Fig. 3: roX RNAs promote gene expression on X but repress gene expression on autosomes.

a Cumulative curves illustrating the fold change (roX-KO/WT) in gene expression on autosomes and the X chromosome following roX loss in male larvae. Significance levels are determined using the two-sided Kolmogorov–Smirnov test. b roX-bound autosomal genes (n = 203) show upregulated expression of in roX-KO larvae while X-chromosomal targets (n = 1346) exhibit decreased expression. The center lines represent the median, the box limits represent the first and third quartiles, and the whiskers indicate 1.5 × the interquartile range (IQR). Significance levels are assessed using the two-sided Wilcoxon test. c The top 10 significantly enriched Gene Ontology (GO) terms in roX-bound autosomal genes are presented. Significance levels are determined using the Fisher’s exact test, with the Benjamini–Hochberg false discovery rate (FDR) correction for multiple testing. d Examples of genes located on autosomes and X chromosomes that exhibit increased and decreased expression, respectively, upon roX loss. Mean ± SD FPKM values from RNA-seq analyses for each gene are plotted (n = 3 independent experiments) and the adjusted P values using Benjamini and Hochberg method are indicated. Source data are provided as a Source Data file.