In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex

During the differentiation process of neurons, their gene transcription pattern changes according to both intrinsic and extrinsic stimuli-induced programs. Chromatin regulation at regulatory elements is involved in this precise control of gene expression. However, developmental changes in chromatin accessibility of the cortical neurons in vivo are less understood, partly because there is no convenient method to genetically label neurons of a specific lineage. Here, we establish a method for labeling the differentiating neurons of specific birthdates. Using this method, we traced the four-day differentiation process of in vivo deep-layer excitatory neurons in mouse embryonic cortex and examined the changes in the genome-wide transcription pattern and chromatin accessibility with RNA-seq and DNase-seq, respectively. The genomic regions of genes associated with mature neuron functions, such as deep layer-specific genes and genes responsive to external stimuli, became open even in the embryonic stage. Moreover, genes with bivalent marks in neural precursor/stem cells (NPCs) became open. Together, our data demonstrate the importance of chromatin regulation in vivo differentiating neurons during the embryonic stage to follow activation of neuronal genes in their maturation process.