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Fig. 3 | Genome Biology

Fig. 3

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

Fig. 3

CpG methylation is reprogrammed only at a small fraction of TF binding sites, at binding sites for specific reprogramming TFs during male PGC and ESC development. a Heatmaps of DNase-seq signal at the indicated sites during PGC development. E9.5-trace, E14.5m-Hi sites are those that have FPKM < 1 in E9.5 PGCs and FPKM > 20 in E14.5m PGCs, while E9.5-Hi, E14.5m-trace sites have FPKM > 20 in E9.5 PGCs and FPKM < 1 in E14.5m PGCs. The two heatmaps are not drawn to scale in order to enable better viewing of both sets. b Average DNA methylation levels of CpGs at the indicated regions and stages of PGC development, weighted by the number of BS-seq reads at each CpG. The numbers displayed correspond to the number of TF binding sequences at which CpG methylation was averaged. P values are by Fisher’s exact test. P value cutoffs (E9.5-trace, E14.5m-Hi vs. E9.5-Hi, E14.5m-trace) *P < 0.01; **P < 10−3; ***P < 10−5; ****P < 10−10. c Heatmaps of DNase-seq signal at the indicated sites during gamete and pre-implantation development. E9.5-trace, E14.5m-Hi sites are those that have FPKM < 1 in E9.5 PGCs and FPKM > 20 in E14.5m PGCs, while E9.5-Hi, E14.5m-trace sites have FPKM > 20 in E9.5 PGCs and FPKM < 1 in E14.5m PGCs. The two heatmaps are not drawn to scale in order to enable better viewing of both sets. d Average DNA methylation levels of CpGs at the indicated regions and stages of pre-implantation development, weighted by the number of BS-seq reads at each CpG. The numbers displayed correspond to the number of TF binding sequences at which CpG methylation was averaged. P values are by Fisher’s exact test. P value cutoffs (E9.5-trace, E14.5m-Hi vs. E9.5-Hi, E14.5m-trace) *P < 0.01; **P < 10−3; ***P < 10−5; ****P < 10−10. e Example showing the DNA methylation across development at an E9.5-trace, E14.5m-Hi site with a CTCF binding sequence. f Example showing the DNA methylation across development at an E9.5-Hi, E14.5m-trace site with a CTCF binding sequence. CpG cov indicates the BS-seq read coverage. g, h Bar plots showing the number of motif hits for each TF at the indicated set of regions. Statistical significance of the enrichment of each TF motif, based on Fisher’s exact test, is indicated by the color purple

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