Gene expression of subtypes of neocortical projection neurons over developmental time is correlated with cell class-specific chromatin accessibility

Excitatory projection neurons of the neocortex can be classified as occupying the upper layers, layers 2-4, or the deep layers, layers 5 and 6. It is still unclear which transcription factors are required to specify one cell fate versus another and which downstream targets confer specific aspects of neuronal identity over developmental time. To identify transcription factors that specify upper layer versus deep layer fate, we analyzed cell type specific gene expression and differential chromatin accessibility over three defined stages of development. We found that transcription factor expression can distinguish upper layers from deep layers, and cell type specific transcription factor genes have differentially accessible chromatin in their regulatory domains, which tends to be correlated with gene expression. Total mRNA was isolated from two specific populations of FACS-purified projection neurons at three defined stages of mouse development.