Nucleosome Dynamics

Bai, Yawen

Abstract

For FY13, we have used multi-dimensional NMR, X-ray crystallography, site-directed mutagenesis coupled with isothermal titration calorimetry to study how nucleosomes and histones are recognized by other proteins. We have determined the crystal structure of the CENP-C-CENP-A nucleosome complex and found a conserved mechanism for recognition of the centromeric nucleosome by the kinetochore protein CENP-C. We have built a structure model for the H1-nucleosome complex with residue-level information, which shows a unique orientation of H1 in the H1-nucleosome complex. In addition, we have investigated how the centromere-specific histone is recognized by its chaperone. We found that the centromere histone in budding yeast (Sc and Kl) has a partially unfolded conformation that is specifically recognized by the chaperone Scm3. We also solve the structure of histone variant H2A.Z in complex with the N-terminal region of the Swr1 subunit of the SWR1 remoldeler. Our results show that Swr1 deliver the H2A.Z-H2B by a chaperone mechanism.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Cancer Institute (NCI)
• Type: Investigator-Initiated Intramural Research Projects (ZIA)
• Project #: 1ZIABC010808-07
• Application #: 8763231
• Support Year: 7
• Fiscal Year: 2013
• Total Cost: $1,230,940

Institution

• Name: National Cancer Institute Division of Basic Sciences

Publications

Zhou, Bing-Rui; Jiang, Jiansheng; Ghirlando, Rodolfo et al. (2018) Revisit of Reconstituted 30-nm Nucleosome Arrays Reveals an Ensemble of Dynamic Structures. J Mol Biol 430:3093-3110

Chittori, Sagar; Hong, Jingjun; Saunders, Hayden et al. (2018) Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N. Science 359:339-343

Fyodorov, Dmitry V; Zhou, Bing-Rui; Skoultchi, Arthur I et al. (2018) Emerging roles of linker histones in regulating chromatin structure and function. Nat Rev Mol Cell Biol 19:192-206

Liu, Chuanbo; Wang, Tianshu; Bai, Yawen et al. (2017) Electrostatic forces govern the binding mechanism of intrinsically disordered histone chaperones. PLoS One 12:e0178405

Zhou, Bing-Rui; Feng, Hanqiao; Ghirlando, Rodolfo et al. (2016) A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome. J Mol Biol 428:3948-3959

Zhou, Bing-Rui; Jiang, Jiansheng; Feng, Hanqiao et al. (2015) Structural Mechanisms of Nucleosome Recognition by Linker Histones. Mol Cell 59:628-38

Hong, Jingjun; Feng, Hanqiao; Wang, Feng et al. (2014) The catalytic subunit of the SWR1 remodeler is a histone chaperone for the H2A.Z-H2B dimer. Mol Cell 53:498-505

Hong, Jingjun; Feng, Hanqiao; Zhou, Zheng et al. (2013) Identification of functionally conserved regions in the structure of the chaperone/CenH3/H4 complex. J Mol Biol 425:536-45

Kato, Hidenori; Jiang, Jiansheng; Zhou, Bing-Rui et al. (2013) A conserved mechanism for centromeric nucleosome recognition by centromere protein CENP-C. Science 340:1110-3

Zhou, Bing-Rui; Feng, Hanqiao; Ghirlando, Rodolfo et al. (2012) Histone H4 K16Q mutation, an acetylation mimic, causes structural disorder of its N-terminal basic patch in the nucleosome. J Mol Biol 421:30-7