Fig. 6: TFAP2C acts as a pioneer factor for late-stage TFs and EVT-active genes. | Nature Communications

Fig. 6: TFAP2C acts as a pioneer factor for late-stage TFs and EVT-active genes.

From: The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation

Fig. 6

a Gene track view displaying TFAP2C and DLX6 signals in TSCs and differentiating cells to EVT on days 2, 5, and 8, along with ATAC-seq, H3K27ac, H3K4me3 signals in TSCs and EVTs. mRNA expression levels are shown near EVT factors. b Heatmaps showing TFAP2C ChIP-seq unique, common, and ATAC-seq unique loci in TSCs. TFAP2C ChIP-seq unique loci are indicated by a black bar. PC peak center. c Enriched GO terms of the top 3000 TFAP2C unique, common, or ATAC-seq unique peaks were determined using GREAT software100. p-values were calculated within the software. d ATAC-qPCR results validating TFAP2C binding to loci near EVT-active genes with low ATAC-seq signal. To account for primer variability, the Ct value was first normalized by subtracting the Ct value of sheared genomic DNA, resulting in a normalized Ct value. The deltaCt value was then calculated by subtracting the normalized Ct value of a genomic locus near an olfactory receptor gene (OR1A1), which exhibits very low ATAC-seq signal and low transcription levels in TSCs. The y-axis represents negative deltaCt values, indicating that an increase in value corresponds to increased openness. Error bars: mean ± SD (n = 3, independent repeats). e ATAC-seq signals at TFAP2C unique and common loci identified by comparing ChIP-seq results of TFAP2C in TSCs and DLX6 in EVTs. Box plots represent the median (black bar) and interquartile range (box boundaries), with whiskers from minimum to maximum values. Significance by two-tailed Wilcoxon rank-sum test. Analysis involved ATAC-seq signals on all TFAP2C unique or common loci in TSCs and EVTs. f Enhancer signals at TFAP2C unique loci in TSCs and EVTs. Box plots represent the median (black bar) and interquartile range (box boundaries), with whiskers from minimum to maximum values. Significance by two-tailed Wilcoxon rank-sum test. Statistical analysis involved signals from enhancer ChIP-seq results on all specified TFAP2C unique loci in both TSCs and EVTs.

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