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Fig. 5 | Genome Biology

Fig. 5

From: Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance

Fig. 5

TF binding site affinity influences the binding patterns of TFs during PGC and embryonic development. a Boxplots showing the distribution of TRAP affinity scores for TFs at DNase-Hi vs. DNase-Lo sites in E14.5m PGCs and TFs at ATAC-Hi vs. TF ATAC-Lo sites in ESCs. P values are by the Wilcoxon rank-sum test. P value cutoffs *P < 0.01; **P < 10−3; ***P < 10−5; ****P < 10−10. b, c Average TF binding signal (DNAse-seq in PGCs and TF ATAC-seq in ESCs) at regions with high and low TRAP affinities in the indicated samples. P values are by Student’s t test. P value cutoffs ***P < 10−5; ****P < 10− 10. d Boxplot comparing TRAP affinity at Nrf1 ChIP-seq peaks to those of DNase-seq peaks. P values are by the Wilcoxon rank-sum test. P value cutoffs ****P < 10−10. e, f Weighted average DNA methylation levels in the indicated samples at sites with high vs. low TRAP affinity scores for PGC TFs at E14.5m PGC DNase-seq peaks (e) and for Nrf1 at Nrf1 ChIP-seq peaks (f). P values are by Fisher’s exact test. P value cutoffs *P < 0.01; **P < 10−3; ***P < 10−5; ****P < 10−10. g Example showing the Nrf1 ChIP-seq and DNA methylation levels during and after growth in 2i medium at two Nrf1 peaks, one with a relatively low TRAP affinity (top) and one with a relatively high TRAP affinity (bottom)

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