Fig. 6: Genes affected in the absence of NELF-B or TDP-43 are critical for SC and RS development. | Nature Communications

Fig. 6: Genes affected in the absence of NELF-B or TDP-43 are critical for SC and RS development.

From: RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis

Fig. 6

a, b Volcano plots of fold changes in gene expression in SG and early meiotic cells (pL, L &Z) versus adjusted p-values, for control mice compared to NELF-B cKO (a) or TDP-43 cKO (e) mice. Dotted lines indicate 2-fold cut-off for significantly increased (red) or decreased (blue) genes, with numbers of genes passing these thresholds and p-values < 0.01 indicated on each plot. P-values from DESeq2, (Wald test adjusted p-value calculated using Benjamin-Hochberg correction). c, d Enriched functional categories among downregulated genes in NELF-B (c) or TDP-43 (d) mice, and their significance determined by ClusterProfiler. Enrichment p-values were calculated by a hypergeometric test, and the p-values were adjusted using a Benjamin-Hochberg correction. e, f Representation of downregulated genes from NELF-B cKO (e) or TDP-43 cKO mice (f), within each cluster (from Fig. 1f). A value of 1 indicates representation expected by chance. g Expression of Cluster 4 genes (n = 3916) in scRNA-seq from control, NELF-B cKO, or TDP-43 cKO mice, in indicated cell types. Line represents median, box represents 25–75th percentile, whiskers represent 10–90th percentile. P-values from two-sided Wilcoxon signed rank test. h Genome browser view of wild type PRO-seq signal in each cell type at Spo11. Note that the y axis is truncated at 50 to highlight PRO-seq gene body signal. Source data are provided as Source Data Fig. 6.

Back to article page