Extended Data Fig. 3: Annotating differentially accessible peaks during neuronal differentiation.

a, Gene ontology (GO) enrichment of differentially accessible peaks at the TSS. Progenitor peaks (left) and neuron peaks (right) showed enrichment for GO terms related to proliferation and differentiation, as expected. b, TFs with significantly differentially enriched conserved binding sites in differentially accessible peaks. The statistical test identifies TFs likely involved in neural progenitor proliferation and maintenance (progenitorTFs; top) or neurogenesis and maturation (neuronTFs; bottom). The top 30 significantly enriched TFs were shown in this figure, and the full list can be found in Supplementary Table 2. Within progenitorTFs, we found TFs previously characterized to have key roles for neural stem cell renewal and reprogramming, such as SOX2^101,102, and those known to be required for the maintenance of stem cells in cortex, such as NR2F1, ETV5, and SP2^103,104,105. Within neuronTFs, NEUROG2 and LMX1A were identified, which are known to drive neuronal differentiation^106,107, as well as TFs shown to induce neuronal identity from fibroblasts, including ASCL2 and the POU family³⁹. NeuronTFs also included CUX1/2, a marker for layer II-III neurons^61,108 and other laminar markers such as TBR1 and FOXP1. c, Schematic of known functions for selected progenitorTFs and neuronTFs.