a, EDC cross-linking network between histones and Swi6. Histones tails and core regions are indicated, as well as the different Swi6 domains. b, Interactions between Swi6 domains, histone tails and core domains mapped by cross-link spectral counts. The number of cross-linked mass spectra matched to a given domain pair is indicated by the colour of the tile as well as the numbers given. c, d, Analysis as in a and b but performed only on the structured domains of Swi6 (CSD and chromodomain) and on the folded core of histones. e, The Swi6 CSD binds to H2B core. Superposition of 1H–15N HSQC spectra of Swi6 CSD with (black) and without (red) H2B peptide. Measurements are representative of three independent experiments. The sequence of the H2B peptide is shown. f, Chemical shift perturbation for assigned resonances between Swi6 CSD alone and with the addition of the H2B peptide shown in e. g, Intra-nucleosome cross-links are altered by Swi6 binding. Each axis maps residue position within a histone, and the red dashed lines indicate the boundaries between histone tail and core domains. A cross-link is represented by a filled circle between two residues, with area proportional to the number of MS2 spectra identifying a given cross-link. Cross-links found in the free nucleosome state are in green, and cross-links found in the Swi6-bound nucleosome are in blue. The red squares highlight changes in the H3–H3 and H4–H4 cross-linking patterns between the free and bound nucleosome states. h, New histone–histone cross-links detected only with Swi6 binding involve buried regions of the nucleosome. The plots report the solvent-accessible surface area (SASA; y axis) versus residues number (x axis) for each histone. Cross-linkable residues (E, D and K) are indicated by a circle. Empty circles represent residues that do not show any cross-linking, and filled circles represent cross-linked residues. The area of the circle reports the number of cross-linked spectra with one peptide mapped to a particular residue. The red ovals highlight buried residues that were observed to cross-link only in the presence of Swi6. Analysis in a–d, g and h is performed on one of two XLMS datasets. Similar results were obtained with the other dataset that used the BS3 cross-linker.