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Position and orientation of the globular domain of linker histone H5 on the nucleosome

Abstract

It is essential to identify the exact location of the linker histone within nucleosomes, the fundamental packing units of chromatin, in order to understand how condensed, transcriptionally inactive chromatin forms. Here, using a site-specific protein–DNA photo-crosslinking method1, we map the binding site and the orientation of the globular domain of linker histone H5 on mixed-sequence chicken nucleosomes. We show, in contrast to an earlier model2, that the globular domain forms a bridge between one terminus of chromatosomal DNA and the DNA in the vicinity of the dyad axis of symmetry of the core particle. Helix III of the globular domain binds in the major groove of the first helical turn of the chromatosomal DNA, whereas the secondary DNA-binding site on the opposite face of the globular domain of histone H5 makes contact with the nucleosomal DNA close to its midpoint. We also infer that helix I and helix II of the globular domain of histone H5 probably face, respectively, the solvent and the nucleosome. This location places the basic carboxy-terminal region of the globular domain in a position from which it could simultaneously bind the nucleosome-linking DNA strands that exit and enter the nucleosome.

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Figure 1: DNase I degestion of H1/H5-depleted chromatosomes.
Figure 2: Characterization of the complex formation between GH5 mutants and linker-histone-depleted chromatosomes and of dimer formation by the mutant proteins.
Figure 3: Analysis of GH5–azidophenacyl crosslinked to chromatosomal DNA.
Figure 4: Representation of the GH5 location on a chromatosome.

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Acknowledgements

We thank T. Hamelryck and Y. Geunes for help with figures, and L. Wyns for helpful discussions. Z.Y.B. received a grant from the VlAB. V.R. was supported by a Public Health Service grant from the NIH. This work was supported by grants from (N)FWO and the OZR-VUB.

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Correspondence to Serge Muyldermans.

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Zhou, YB., Gerchman, S., Ramakrishnan, V. et al. Position and orientation of the globular domain of linker histone H5 on the nucleosome. Nature 395, 402–405 (1998). https://doi.org/10.1038/26521

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