A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome

Abstract

Linker histones bind to the nucleosome and regulate the structure and function of chromatin. We have previously shown that the globular domains of chicken H5 and Drosophila H1 linker histones bind to the nucleosome with on- or off-dyad modes, respectively. To explore the determinant for the distinct binding modes, we investigated the binding of a mutant globular domain of H5 to the nucleosome. This mutant, termed GH5_pMut, includes substitutions of five globular domain residues of H5 with the corresponding residues in the globular domain of Drosophila H1. The residues at these five positions play important roles in nucleosome binding by either H5 or Drosophila H1. NMR and spin-labeling experiments showed that GH5_pMut bound to the nucleosome off the dyad. We further found that the nucleosome array condensed by either the GH5_pMut or the globular domain of Drosophila H1 displayed a similar sedimentation coefficient, whereas the same nucleosome array condensed by the wild-type globular domain of H5 showed a much larger sedimentation coefficient. Moreover, NMR and spin-labeling results from the study of the nucleosome in complex with the full-length human linker histone H1.0, whose globular domain shares high sequence conservation with the corresponding globular domain of H5, are consistent with an on-dyad binding mode. Taken together, our results suggest that a small number of residues in the globular domain of a linker histone can control its binding location on the nucleosome and higher-order chromatin structure.

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1

“…By contrast, the Drosophila GH1 domain (43–46% identical to chicken GH5, Xenopus GH1.0 and human GH1.5; Figure S6A) has been observed to bind off the dyad (Zhou et al, 2013). Moreover, a chicken GH5 mutant could be engineered to adopt an off-dyad binding mode by replacing five surface-exposed residues with the corresponding Drosophila GH1 residue, confirming that GH1 sequence variation can modulate binding mode (Zhou et al, 2016). Interestingly, human GH1.5 matches Drosophila GH1 at two of these mutated positions (Figure S6B), raising the possibility that the H1.5 on-dyad configuration may be less stable than that of the H1.0 isoform.…”

“…In contrast, an NMR study reported an off-dyad binding mode for the Drosophila H1 globular domain (GH1) (Zhou et al, 2013). The different binding modes observed for these two histone isoforms have been ascribed to differences in a few DNA-contacting residues (Zhou et al, 2016). A distinct off-dyad binding mode was reported for human histone H1.4 in the cryo-EM structure of a condensed 12-nucleosome array (Song et al, 2014).…”

Emerging roles of linker histones in regulating chromatin structure and function

“…2f,g). The different binding modes were explained by a subsequent study, which identified five key residues in the globular domains of H5 and D. melanogaster H1 that determine the binding location of the globular domain in the chromatosome (on-dyad versus off-dyad binding) 43 , suggesting that a small number of residues in the globular domain of a linker histone variant can determine its binding mode.…”

“…This crystal structure is in agreement with previous in vitro experimental data investigating the binding of the H5 globular domain to nucleosomes 41,42 , as well as data showing the binding of the globular domain of mouse H1.0 and its mutants to chromatin in vivo 36 , suggesting that the linker histone binds to the nucleosome in the same way in vitro and in vivo . Using longer linker DNA and full-length linker histone H1.0, it was further shown by NMR and cryo-electron microscopy (cryo-EM) that the tails of the linker histones and the longer linker DNA in the chromatosome do not have a role in determining the binding mode between the nucleosome and the globular domain of the linker histone 43,44 . However, measurements of binding affinity and cryo-EM structural studies showed that within a single chromatosome, the C-terminal tail of H1.0 appears to be preferentially associated with only one of the two available linker DNAs 44,45 , which was speculated to have a role in influencing the assembly and properties of higher-order chromatin structures 44 .…”

“…The observation that linker histone variants may bind to the nucleosome in different modes, which is associated with distinct structures of condensed nucleosome arrays — with on-dyad binding corresponding to more condensed chromatin architecture 40,43 — is also likely to be related to chromatin function.…”