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 age‐dependent 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 growth‐associated 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. © 2018 Wiley Periodicals, Inc. Develop Neurobiol 00: 000–000, 2018
An important question, however, is whether changes in chromatin accessibility are the cause or consequence of gene transcription.
local changes in accessibility precede and are a prerequisite for enhanced transcriptional output
changes in accessibility during CNS maturation are not merely passive indicators of
transcriptional activity, but rather contribute functionally to changes in gene expression
the relationship between accessibility and TF-evoked growth is striking and has potentially important implications for the use of TFs as pro-regenerative tools.
Chromatin structure is influenced by two main classes of proteins: histone-modifying enzymes, which ultimately regulate the degree of histone/DNA association, and ATP-dependent remodeling complexes that actively restructure chromatin
during cellular reprogramming events, a class of molecules called Pioneer TFs initially engage with compacted chromatin at specific loci, flagging these regions for subsequent chromatin relaxation and gene expression
pioneer factor binding marks the first in a sequence of events that culminates in
recruitment of chromatin remodelers and transcriptional activators
efficient cellular reprogramming requires an optimal combination of both pioneer factors and cell-specific TFs, which act co-operatively to initiate transcriptional activation at specific genomic loci.
the 3D spatial organization of the accessible genome is increasingly appreciated as critical regulatory mechanism
as improved input data become available it will be essential to continually update this workflow and reevaluate conclusions
optimal combination of pioneer factors/pro-regenerative TFs may be needed to
reverse age-related epigenetic constraints at specific pro-growth genomic loci
integrated assessment of gene expression, chromatin status, and axon growth phenotypes strongly supports a central role for chromatin accessibility in regulating axon growth.
Common Design 