Fig. 6: FOXG1 drives common molecular determinants to control pallial versus subpallial fate across MGE and dLGE/CGE lineages.

a Venn plot showing the counts of overlapping genes among the union set of the three category DEGs in the MGE lineage with that in the FOXP2^highSP8^low and FOXP2^lowSP8^high lineages. b Identification of the 40 overlapping genes driven by FOXG1 to control the fate of pallial versus subpallial GABAergic neurons across the MGE and dLGE/CGE lineages. “┫” indicates the repression of subpallial GABAergic neuron fate by FOXG1. The arrow indicates the activation of pallial GABAergic neuron fate by FOXG1. Highlighted genes are direct targets of FOXG1. c Triple immunostaining for FOXG1, NKX2-1, and LHX6 at E13.5, E16.5 and E18.5 wild type mice. Quantification of FOXG1 expression levels by measuring fluorescence intensity in NKX2-1^highLHX6^- progenitors positioned in the MGE ventricular zone (white-boxed region1) at E13.5, in NKX2-1^lowLHX6^high pre-CINs (white-boxed region2, 5, 8) and NKX2-1^highLHX6^high pre-SINs/GP prototypical neurons positioned in the MGE subventricular zone (white-boxed region2, 5, 8), in NKX2-1^highLHX6^high SINs/GP prototypic neurons located in the subpallium (white-boxed region3, 6, 9), and in NKX2-1^-LHX6^high CINs dispersed in the cortex (white-boxed region4, 7, 10) at E13.5, E16.5, E18.5 (n = 3 mice per time point). Data are presented as means ± SEM. One-way ANOVA with Tukey post hoc test; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001; NKX2-1^highLHX6^- MGE progenitors vs. NKX2-1^low/-LHX6^high pre^-CINs (E13.5: **P = 0.0093); NKX2-1^highLHX6^- MGE progenitors vs. NKX2-1^highLHX6^high pre^-SINs/GP prototypical neurons (E13.5: **P = 0.003); NKX2-1^low/-LHX6^high pre-CINs vs. NKX2-1^highLHX6^high pre-SINs/GP prototypical neurons (E13.5: ****P < 0.0001; E16.5: **P = 0.0043; E18.5: *P = 0.0458); NKX2-1^highLHX6^high SINs/GP prototypical neurons vs. NKX2-1^-LHX6^high CINs (E13.5: ****P < 0.0001; E16.5: **P = 0.0014; E18.5: ***P = 0.0004). Source data are provided as a Source Data file. Blue arrows: low levels of FOXG1 in NKX2-1^highLHX6^high pre-SINs/GP prototypical neurons and NKX2-1^highLHX6^high SINs/GP prototypical neurons, yellow arrows: high levels of FOXG1 in NKX2-1^highLHX6^- MGE progenitors, NKX2-1^lowLHX6^high pre-CINs, and NKX2-1^-LHX6^high CINs.