Fig. 6: Chromatin buffers transcription-dependent superhelicity.

A MA plot of gene expression changes between cells growing in raffinose (Raff.) media, and those induced with Galactose (Gal.) for 60 min. Grey and blue circles indicate nonsignificant and significant genes (negative binomial GLM two-sided likelihood ratio test FDR-adjusted P-value < 0.05), respectively. GAL1,2,7 and 10 are labelled. B Average (pileup) analysis of Hi-C maps of chromosome contact signals at the GAL7−10−1 and GAL2 loci, expressed as log2 fold change in contacts in cells growing in galactose for 60 min vs raffinose. C 500 bp binned CC-seq-v2 maps of physiological Top2ccs across a 300 kb region centred on the GAL7−10−1 locus, in raffinose and galactose growth conditions ± osmotic shock for 2 min. In (C, E) data from individual timepoints (see Fig. 6D and Supplementary Fig.8A, B) were averaged. D Sum CC-seq-v2 signal in a 20 kb region centred on the GAL7−10−1 locus (left), and GAL2 locus (right), in cells incubated in raffinose or galactose at 0, 30, 60 and 90 min, with or without subsequent osmotic shock for 2 min. Points indicate independent biological replicates and bars indicate the mean average of these (n = 4 for raffinose + OS at 0 min and 90 min; n = 4 for galactose + OS at 30 min, 60 min and 90 min), or single replicate values for other conditions. E Zoom in to CC-seq-v2 maps of physiological Top2ccs over a 20 kb region centred on the GAL7-10-1 locus, from cells growing in raffinose (top) vs galactose (bottom), without (left) and with (right) osmotic shock for 2 min. Single-nucleotide resolution signals are plotted as dark red and blue histograms, and a 1 kb-smoothed representation is overlaid in lighter shades. Arrows indicate the orientation of genes (pink and yellow) with stranded RNA-seq data from cells grown in raffinose or induced for 90 min with galactose plotted below them. A GapR-ChIP enrichment map is plotted in green³⁶. Source data are provided as a Source Data file.