Developmental chromatin restriction of pro-growth gene networks acts as an epigenetic barrier to axon regeneration in cortical neurons

Abstract

Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the agedependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility. When applied to the developing cortex, this pipeline detected overall closure of chromatin in sub-networks of genes associated with axon growth.We next analyzed mature CNS neurons that were supplied with various pro-regenerative transcription factors. Unlike prior results with SOX11 and KLF7, here we found that neither JUN nor an activated form of STAT3 promoted substantial corticospinal tract regeneration. Correspondingly, chromatin accessibility in JUN or STAT3 target genes was substantially lower than in predicted targets of SOX11 and KLF7. Finally, we used the pipeline to predict pioneer factors that could potentially relieve chromatin constraints at growthassociated loci. Overall this integrated analysis substantiates the hypothesis that dynamic chromatin accessibility contributes to the developmental decline in axon growth ability and influences the efficacy of pro-regenerative interventions in the adult, while also pointing toward selected pioneer factors as high-priority candidates for future combinatorial experiments.peer-reviewed)

Intrinsic Determinants of Axon Regeneration

“…Several papers in this special issue address the question “Why do most CNS neurons not have the ability to activate the RAG‐program and enhance GAP expression in response to injury?” (Moon , Venkatesh et al , Danzi et al, ). These papers describe multiple layers of regulation that are different in CNS and PNS neurons, including differences in cytoplasmic RNA metabolism (a.k.a.…”

“…Despite these recent insights, significant gaps in our knowledge remain. To better understand the core mechanisms that drive expression of genes that support axon extension in developing cortical neurons, Ishwariya Venkatesh and colleagues (Venkatesh et al, ; this special issue) describe a bioinformatics workflow that integrates the assessment of gene regulation by RAG‐TFs and chromatin accessibility. Previous work of these authors pointed to a developmental decline in chromatin accessibility in the promoter regions of particular RAGs in cortical neurons (Venkatesh et al, ).…”

“…Epigenetic modifications such as histone (de)acetylation or (de)methylation, or direct DNA methylation are involved in long‐term modulation of gene expression during organ development and in cancer. Evidence for a role of epigenetic factors in axon outgrowth has been obtained in studies on the developmental decline in axon growth capacity (Venkatesh et al, ; ) as well as in DRG neurons following injury (Finelli et al, , Loh et al, ). The DRG model system is particularly well‐suited to study neuron‐intrinsic differences between PNS and CNS axons (Attwell et al, ).…”

Can Chromatin Accessibility be Exploited for Axon Regeneration?

“…Several transcription factors, including Jun, Stat3, Sox11, and CREB, have been deemed necessary for axon regeneration through knockdown or knockout experiments that decrease growth in experimental models of axon regeneration (Lonze et al, ; Raivich et al, ; Di Giovanni et al, ; Seijffers et al, ; Jankowski et al, ; Leibinger et al, ). Interestingly, the only one of these transcription factors whose overexpression without modification is sufficient to promote axon regeneration in the Central Nervous System in vivo is Sox11 (Wang et al, ). The known binding sites of Sox11 were recently shown to be accessible in adult cortical neurons, while the binding sites of other factors such as Jun and Stat3 were much less accessible (Venkatesh et al, ).…”

“…Interestingly, the only one of these transcription factors whose overexpression without modification is sufficient to promote axon regeneration in the Central Nervous System in vivo is Sox11 (Wang et al, ). The known binding sites of Sox11 were recently shown to be accessible in adult cortical neurons, while the binding sites of other factors such as Jun and Stat3 were much less accessible (Venkatesh et al, ). This finding suggests that other regeneration‐associated transcription factors are not sufficient to promote axon regeneration in vivo because the appropriate binding sites are not accessible.…”