Fig. 1: ZNF143 stabilizes CTCF binding on promoter and enhancer regions to regulate gene transcription. | Nature Communications

Fig. 1: ZNF143 stabilizes CTCF binding on promoter and enhancer regions to regulate gene transcription.

From: ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

Fig. 1

a Heatmaps of ZNF143 and CTCF ChIP-seq in ZNF143 wild type (Znf143 f/f) and ZNF143 knockout (Znf143 −/−) murine HSPCs. b Reciprocal co-IP of ZNF143 and CTCF in murine HSPCs. Experiment is repeated independently for three times with similar results. c Histogram describing the distance between CTCF and ZNF143 motifs on the murine genome (mm10). The X-axis represents the relative distance between ZNF143 and CTCF motif, while the Y-axis represents the number of ZNF143 motifs in each bin. Each bin size is 1 bp. The table presents the number of ZNF143 motifs in the different orientation patterns to the nearest CTCF motifs within 10,544 ZNF143 motifs located 37 bp apart from the nearest CTCF motifs. d Heatmap of H3K27ac, ZNF143, and CTCF ChIP-seq in Znf143 f/f murine HSPCs within the regions ±4 kb from the transcription start site (TSS). Gene order is ranked by RNA expression from high to low in Znf143 f/f cells (heatmap from top to bottom). e Heatmap of H3K27ac, ZNF143, and CTCF ChIP-seq in Znf143 f/f murine HSPCs within ±4 kb from CTCF-bound enhancer regions. f ChIP-reChIP of ZNF143 and CTCF on a negative intergenic control region (NC), Cebpa promoter region (mCa pro), and Cebpa +37 kb enhancer region (mCa + 37 kb) in Znf143 f/f murine HSPCs. Y-axis: the mean ± SD from triplicate experiments. g MA plot demonstrating gene expression changes between Znf143 f/f and ZNF143 −/− murine HSCs. Red dots represent differentially expressed genes (p < 0.05). n = three biological replicates. P-value is determined by the Wald test. h The mean plot of ZNF143 ChIP-seq within ±4 kb TSS regions in Znf143 f/f murine HSPCs. Genes are divided into (1) differentially expressed genes (DEG), (2) non-differentially expressed genes (un-DEG), and 3) non-expressed genes (non-expressed) as defined in (g). HSPCs: c-kit+, lineage- cells; HSCs: LSK+ (lineage-, Sca-1+, c-kit+), CD150+, CD48- cells. ChIP-seq in panels (a), (c), (d), (e), and (h) was performed in two biological replicates. Result was shown in one replicate.

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