Fig. 1
TF binding at CpGs in E14.5m PGCs predicts DNA methylation patterns throughout male PGC development. a Heatmaps of % methylation from BS-seq signal in E6.5 epiblasts and sperm. Each row represents a CpG with at least 10 BS-seq reads in both samples. The heatmaps are divided as follows: CpGs with very high methylation (> 80%) in epiblast (top left), CpGs with very low methylation (< 20%) in epiblasts (bottom left), CpGs with very high methylation in sperm (top right), and CpGs with very low methylation in sperm (bottom right). Heatmap heights are scaled to the total number of CpGs. b DNase-seq signal centered at binding sequences called by fimo that overlap a peak summit in at least one of the samples displayed, ordered by hierarchical clustering. Vertical blue lines at the right show regions of high DNAse signal across PGC development. c RPKM values within binding sequences called by fimo, separated into those that have high DNase signal in E14.5m (DNase-Hi, RPKM > 20) and those that have RPKM = 0 (DNase-Lo). d Average methylation of CpGs within E14.5m DNase-Hi and DNase-Lo regions, 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 (E14.5 DNase-Hi vs. E14.5 DNase-Lo) *P < 0.01; **P < 10−3; ***P < 10−5; ****P < 10−10. e Region with DNase accessibility and low local DNA methylation throughout PGC development. CpG cov indicates the BS-seq read coverage. f Changes in DNA methylation between E14.5m and E16.5m PGCs. Each point represents the average DNA methylation change (E16.5m minus E13.5m PGCs) at CpGs overlapping a binding sequence for a specific TF. The x-axis gives the average value for E14.5m PGC DNase-Hi sites, while the y-axis gives the average value for DNase-Lo sites. g Significantly enriched motifs at E14.5m DNase-Hi sites. P values are by Fisher’s exact test