Fig. 2

Foxg1 suppresses COUP-TFI through an H3K4me1-enriched enhancer. a Schematic diagram of in utero electroporation. b COUP-TFI (red) and GFP (green) immunohistochemistry of E14.5 cortices. Closed arrowheads indicate GFP cells with COUP-TFI expression, open arrowheads indicate GFP cells without COUP-TFI expression. Dashed lines indicate the ventricular surface. c Quantitative analysis of the percentage (±SEM) of GFP cells that express COUP-TFI. Brains were introduced with pCAG:GFP and pCAG:empty (Control) or pCAG:GFP and pCAG:Foxg1 (Foxg1 GOF). d Schematic diagram showing the strategy of conditional Foxg1 loss-of-function (Foxg1 cKO) using Emx1^Cre/+ mice. e Foxg1 (red), GFP (green), COUP-TFI (red), and Hoechst 33342 (blue) staining of E14.5 cortices. Dashed lines indicate the ventricular surface. f Schematic view of the COUP-TFI gene loci (chr13:78,316,360-78,342,718, UCSC genome browser, NCBI37/mm9). The data represent two independent ChIP-seq analyses (Foxg1-ChIP-1 and Foxg1-ChIP-2 from Kumamoto et al.²⁰). Mammal Cons represents Placental Mammal Basewise Conservation by PhyloP. MACS peaks overlapping in the two ChIP-seq analyses are marked in gray boxes. Two putative binding sites, PBS1 and PBS2, and primers designed for ChIP-qPCR analysis are indicated (see Methods for details). g ChIP-qPCR analyses of PBS1 and PBS2 of cells isolated from E14.5 neocortex using anti-Foxg1 (TaKaRa) and anti-H3K4me1 (Abcam) antibodies. For negative controls, Foxg1^LacZ/LacZ (Foxg1 KO) neocortex (Foxg1-ChIP analysis) and IgG (H3K4me1-ChIP analysis) were used. h Quantitative COUP-TFI promoter activity (±SEM) in the presence of PBS1 by in vitro reporter analysis in U87 human glioblastoma cell line. Value indicates RLU compared to COUPTFIpro (COUP-TFI promoter) only. i Schematic diagram showing two gRNAs, g1386 and g1889, designed to target PBS1. j Schematic diagram of in utero electroporation. k Foxg1 (blue), GFP (green), and COUP-TFI (red) staining of E15.5 cortices. Closed arrowheads indicate GFP cells with COUP-TFI expression and open arrowheads indicate GFP cells without COUP-TFI expression. Brains were introduced with pCAG:GFP and pCAG:empty (Control) or pCAG:GFP and pCAG:Foxg1 (Foxg1 GOF). Dashed lines indicate the ventricular surface. l Quantitative analysis of the percentage (±SEM) of GFP cells that express COUP-TFI. * indicates P value <0.05 by Student’s t-test. Source data are provided as a Source Data file