Extended Data Fig. 3: HDX-MS with nucleosome–Swi6 complex and nucleosomes alone.
From: HP1 reshapes nucleosome core to promote phase separation of heterochromatin
a, Experimental scheme for HDX-MS. b, Changes in deuterium incorporation are reported for every histone at five different time points. Each horizontal bar represents an individual peptide, and peptides are placed beneath the schematic of secondary structure elements of the histones. Peptides are coloured as specified, showing the mean of deprotection derived from multiple peptides obtained from one of two independent experiments with similar results. Specifically, more than a 35% increase in deuterium incorporation compared to nucleosomes alone is observed in: (i) residues 74–90 of H3, corresponding to a portion of helix α1 and α2, and the connecting loop 1; (ii) residues 48–61 of H3, corresponding to helix αN of H3; and (iii) residues 85–102 of H4, corresponding to helix α3. Other regions with a marked increase in deuterium uptake are the C-terminal region and helix α2 of H2A (residues 113–129 and 40–51), the C-terminal of H2B (helix αC, residues 104–122), and H4 helix α2 and loop 2 (residues 50–60 and 72–84). These increases in the rates of deuterium incorporation caused by Swi6 binding indicate extensive changes in the backbone hydrogen bonding of histones within the nucleosome and partial unfolding of the helices in the histones. c, Kinetics of deuterium uptake of example histone peptides (residue numbers indicated) over the time course. Data are mean and s.d. of multiple peptides obtained from one of two independent experiments with similar results. Error bars not shown for points when shorter than the height of the symbol.
