9 (H3K9me2), a hallmark of repressive heterochromatin, supports the axonal specification of neurons. However, neuronal maintenance of H3K9me2 equilibrium remains understudied. In this work, we unveil a dynamic equilibrium of H3K9me2 regulated by the epigenetic factor CoREST-2 and RE-1 DNA motifs, sustaining axonal and dendritic outgrowth. Using primary cultures of rat hippocampal neurons and a combination of advanced imaging techniques, we observed an enriched nuclear accumulation of CoREST-2 and H3K9me2 along neuronal development. Genetic silencing of CoREST-2 induced axon-dendrite retraction, accompanied by an increase in nuclear levels of H3K9me2. To further investigate heterochromatin structure at the nanoscale, we employed STED nanoscopy and discovered that H3K9me2 is organized into small nanodomains, which were notably enlarged following the suppression of CoREST-2. In contrast, the genetic blockade of RE-1 DNA motifs led to axon-dendrite retraction alongside the disassembly of H3K9me2 nanodomains. These findings highlight that CoREST-2 and RE-1 sites actively shape neuronal H3K9me2 heterochromatin. Moreover, they uncover that maintaining a precise balance of H3K9me2 is essential for the extension of axons and dendrites, underpinning the connectivity and plasticity of brain neurons.