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. 2022 Apr 22;13:789349. doi: 10.3389/fimmu.2022.789349

Figure 1.

Figure 1

SOX4 and RELA interact on the chromatin (A) Immunoprecipitation of nuclear extracts from wildtype FLS treated with or without 10ng/mL TNF for 16 h. Western blot showing lysates and immunoprecipitates detected with the indicated antibodies. (B) Heatmap of the read coverage density (more red means more reads at that location) around the transcription start site (TSS) in wildtype FLS treated with or without TNF. (C) Box plot representation of normalized read counts in of SOX4 and RELA ChIP-seq peaks. ****p-value < 0.0001 (pairwise t-test adjusted by the Benjamini-Hochberg method). (D) Genome wide distribution of SOX4 and RELA ChIP-seq peaks in wildtype FLS treated with or without TNF. (E) Venn diagram showing overlap between SOX4 and RELA ChIP-seq peaks that are located within 50bp of each other. (F) TSS profile plot and (G) Heatmap showing the pattern of binding at the overlapped locations identified by the Venn Diagram in (F). The color bars on the left correspond to Venn Diagram grouping of peaks. (H) Genome tracks of SOX4 and RELA ChIP-seq peaks at the loci of representative examples of Group 1, 2 and 3 genes. (I) Enriched motifs in the RELA-SOX4 overlapping ChIP-seq peaks in TNF-treated FLS.