Structural Mechanisms of Nucleosome Recognition by Linker Histones Bing-Rui Zhou, Jiansheng Jiang, Hanqiao Feng, Rodolfo Ghirlando, T. Sam Xiao, Yawen Bai  Molecular Cell  Volume 59, Issue 4, Pages 628-638 (August 2015) DOI: 10.1016/j.molcel.2015.06.025 Copyright © 2015 Elsevier Inc. Terms and Conditions

Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 1 Overall Structure of the H5 Globular Domain in Complex with the Nucleosome and Omit Electron Density Maps (A) Overall structure. The globular domain of H5 (red), H2A (light orange), H2B (salmon), H3 (light blue), H4 (light green), and DNA (gray). (B) Omit map calculated using the nucleosome core particle and the original diffraction data (gray, 2Fo − Fc at σ = 1.0; green, Fo − Fc at σ = 3.0). (C) Omit map in (B) was overlaid with the globular domain (red) and the linker DNA in the final structure of the globular domain in complex with the nucleosome. (D) Omit map of the α3 helix of the globular domain. (E) Omit map of the L1 loop of the globular domain. (F) Overlay of the structures of the nucleosome core particle region in our complex and the free nucleosome core particle (PDB ID: 3LZ0) with a root mean square deviation of 0.9. See also Figure S1. Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 2 Side-Chain Methyl NMR and Spin Labeling Experiments Support the On-Dyad Binding of the H5 Globular Domain (A) 1H-13C heteronuclear multiple quantum coherence spectrum of the globular domain bound to the nucleosome and the assignment of the methyl groups. Asterisks indicate natural abundance of methyl groups from histone tails. The two methyl groups in Leu or Val residues are labeled with a and b arbitrarily. (B) Effects of spin label MTSL at H3 Lys37 in the nucleosome on the methyl groups of the H5 globular domain. Data are presented as mean ± SD from three experiments. (C) Effects of spin label MTSL at H2A Thr119 on the methyl groups of the H5 globular domain. Data are presented as mean ± SD from two experiments. (D) The observed spin label effects versus the distances from the methyl groups of the globular domain to the spin label sites are consistent with the crystal structure (see E and F). The distances were measured using a structural model built by overlaying the nucleosome core particle region of our structure over the nucleosome core particle (PDB: 1KX5) that includes the coordinates of H2A 119 and H3 37 residues. The Cys-MTSL was modeled at these sites by choosing the rotamers that are close to the globular domain. The dashed line is the fitting curve generated using the equation: Ipara/Idia = exp(α × r−6)/[1 + β/(1 + r −6)]. Ipara and Idia are the NMR peak intensities of the methyl group when MTSL is in the paramagnetic and diamagnetic states, respectively. α and β are fitting parameters. r is the distance from the carbon atom of a methyl group in the globular domain to the paramagnetic oxygen atom of MTSL. (E and F) Illustration of distances from typical methyl groups to spin label sites. The MTSL was shown with sticks (blue) and spheres (magenta) for the oxygen atom bearing the paramagnetic electron. The carbon atoms in the methyl groups are shown in red spheres, with the exception of those with distances of less than 20 Å, which are shown in cyan. See also Figure S2. Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 3 Interactions between the Globular Domain of H5 and DNA and Measurement of Binding Affinity by ITC (A) Distribution of positively charged globular domain residues that are close to DNA in the crystal structure. (B) Distribution of non-charged globular domain residues that are close to DNA in the crystal structure. Nitrogen, carbon, and oxygen atoms in the stick model are colored in blue, green, and red, respectively. (C) Effects of mutations in the globular domain on the binding affinity of H522–142 to the nucleosome. The dashed line indicates the value that is a factor of two less than that of the wild-type. The values are the mean and one SD generated from fitting of the ITC curves (see D and Table 2). (D) Typical ITC data with the fitting curves. See also Figures S3 and S4. Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 4 Structural Re-analysis of Previous Models (A) Sequence alignment of the globular domains of H5 and mouse H1°. (B) Mapping of the important nucleosome-binding residues identified in the earlier mutation-FRAP studies of H1° to our structure. (C) Structural re-interpretation of earlier cross-linking results. In our structure, the Cα atoms (orange sphere) of residues Ser29 and Ser71 in the globular domain of H5 are ∼10–12 Å away from an atom (cyan sphere) in the third nucleotide from the end of linker-α3. The Cα atom (orange sphere) of residue Ser41 is ∼11 Å away from a DNA atom (cyan sphere) near the dyad. See also Figure S4. Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 5 Structural Changes in the Globular Domain and Linker DNA (A) Overlay of the conformer A and B of the crystal structure of the free globular domain (blue) (PDB: 1HST) with the structure of the globular domain (red) bound to the nucleosome. (B) Comparison of the linker DNA conformations in the H5 globular domain-nucleosome structure (gray) and in the H1.4-condensed nucleosome array (blue). (C) Comparison of linker DNA conformation in the H5 globular domain-nucleosome structure (gray) and in the tetra-nucleosome (orange) (PDB: 1ZBB). See also Figure S5. Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions

Figure 6 The On- and Off-Dyad Binding Modes of Globular Domains Lead to Distinct Structures of Condensed Nucleosome Arrays (A) Sedimentation coefficients of nucleosome arrays (12 nucleosomes with a nucleosome repeat length of 177 bp DNA) in the presence of the globular domains of H5 (22–102), Drosophila H1 (44–118), full-length Xenopus H1.0, or full-length Drosophila H1 with the molar ratio of each linker histone over the nucleosome at approximately one. These values are the average of results from two (for the globular domains) or three experiments (for full-length linker histones) and the error bars represent one standard deviation (see also C and D). (B) Sequence alignment of the globular domains of H5 and Xenopus H1.0. (C) Sedimentation coefficients of the nucleosome arrays in the presence of 0.3 mM Mg2+ and the globular domain of H5 or Drosophila H1 with molar ratios of the globular domain over the nucleosome at 0.0, ∼0.5, and ∼1.0. Each value at the molar ratio of ∼1.0 is the average of results from two experiments, and the error bars represent one SD. (D) Sedimentation coefficients of the nucleosome arrays in the presence of full-length H1.0 or Drosophila H1 at different molar ratios of linker histones over the nucleosome. Each value with an error bar is the average of results from three experiments and the error bar represents one SD. (E–H) c(s) versus S20,w (S). The sedimentation coefficients at the peak maxima were plotted in (A), (C), and (D). The numbers near the curves correspond to the lane number in (J) and (K) (see below), which have different ratios of linker histone over the nucleosome. (I) Confirmation of saturated nucleosome arrays. ScaI digestion of the nucleosome array yielded mono-nucleosome only, indicating that the nucleosome array is saturated. (J–L) SDS gels for the arrays used for the sedimentation experiments. The band intensities were used to calculate the molar ratios of linker histones over the nucleosome shown in (C) and (D). The molar ratios of linker histone over the nucleosome described below are input values (before dialysis). Dashed lines indicate related nucleosome arrays are used in the experiments. The peak numbers in (E)– (H) correspond to the lane numbers in (J)–(L). (J) Lane 1, protein marker; lane 2, GH1; lane 3, mixture of Drosophila GH1 and the core histone octamer with molar ratio of Drosophila GH1 over the octamer at 1.0 (as reference); lanes 4 and 5, molar ratios of Drosophila GH1 over the nucleosome at 0.5 and 1.0, respectively; lane 6, protein marker; lane 7, GH5; lane 8, mixture of GH5 and the core histone octamer with molar ratio of GH5 over the octamer at 1.0 (as reference); lanes 9 and 10, molar ratios of Drosophila GH5 over the nucleosome at 0.5 and 1.0, respectively. (K) Lanes 1 and 2, mixture of the full-length linker histone Drosophila H1 and the core histone octamer with a molar ratio of linker histone over the octamer at 1.0; lane 3, protein marker; lanes 4–11, nucleosome arrays in the presence of full-length Drosophila H1 with increasing molar ratios (0, 0.25, 0.5, 0.75, 1.0, 1.1, 1.2, and 1.3) of the linker histone over the nucleosome. (L) Same as in (K), except full-length Xenopus H1.0 is used. See also Figure S6. Molecular Cell 2015 59, 628-638DOI: (10.1016/j.molcel.2015.06.025) Copyright © 2015 Elsevier Inc. Terms and Conditions