Extended Data Fig. 10: Condense-seq measurements of nucleosomes purified from mouse CD8+ T cells.
From: Native nucleosomes intrinsically encode genome organization principles
a, Soluble fractions were measured via UV-VIS spectroscopy and run in 2% agarose gel after condensation in various spermine concentrations (the titration curves were plotted as the mean of three replicates with error bar as the standard deviation, and there were no significant differences between wild-type/DFMO-treated/ODC-KO as shown p-value > 0.05 for any-pair). (Ladder: NEB Low Molecular Weight DNA ladder used for the first lane of gels) b, Condensation point (c1/2) is defined by the concentration of condensing agent when the soluble fraction is half the input, so it is reversely correlated with condensability score. c–h, Soluble fractions of nucleosomes in various spermine concentrations were calculated and plotted over chromosome 1 in 10 kb resolution. C1/2 was computed for each bin after fitting the soluble fraction change with a logistic function as shown fitting curves of all bins (d, f, h), and polyamine deficient conditions show broader distribution of condensation points. (c, d: wild type control, e, f: +DFMO, g, h: ODC KO) i, Condensability point (c1/2) has inverse relationship with condensability scores of nucleosomes in mouse CD8 + T cells. j, The scatter plot of Δ z-score of condensability near TSS shows a high correlation between +DFMO and ODC KO. k, The Δ z-score of condensabilities is computed as the difference between the standardized condensability of +DFMO or ODC KO conditions and the wild type control and then categorized into the corresponding ChromHMM chromatin states over more than 300 nucleosomes of each state from two biological replicates (boxplot: the center is median and the lower/upper bound is the 1st/3rd quartile of data). Flow cytometry data show the global changes of PTM marks in ODC knockout (ODC KO) CD8+ T cells vs wild type (WT) expressed as mean intensity fluorescence (MFI) from three biological replicates (p-values were computed via the two-sided Welch’s t-test). (l) and also further verified using calibrated histone ChIP-seq for H3K27ac (m) and H3K27me3 marks (n) (the statistics were computed via the two-sided Welch’s t-test over more than 10000 nucleosomes of each state from three biological replicates).
