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Significance Neurons of the cerebral cortex arise from a common progenitor pool that progressively generates different cell subtypes with distinct features, including deep layer (DL) and upper layer (UL) projection neurons. Several transcription factors (TFs) are known to specify whether a progenitor cell will become UL or DL; however, it is still unknown which upstream and downstream factors contribute to this fate decision. Here, we deeply characterize differential gene expression and chromatin accessibility of UL and DL neurons. We identify TFs that are highly differentially expressed and densely regulated and find that UL neurons retain the transcriptomic signature of their mother cells. We also discover a previously unknown role for the TF Myt1l in cell fate specification.

Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes