Fig. 3. Transcriptional downregulation near SAHF-forming regions.

a GSEA of the 495 genes located within the 500–700 kb range from SAHF, from all chromosomes (Methods). All human genes were ranked by expression fold changes (FC), calculated as levels of gene expression in OIS cells divided by levels of expression in growing cells (blue distribution). The distribution of the target genes (n = 495) is shown by the row of black tick marks (also green line). The target genes were frequently downregulated in OIS cells compared to growing cells, indicated by the negative normalized enrichment score (NES). The significance of the biased distribution was assessed by an empirical phenotype-based permutation test⁴⁶. b Statistical significance and NES of changes in gene expression, between OIS and growing cells, for groups of genes positioned within the indicated distances from SAHF, as analyzed using GSEA. c Same data as panel b, but GSEA was performed on groups of genes positioned within the indicated 200 kb windows from SAHF. d Percent of downregulated genes positioned within the indicated 200 kb windows. Note that 48% of all human genes were downregulated upon OIS, serving as a control distribution for downregulated genes. e Expression ratios between OIS and growing cells were calculated for the genes located within the 500–700 kb range from SAHF, and the distribution was plotted against the ratio. All human genes were also subjected to the same analysis (control). P-value was calculated by a two-sided Mann–Whitney U test. f Percent of chromosome occupied by SAHF in chromosomes 1–14 and 15–22 shown as boxplots (central bar represents the median with boxes indicating the upper and lower quartiles, and whiskers extend to the data points, which are no more than 1.5× the interquartile range from the box). P-value was calculated by a two-sided Mann–Whitney U test. BA- and AB-switching regions were analyzed identically. g Correlation between percent of chromosome occupied by SAHF and by BA-switching regions, in the indicated chromosome groups. The coefficient of determination (R²) for a linear model fit (red line) was shown.