Neocortical projection neurons consist of intracortical connected upper layer (UL, layer II–IV) neurons and subcortical connected lower layer (LL, layer V–VI) neurons. Afferent activity from the thalamus regulates layer-specific gene expression during postnatal development, which is critical for the formation of proper neocortical cytoarchitecture. Here, we show that activity-dependent gene regulation is confined to UL cortical neurons, but not LL neurons, and that this distinction is likely due to epigenetic modifications of chromatin. We found that the immediate early genes (IEGs), EGR1 and c-FOS, are downregulated in all cortical laminar layers in the absence of afferent activity in vivo. Transcriptional assays demonstrated that EGR1 and c-FOS are able to bind to the promoters of UL- and LL-specific genes to induce transcription. Furthermore, we discovered that LL neurons express higher levels of heterochromatin markers, such as H3K9m3 and H4K20m3, compared to UL neurons. Our results suggest that differential epigenetic modifications of chromatin is an intrinsic mechanism that underlies the different sensitivities of cortical neurons to activity-dependent gene regulation.

新皮层投射神经元由皮层内连接的上层（UL，II–IV层）神经元和皮层下连接的下层（LL，V–VI层）神经元组成。丘脑的传入活动调节出生后发育期间的层特异性基因表达，这对于适当的新皮层细胞结构的形成至关重要。在这里，我们显示了活动依赖的基因调节仅限于UL皮质神经元，而不是LL神经元，并且这种区别很可能是由于染色质的表观遗传修饰。我们发现，立即早期基因（即早基因），EGR1和Ç -FOS，在所有皮质层的层下调在没有传入活动的体内。转录分析表明EGR1和c-FOS能够与UL和LL特异性基因的启动子结合以诱导转录。此外，我们发现，与UL神经元相比，LL神经元表达更高水平的异染色质标记，例如H3K9m3和H4K20m3。我们的结果表明，染色质的不同表观遗传修饰是一种内在机制，是皮层神经元对活性依赖基因调控的不同敏感性的基础。