Epigenetic profiling reveals a developmental decrease in promoter accessibility during cortical maturation in vivo

Abstract

Axon regeneration in adult central nervous system (CNS) is limited in part by a developmental decline in the ability of injured neurons to re-express needed regeneration associated genes (RAGs). Adult CNS neurons may lack appropriate pro-regenerative transcription factors, or may display chromatin structure that restricts transcriptional access to RAGs. Here we performed epigenetic profiling around the promoter regions of key RAGs, and found progressive restriction across a time course of cortical maturation. These data identify a potential intrinsic constraint to axon growth in adult CNS neurons. Neurite outgrowth from cultured postnatal cortical neurons, however, proved insensitive to treatments that improve axon growth in other cell types, including combinatorial overexpression of AP1 factors, overexpression of histone acetyltransferases, and pharmacological inhibitors of histone deacetylases. This insensitivity could be due to intermediate chromatin closure at the time of culture, and highlights important differences in cell culture models used to test potential pro-regenerative interventions.

Intrinsic mechanisms of neuronal axon regeneration

“…Importantly, co-expression of ATF3 and JUN can cooperate to improve regeneration in DRG neurons to a greater extent than can be achieved by the expression of either transcription factor alone 114 . However, this cooperative effect does not occur in cortical neurons 110 . These results make it clear that the extent to which genetic manipulation can impact regeneration is strongly influenced by cellular context and the competency of the neurons to respond (BOX 3).…”

“…Interestingly, JUN and ATF3 are sufficient to promote regeneration only under certain cellular conditions. Although overexpression of ATF3 can promote peripheral nerve regeneration 109 , it fails to do so in several models of CNS injury 110,111 . Conversely, JUN overexpression can promote regeneration in cultured cortical 110,112,113 and DRG neurons 114 ; however, as described above, its activation downstream of DLK also promotes cell death in RGCs 66 .…”

“…Although overexpression of ATF3 can promote peripheral nerve regeneration 109 , it fails to do so in several models of CNS injury 110,111 . Conversely, JUN overexpression can promote regeneration in cultured cortical 110,112,113 and DRG neurons 114 ; however, as described above, its activation downstream of DLK also promotes cell death in RGCs 66 . Whereas neuronal JUN is clearly necessary for peripheral axon regeneration 115 , JNK-mediated phosphorylation of JUN appears to not be required for its full function in facial nerve regeneration 116 .…”

“…Although interactions between the known pro-regenerative transcription factors have been extensively studied in other cell types, it is critical to understand their interactions in the context of axon injury. This need is further highlighted by recent studies in which combinatorial co-expression of a few of these transcription factors had limited to no ability to boost regeneration above single-factor overexpression in poorly regenerating neurons 110,148 .…”

“…However, it is also possible that even the addition of pioneer transcription factors is insufficient to reprogramme CNS neurons to grow owing to the presence of a growth-repressive chromatin landscape in these cells 153,156 . Indeed, a decrease in promoter accessibility during cortical development has been observed 110 , revealing a potential intrinsic constraint to axon growth and regeneration. This constraint may cause a failure reminiscent of the low efficiency observed in cell reprogramming, in which repressive chromatin remains a barrier to deterministic reprogramming 153 .…”