Fig. 6: Diminished TAD organization and reduced CTCF binding in PGCs.
From: Global reorganization of genome architecture at the transition to gametogenesis
a, Normalized Hi-C interaction frequencies (40–50 Mb, chromosome 2) in somatic cells (top) and PGCs (bottom), male (right) and female (left). b, TAD aggregate plots showing diminished TADs in both male and female PGCs. TAD strength values (median) are indicated for each group. c, Boundary strength was calculated at boundaries identified in our Hi-C libraries. Boundary strength is significantly reduced in PGCs compared with somatic cells. P values were calculated using a two-sided Student’s paired t-test (female, n = 5,512 boundaries; male, n = 6,251 boundaries). Outliers are not depicted. d, Loop aggregate plots for somatic cells (left) and PGCs (right). Loop strength is shown by the genome-wide averaged contact signals (Methods). The contact map was normalized using matrix balancing and distance (O/E). Positive enrichment is shown in red and negative signals are displayed in blue. The ratio of contact enrichment for the center pixels is annotated within each plot. e, Normalized Hi-C interaction frequencies (50.7–52.7 Mb, chromosome 6) in somatic cells and PGCs, male and female. Bottom: insulation plot. Identified TADs and subTADs are labeled with different colors. Loops are indicated by circles. f, Left: Gaudí plot generated by METALoci (Methods) showing genomic regions at 10-kb resolution, overlaid with corresponding TADs (as shown in e). Different colors represent distinct TADs. Right: log10-transformed sum of ATAC-seq signal within each 10-kb bin is mapped onto the same graph layout, illustrating chromatin accessibility. g, Representative IF image of CTCF (n = 3 biological replicates). Germ cell markers, AP2γ and OCT4. Yellow arrowheads indicate PGCs. DNA was stained with DAPI (blue). Scale bar, 10 µm. h, Image quantification analysis showing normalized CTCF intensity (Methods) from three biological replicates (mean ± s.d.). P values were calculated using a two-tailed Mann–Whitney U-test. i, CTCF footprints of corrected ATAC-seq signal at CTCF-binding sites in TAD boundaries (mild, severe and total loss categories). CTCF footprint scores were calculated from published ATAC-seq data for E13.5 PGCs27. j, CTCF motif score for TAD boundaries with mild loss, severe loss and total loss. The motif with the highest score was considered for each TAD boundary. P values were calculated using a two-sided Student’s t-test. Box plots were plotted using Tukey’s method. The median and the first and third quartiles are indicated. Whiskers represent the furthest value within 1.5× the IQR.
