We are only just beginning to catalog the vast diversity of cell types in the cerebral cortex. Such categorization is a first step toward understanding how diversification relates to function. All cortical projection neurons arise from a uniform pool of progenitor cells that lines the ventricles of the forebrain. It is still unclear how these progenitor cells generate the more than 50 unique types of mature cortical projection neurons defined by their distinct gene-expression profiles. Moreover, exactly how and when neurons diversify their function during development is unknown. Here we relate gene expression and chromatin accessibility of two subclasses of projection neurons with divergent morphological and functional features as they develop in the mouse brain between embryonic day 13 and postnatal day 5 in order to identify transcriptional networks that diversify neuron cell fate. We compare these gene-expression profiles with published profiles of single cells isolated from similar populations and establish that layer-defined cell classes encompass cell subtypes and developmental trajectories identified using single-cell sequencing. Given the depth of our sequencing, we identify groups of transcription factors with particularly dense subclass-specific regulation and subclass-enriched transcription factor binding motifs. We also describe transcription factor-adjacent long noncoding RNAs that define each subclass and validate the function of Myt1l in balancing the ratio of the two subclasses in vitro. Our multidimensional approach supports an evolving model of progressive restriction of cell fate competence through inherited transcriptional identities.

我们才刚刚开始对大脑皮层中多种细胞类型进行分类。这种分类是了解多元化与功能之间关系的第一步。所有皮质投射神经元均来自在前脑室内衬的统一祖细胞库。尚不清楚这些祖细胞如何产生其独特的基因表达谱所定义的50多种独特类型的成熟皮层投射神经元。此外，尚不清楚神经元在发育过程中如何以及何时使其功能多样化。在这里，我们将投射神经元的两个子类的基因表达和染色质可访问性联系在一起，因为它们在胚胎第13天到出生后第5天之间在小鼠大脑中发育，因此具有不同的形态和功能特征，以便识别使神经元细胞命运多样化的转录网络。我们将这些基因表达谱与从相似种群中分离出的单个细胞的已发表谱进行比较，并确定层定义的细胞类别涵盖了使用单细胞测序鉴定的细胞亚型和发育轨迹。鉴于测序的深度，我们确定了具有特别密集的亚类特异性调节和富含亚类的转录因子结合基序的转录因子组。Mytll在体外平衡了两个亚类的比例。我们的多维方法支持通过继承的转录身份逐步限制细胞命运能力的进化模型。