Fig. 5: Cross-links identified for histones.

a Example fragment spectrum of an inter-protein cross-link between histone H4 and histone H2B. The m/z and charge state of the precursor ion are given. Y-ions (light red), y-ions including the mass shift of 12 Da (dark red), a-ions (orange) and b-ions (yellow) of the peptide originating from histone H4 as well as y-ions (light blue), y-ions including the mass shift of 12 Da (blue), b-ions (dark blue) and a-ions (cyan) of the peptide originating from histone H2B type 1-L are assigned. Note that not all observed fragment ions are annotated. b–d High-resolution structure of the nucleosome core particles containing two copies of histones H3, H4, H2A and H2B (PDB ID: 3x1s⁵⁶) are shown. Identified cross-links are visualised in the structure (red and blue lines). Cross-linking distances >30 Å (red) and <30 Å (blue) are indicated. b Cross-links identified in RA-differentiated cells. c Cross-links identified in RA/PMA-differentiated cells. d Cross-links identified in undifferentiated cells. Figure generated using Supplementary Data 4.