Fig. 7: INO80 synergistically integrates nucleosome positioning information from DNA shape/mechanics and Reb1 barriers.

a Composite plots as in Fig. 6b, but merge of four replicates (Supplementary Data 1) of SGD chromatin with recombinant human histones at histone-to-DNA mass ratio 0.4 incubated with recombinant S. cerevisiae WT INO80 plotted for either 456 genes with promoter Reb1 PWM sites or for a randomly selected but same number of genes with no GRF-PWM sites (Reb1, Abf1, Rap1, Mcm1, Cbf1⁸⁸) in their promoters. b As in a but for matched replicate (replicate 8, Supplementary Data 1) comparing SGD chromatin with embryonic fly (D. m.) or recombinant human (H. s.) histones, ± 20 nM Reb1 and for 620 genes with promoter anti-Reb1-SLIM-ChIP sites (as in Fig. 6a, red shading, and in Fig. 6b, top). c Distributions of distances between +1 nucleosome positions at 620 Reb1 site-containing promoters in vivo and reconstituted by incubation of SGD chromatin with the indicated histone-to-DNA mass ratios with recombinant S. cerevisiae WT INO80 in the presence (Reb1) or absence (none) of 20 nM Reb1. Dots show independent replicates (n = 4 or 12 or 7 for histone-to-DNA ratio of 0.2 or 0.4 or 0.8, respectively, and for ±Reb1 each; either recombinant human or endogenous fly embryo histones were used, see Supplementary Data 1 and GEO deposition at GSE140614. For histone-to-DNA ratio 0.2 and 0.8 data and for detailed description and more examples of such distances between nucleosomes and barriers and their dependencies on nucleosome density and remodelers see accompanying paper³⁹. Larger horizontal bars represent mean, error bars standard deviation. d As in b but only SGD chromatin with recombinant human histones incubated with recombinant S. cerevisiae WT INO80 ± 20 nM Reb1.MNase-seq data were merged (four replicates without and seven replicates with Reb1 (Supplementary Data 1)) and aligned at Reb1 PWM sites of groups, which were defined according to promoter uni- versus bidirectionality and Reb1 PWM orientation as indicated. Only Reb1 sites in promoters and only if identified by both anti-Reb1-SLIM-ChIP and Reb1 PWM were used (see also accompanying paper³⁹). e Reb1 PWM-aligned composite plots for gene groups as in d. From top to bottom: anti-Reb1-SLIM-ChIP signal (Reb1 signal) and zoom in on distribution of DNA rigidity, propeller twist and helix twist DNA shape features, and positions of poly(dA) or poly(dT) elements (hexa-homopolymeric stretches) around Reb1 sites, each with Reb1 signal. Gray background in all panels shows composite plot of MNase-seq data with Reb1 as in d.