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

Journal: bioRxiv

Article Title: LSD1 acts as an epigenetic barrier against glucocorticoid-induced atrophy and exercise-induced hypertrophy in skeletal muscle

doi: 10.1101/2022.10.08.509614

Figure Lengend Snippet: ( A ) ChIP-qPCR analyses of H3K4me3 at Sln, Gadd45a , and Ddit4 gene promoters in LSD1-mKO Gas muscles after Dex treatment. The data are from three independent experiments. The enrichment levels of H3K4me3 were normalized to the input DNA and presented as fold differences in the LSD1-mKO against that of WT. ( B ) Motif analyses of the promoter regions of genes that were upregulated in Dex-treated LSD1-mKO Gas muscles. Analysis of the atrophy-associated genes identified Foxk1 and PITX1 motifs, while significant enrichment of NFATc1 motif was found when all the upregulated genes were scanned. ( C ) Expression of genes encoding the TFs identified by the motif analyses. qRT-PCR values (n = 4) are shown as the fold differences, compared with those of the Gas muscles. ( D ) Effects of treatment with Dex and LSD1 inhibitor (T-3775440) on the expression of Foxk1 in C2C12 myotubes. Foxk1 and DAPI co-staining revealed Foxk1 positive nuclei, which are indicated by arrowheads (scale bars, 20 μm). The graph shows the percentage of Foxk1-positive nuclei (n = 3). ( E ) Co-immunoprecipitation of LSD1 and Foxk1. C2C12 myotubes were treated with insulin for 6 h before harvest to enhance the nuclear retention of Foxk1. Input lane contains 10 % amount of the whole-cell extract. (F and G) Effects of Foxk1-KO on the expression of atrophy-( F ) and slow fiber-associated genes ( G ) in C2C12 myotubes (n = 6). qRT-PCR values are shown as the fold differences, compared with those in the control-transfected cells (n = 6). Values are mean ± SD. * p < 0.05, ** p < 0.01.

Article Snippet: The primary antibodies used for western blot, co-immunoprecipitation (co-IP), immunohistochemistry, and immunocytochemistry experiments were as follows: anti-LSD1 (Abcam, ab17721), anti-FOXK1 (Abcam, ab18196), anti-ERRγ (Abcam, ab12893), anti-MHC type I (Developmental Studies Hybridoma Bank (DHSB), BA-F8), anti-MHC type IIA (DHSB, SC-71), anti-Laminin (Sigma-Aldrich, L9393), anti-Akt (Cell Signaling Technology (CST), #9272), anti-Phospho-Akt (Ser473) (CST, #9271), anti-GAPDH (Santa Cruz, sc-25778), anti-LC3(MBL, PM036), and anti-Sin3A (Santa Cruz, sc-994).

Techniques: Expressing, Quantitative RT-PCR, Staining, Immunoprecipitation, Transfection

Journal: The Journal of allergy and clinical immunology

Article Title: Progression of acute-to-chronic atopic dermatitis is associated with quantitative rather than qualitative changes in cytokine responses

doi: 10.1016/j.jaci.2019.11.047

Figure Lengend Snippet: a) immunostaining for FOXK1 in normal, acute, and chronic AD lesional skin; b) RNA expression (from RT-PCR) of FOXK1, IL4R, CCL5, and IL32 upon the indicated cytokine stimulation in keratinocytes under control (NC) or FOXK1 knockdown (siFOXK1). *p<0.05; **p<0.01; ***p<0.001.

Article Snippet: For immunohistochemistry, FFPE human skin biopsy specimens (independent of the RNA-seq samples) on slides were heated for 30 minutes at 65°C, rehydrated, epitope retrieved, blocked and incubated with primary antibody against FOXK1(ATLAS ANTIBODIES #HPA017998) overnight at 4°C.

Techniques: Immunostaining, RNA Expression, Reverse Transcription Polymerase Chain Reaction