Extended Data Fig. 5: A mechanistic basis of the Stag3 KO phenotypes in GSCs.
From: The mitotic STAG3–cohesin complex shapes male germline nucleome
a, ChIP-seq read density for RAD21 in WT and Stag3 KO GSCs (2 kb window) around the CTCF-colocalized and CTCF-non-colocalized RAD21 peak centers. b, Differential Hi-C contact map between WT and Stag3 KO GSCs (top) and CTCF-binding profile in WT GSCs (bottom). Red circles, more frequent interactions between CTCF-binding sites (pink) in Stag3 KO GSCs. c, Genome-wide contact probability (P(s)) curves (top) and their slopes (P’(s)) (bottom) for E11.5 mitotic pro-spermatogonia20 and WT and Stag3 KO GSCs. d, Overlap of CTCF-binding sites between WT and Stag3 KO GSCs. e, Comparison of the normalized CTCF-binding intensity in CTCF/cohesin co-occupied regions between WT and Stag3 KO GSCs. f, Differential interaction strength, as measured by chromosight84, for enhancer–promoter (left two panels) and Polycomb-associated loops (right two panels) between WT and Stag3 KO GSCs. p-values are measured by two-sided Welch’s t-test. Control genes, expression-matched genes with the genes of interest as defined in Fig. 3i, j. Box plots are as in Fig. 2d. Gene numbers analyzed are as follows: E–P interaction (left panel) — DEG-Control: Upregulated genes (left): 218-95, 174-91, 135-86, 125-73, 297-224; Downregulated genes (right): 297-134, 354-251, 271-180, 213-141, 397-378. Polycomb interaction (right panel) — Upregulated genes (left): 22-13, 14-8, 16-14, 8-8, 345-158; Downregulated genes (right): 42-15, 16-8, 26-15, 35-33, 934-456. p-values (ordered left to right) for each panel are as follows: E–P interaction (left panel) — Upregulated genes (left): 0.44, 0.0035, 0.15, 0.022, 0.55; Downregulated genes (right): 0.00012, 0.015, 0.00036, 0.94, 0.0068. Polycomb interaction (right panel) — Upregulated genes (left): 0.14, 0.13, 0.14, 0.71, 0.00039; Downregulated genes (right): 0.26, 0.010, 0.059, 0.62, 0.70. g, Violin and box plots of the expression of down-regulated genes in Stag3 KO GSCs defined in E12.5 male germ cells38 and P7 Kit− spermatogonia24. The p-value (<2.22e−16) was measured by two-sided Welch’s t-test. Box plots (471 genes each) are as in Fig. 2d. h, Virtual 4 C plot from the transcription start site (TSS: yellow shade) of Ddx4 in E13.5 male germ cells20 and undifferentiated spermatogonia151. Red shading, Ddx4 enhancer19.
