Journal: bioRxiv

Article Title: Neocortical temporal patterning by a two-layered regulatory network

doi: 10.64898/2025.12.18.695250

Figure Lengend Snippet: Hierarchical functional coordination of key processes by transition hub TFs. (a) Left: scatter plot showing the number of enriched KEGG and GO biological processes by TF direct targets versus the number of regulatory links in E11-E12 transition. Right: heatmap showing the enrichment score of representative KEGG and GO biological processes by direct targets of indicated TFs. Top: bar plots showing the number of regulatory links in E11-E12 transition. (b) Bar plots showing Foxk1 promoted in TF ranking in E11-E12 transition. (c) Left: schematic showing the role of Hbp1 and its downstream TF Foxk1 in regulating adhesion in the E11-E12 transition. Right: ATAC-seq signal at the Foxk1 promoter. Grey box indicates an identified Hbp1 motif occurrence in the Foxk1 promoter. The identified motif occurrence is a valid Hbp1 binding site, as shown by enrichment of HBP1 ChIP-seq signal (GSE104247) in a cell line. (d) UMAP visualization of scRNA-seq from control and Hbp1 overexpression samples. Cell shape indicates experimental conditions, and color indicates cell type assignment. (e) KEGG biological processes associated with differentially expressed genes in RGPs overexpressing Hbp1 . (f) UMAP visualization of scRNA-seq from control and Foxk1 overexpression samples. Cell shape indicates experimental conditions, and color indicates cell type assignment. (g) KEGG biological processes associated with down-regulated genes in RGPs overexpressing Foxk1 . (h) Experimental timeline for Hbp1 and Foxk1 manipulation and phenotyping. (i) Representative coronal sections of dorsolateral telencephalon triple stained using anti-GFP (green), anti-PAX6 (red) antibodies, and a DNA dye (blue), following the experimental scheme shown in (h). Zoomed in view of VZ and IZ showing substantial discharging from the VZ and repositioning to the IZ. (j) Representative coronal sections of dorsolateral telencephalon triple stained using anti-GFP (green), anti-PAX6 (red) antibodies, and a DNA dye (blue), following the experimental scheme shown in (h). Zoomed in view of VZ and IZ. (k-l) Quantification of the distribution of PAX6 + EGFP + cells (k), and percentage of PAX6 + EGFP + cell on the ventral surface in EGFP+ cells (l). Data are shown as mean ± SEM. (j) **** P<0.0001, ***P=0.0004, **P=0.007; (k) **** P<0.0001; (l) **P=0.0067; Student’s t-test. N.S., not significant. (m) Quantification of distribution of percentage of PAX6 + EGFP + cell on the ventral surface in PAX6 + EGFP + cells in VZ. Data are shown as mean ± SEM. **P=0.008; Student’s t-test; N.S., not significant. (n) Summary of experimental results in the perturbation of Foxk1 .

Article Snippet: The following primary antibodies were used in this study: rabbit polyclonal anti-FOXK1 antibody (Sino Biological, 101153-T10; 1:1,000 dilution), mouse monoclonal anti-HA antibody (BioLegend, #MMS-101P; 1:2,000 dilution) and mouse monoclonal anti-α-Tubulin antibody (Santa Cruz Biotechnology, sc-8035; 1:10,000 dilution).

Techniques: Functional Assay, Binding Assay, ChIP-sequencing, Control, Over Expression, Staining