Fig. 1: Reb1-guided nucleosome positioning in vitro by individual remodelers at varying nucleosome density.

a Overview of genome-wide in vitro reconstitution system. (GRF general regulatory factor, RE restriction enzyme). b Comparison of SGD (salt gradient dialysis) chromatin reconstituted at indicated histone-to-DNA mass ratios. DNA fragments after Micrococcal Nuclease-digest under the same conditions were resolved by agarose gel electrophoresis. Arrow heads on right point to subnucleosomal, mono- and dinucleosomal fragments (bottom to top). MNase digest and agarose gel electrophoresis was performed for every SGD chromatin sample. Results were similar to those shown here. c Heat maps of MNase-seq data for SGD chromatin of the indicated nucleosome density (low, medium, high) and after incubation with indicated remodelers and Reb1. Chd1 refers to the Chd1/FACT complex. Heat maps are aligned at in vivo +1 nucleosome positions and sorted according to decreasing (top to bottom) anti-Reb1 SLIM-ChIP score⁴⁹ (Reb1 signal) as measure for in vivo Reb1 binding and shown in leftmost heat map. Horizontal red shading highlights genes with strong in vivo Reb1 binding at promoters. Merged data of replicates are shown, individual replicates in Supplementary Fig. 1b, c. d Composite plots for data as in c averaged over the indicated number of replicates (n) and only for genes highlighted in red in c. Gray background shows in vivo MNase-seq data generated in this study.