Extended Data Fig. 7: Amplified views of the bottom-up first-principle coarse-grained model of the nucleosome fiber and the distribution of fitting values when the sampled conformations are confronted to iOS localizations.
a A representative folded GAPDH gene is amplified until consecutives centroids are shown. Each individual DNA centroid is located at the base pair reference frame (BPRF) following Cambridge and Tsukuba conventions72,73,74. These centroids represent the monomer length defined in our implementation, whose arbitrariness was based on a detailed knowledge on the structure and dynamics of B-DNA at the atomistic level42,75,76. In the first amplification, each DNA centroid is roughly represented considering its spherical exclusion volume (radius of van der Waals) centered at the BPRF. In the last two amplifications, the DNA-excluded volume is no longer depicted, and only the center of the BPRF is shown. Note that on average, being B-DNA, the distance between two consecutives base pairs is ~3.3 Å, although the experimentally falsifiable resolution of our predictions ranges from nucleosome clutches to near single nucleosome particles. b Distribution of the fitting values obtained from the filtered ensembles of GAPDH and NANOG folded conformations in hFibs and hiPSCs when confronted to iOS localizations. The top 10 structures with the highest fitting numbers, for which physical descriptors were computed and reported in Fig. 7 and Supplementary Table 2, are found at the right of the vertical dashed lines.
