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. Overall design: Total mRNA was isolated from two specific populations of FACS-purified projection neurons at three defined stages of mouse development.

大脑新皮层（neocortex）的兴奋性投射神经元（excitatory projection neurons）可分为两类：一类占据皮层上层（2~4层），另一类占据皮层深层（5、6层）。目前学界仍未明确，究竟哪些转录因子（transcription factor）参与了两类神经元的命运特化，以及哪些下游靶标在发育进程中赋予神经元身份的特异性特征。为鉴定调控皮层上层与深层细胞命运的转录因子，本研究分析了三个明确发育阶段下的细胞类型特异性基因表达谱与差异染色质可及性（differential chromatin accessibility）。研究发现，转录因子的表达模式可有效区分皮层上层与深层神经元；细胞类型特异性转录因子基因的调控区域存在染色质开放差异，且该差异通常与基因表达水平呈显著相关。实验设计概述：本研究从小鼠发育的三个既定阶段中，分离了经荧光激活细胞分选（FACS, fluorescence-activated cell sorting）纯化得到的两类特异性投射神经元群体的总mRNA。