Extended Data Fig. 4: Nucleosome methyl-TROSY NMR.

a, The methyl-TROSY spectra of H3 and H2B are well resolved and the chemical shift differences between the cross-peaks of our spectra and of the published spectra of Drosophila nucleosomes are small (less than 0.1 ppm)⁴¹. Owing to these small changes and the high protein conservation between the two species, we were able to transfer the assignments to all the cross-peaks of H3 and most of the cross-peaks of H2B. The chemical shift change (Δδ) plot reports the differences in chemical shift of the cross-peaks for conserved Ile, Leu and Val (ILV) residues in Drosophila and Xenopus histones. Δδ values were calculated from the equation:\(\sqrt{0.5({({\delta {\rm{H}}}_{Drosophila}-{\delta {\rm{H}}}_{Xenopus})}^{2}+{(0.2({\delta {\rm{C}}}_{Drosophila}-{\delta {\rm{C}}}_{Xenopus}))}^{2})}\) in which the factor of 0.2 is used as a scaling factor for the carbon spectral width. The average Δδ value is shown as a red dashed line. Experiments were performed twice to optimize conditions; data from one experiment are reported. b, Amino acid sequence alignment of Drosophila and Xenopus H2B and H3 histones. ILV residues conserved between the two species are coloured in blue, and non-conserved ILV residues are in red. Ile residues are fully conserved between H3 histones. Leu and Val are conserved between H2B histones, except for V15, V38 and V66, which are present only in the Xenopus histone. V15, V38 and V66 are not included in our NMR analysis. c, Quantification of the SASA of the residues indicated (x axis) in histone H2B (left) and H3 (right). The SASA was calculated from the PDB structure file 1KX5 using the program POPS. The SASA values are for the entire residue and represent fraction of exposed surface area. Bars corresponding to ILV residues are coloured in red with shading as specified, reflecting changes reported from the methyl-TROSY experiments due to Swi6 binding. ILV residues not assigned or not included in the analysis are in blue. The schematic of secondary structure elements is shown below the x axis.