Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures

• Published in: Journal of molecular biology 2018-09, Vol.430 (18), p.3093-3110
• Main Authors: Zhou, Bing-Rui, Jiang, Jiansheng, Ghirlando, Rodolfo, Norouzi, Davood, Sathish Yadav, K.N., Feng, Hanqiao, Wang, Rui, Zhang, Ping, Zhurkin, Victor, Bai, Yawen
• Format: Article
• Language: English
• Subjects: 30-nm chromatin fiber; Chromatin - chemistry; Chromatin - genetics; Chromatin - metabolism; crosslinking; cryo-electron microscopy; Crystallography, X-Ray; Disulfides - chemistry; glutaraldehyde; histones; Models, Molecular; Molecular Conformation; NMR; nuclear magnetic resonance spectroscopy; nucleosome; nucleosome arrays; nucleosomes; Nucleosomes - chemistry; Nucleosomes - metabolism; physical properties; small-angle X-ray scattering; Solutions; Structure-Activity Relationship; ultracentrifugation; X-ray crystallography; X-ray diffraction
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2018.06.020

It has long been suggested that chromatin may form a fiber with a diameter of ~30 nm that suppresses transcription. Despite nearly four decades of study, the structural nature of the 30-nm chromatin fiber and conclusive evidence of its existence in vivo remain elusive. The key support for the existence of specific 30-nm chromatin fiber structures is based on the determination of the structures of reconstituted nucleosome arrays using X-ray crystallography and single-particle cryo-electron microscopy coupled with glutaraldehyde chemical cross-linking. Here we report the characterization of these nucleosome arrays in solution using analytical ultracentrifugation, NMR, and small-angle X-ray scattering. We found that the physical properties of these nucleosome arrays in solution are not consistent with formation of just a few discrete structures of nucleosome arrays. In addition, we obtained a crystal of the nucleosome in complex with the globular domain of linker histone H5 that shows a new form of nucleosome packing and suggests a plausible alternative compact conformation for nucleosome arrays. Taken together, our results challenge the key evidence for the existence of a limited number of structures of reconstituted nucleosome arrays in solution by revealing that the reconstituted nucleosome arrays are actually best described as an ensemble of various conformations with a zigzagged arrangement of nucleosomes. Our finding has implications for understanding the structure and function of chromatin in vivo. [Display omitted] •Disulfide cross-linking can alter nucleosome array conformation population.•Crystal packing conduces tetra-nucleosome array compaction.•Glutaraldehyde cross-linking can perturb nucleosome array conformation.•A novel ladder-like nucleosome packing mode•Thirty-nanometer nucleosome arrays exist as an ensemble of dynamic structures.