Fig. 5

The dynamics of chromatin loop location during spermatogenesis and the impact of looping on gene expression change. In (A) and (B), chromosomes were divided into 100 even-sized bins; the X axis shows the distance of a given bin to the nearest telomere, relative to chromosome length. On the Y axes, we plot, on a per-cell type basis and across all chromosomes: (A) the proportion of footprinted CTCF sites in a given bin, relative to the total number of footprinted CTCF sites; (B) the proportion of predicted loops in a given bin, relative to the total number predicted loops. C The distance to the nearest telomere, relative to chromosome length, is shown for CTCF motifs (light blue) and predicted loops (dark blue). An average relative distance of 0.25 is expected if elements are evenly distributed with respect to telomeric distance, indicated by the dashed line. D Looping does not result in gene activation in early primary spermatocytes. Y axis: log2 fold-change of gene expression, with log2 fold-values > 0 indicating higher expression in early primary spermatocytes. The number (N) of promoters located in cell-type specific loops is indicated in each comparison, and the Wilcoxon signed-rank test was used to compare the median log2 fold-change between categories. Green boxplots: early primary spermatocytes versus differentiating spermatogonia; promoters are either in early primary spermatocyte-specific loops (left) or in differentiating spermatogonia-specific loops (right). Blue boxplots: early versus late primary spermatocytes; promoters are either in early (left) or late (right) primary spermatocyte-specific loops