A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers

Authors

Dong, A., Wang, Y., Yang, S., Wang, J., Wu, X., Zhou, D., Liu, P., Zha, R., Sun, J., Zhang, J., Lin, J., Zhou, H., Gan, J.

Abstract

Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron microscopy structures of Arabidopsis dodeca-nucleosome fibers containing distinct H2A/H3 variants and linker histone H1.3, revealing a noncanonical binding mode that a laterally positioned H1.3 connects the acidic patch of one nucleosome and the DNA of the neighboring nucleosome, thereby scaffolding dinucleosomes into two-start chromatin fibers. This noncanonical binding mode is structurally conserved when H1.3 is replaced by Gallus gallus H5. Furthermore, incorporation of H2A.W and H3.3 further induces back-to-back fiber dimerization. Cryo-electron tomography and in vivo cross-linking mass spectrometry analyses support the physiological relevance of H1 lateral engagement. Our findings establish that linker histones act as active architectural scaffolds in higher-order chromatin organization.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 01 Apr 2026.

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