Fig. 3: Long-range TFs and short-range TFs have distinct regulatory properties. | Nature Communications

Fig. 3: Long-range TFs and short-range TFs have distinct regulatory properties.

From: Determinants of transcription factor regulatory range

Fig. 3

a Right: increase of H3K27ac levels in TEAD1 target TADs in cell lines with high TEAD1 expression (p value 0.003; two-tailed Pearson correlation). Left: no increase of H3K27ac levels in YY1 target TADs with YY1 expression. x-axis: CCLE cell lines ranked by YY1 (left) or TEAD1 (right) gene expression. y axis: YY1 (left) or TEAD1 (right) target TADs. Heatmap colors represent H3K27ac ChIP-seq signal for cell line – TAD pairs. b Strong correlation between TF expression and H3K27ac ChIP-seq signal in TF target TADs for long-range TFs but not for short-range ones. (p value = 0.0002; two-tailed Student’s t test). c Right: the average expression of genes in TEAD1 target TADs is high in cell lines with high TEAD1 expression. Left: there is no association between YY1 gene expression and gene expression in YY1 target TADs. d Strong correlation between TF expression and expression of genes in TF target TADs for long-range TFs but not for short-range ones. (p value 7.9e−6; two-tailed Student’s t test). e Tissue-restricted expression of long-range TFs. Compared with short-range TFs, long-range TFs have higher expression coefficients of variation across 48 GTEx tissues. f Long-range TFs (green) have more binding sites within the TAD harboring the TF gene itself (p value 0.008; two-tailed Student’s t test). g Right: ChIP-seq peaks of TFs besides TEAD1 are more highly enriched with the TEAD1 motif in cell lines with higher TEAD1 expression. Left: no such association is observed in the YY1 case. x axis: CCLE cell lines ranked by YY1 (left) or TEAD1 (right) gene expression. y axis: ChIP-seq of TFs besides TEAD1 or YY1. Each cell represents the enrichment of YY1 (left) or TEAD1 (right) motifs in the ChIP-seq peaks of the corresponding TF-cell line pair. h Long-range TFs tend to possess pioneer-like properties. The “pioneer-like” property of a TF is defined as the association between the level of that TF’s expression and its motif enrichment in the ChIP-seq peaks of other TFs (p value 0.02; two-sided Fisher’s exact test). Source data are provided as a Source Data file.

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