Cryo-EM Structure and Biochemical Analyses of the Nucleosome Containing the Cancer-associated Histone H3 Mutation E97K

Overview

Journal Genes Cells

Specialties Cell Biology
Molecular Biology

Date 2024 Jul 7

PMID 38972377

Authors

Tomoaki Kimura

Seiya Hirai

Tomoya Kujirai

Risa Fujita

Mitsuo Ogasawara

Haruhiko Ehara

Shun-Ichi Sekine

Yoshimasa Takizawa

Hitoshi Kurumizaka

Affiliations

Soon will be listed here.

Abstract

The Lys mutation of the canonical histone H3.1 Glu97 residue (H3E97K) is found in cancer cells. Previous biochemical analyses revealed that the nucleosome containing the H3E97K mutation is extremely unstable as compared to the wild-type nucleosome. However, the mechanism by which the H3E97K mutation causes nucleosome instability has not been clarified yet. In the present study, the cryo-electron microscopy structure of the nucleosome containing the H3E97K mutation revealed that the entry/exit DNA regions of the H3E97K nucleosome are disordered, probably by detachment of the nucleosomal DNA from the H3 N-terminal regions. This may change the intra-molecular amino acid interactions with the replaced H3 Lys97 residue, inducing structural distortion around the mutated position in the nucleosome. Consistent with the nucleosomal DNA end flexibility and the nucleosome instability, the H3E97K mutation exhibited reduced binding of linker histone H1 to the nucleosome, defective activation of PRC2 (the essential methyltransferase for facultative heterochromatin formation) with a poly-nucleosome, and enhanced nucleosome transcription by RNA polymerase II.

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Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K.

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References

Stark H . GraFix: stabilization of fragile macromolecular complexes for single particle cryo-EM. Methods Enzymol. 2010; 481:109-26. DOI: 10.1016/S0076-6879(10)81005-5. View

Olins A, Olins D . Spheroid chromatin units (v bodies). Science. 1974; 183(4122):330-2. DOI: 10.1126/science.183.4122.330. View

Wang H, Xiong L, Cramer P . Structures and implications of TBP-nucleosome complexes. Proc Natl Acad Sci U S A. 2021; 118(30). PMC: 8325331. DOI: 10.1073/pnas.2108859118. View

Peterson C, Kruger W, Herskowitz I . A functional interaction between the C-terminal domain of RNA polymerase II and the negative regulator SIN1. Cell. 1991; 64(6):1135-43. DOI: 10.1016/0092-8674(91)90268-4. View

Ehara H, Umehara T, Sekine S, Yokoyama S . Crystal structure of RNA polymerase II from Komagataella pastoris. Biochem Biophys Res Commun. 2017; 487(2):230-235. DOI: 10.1016/j.bbrc.2017.04.039. View

Bednar J, Garcia-Saez I, Boopathi R, Cutter A, Papai G, Reymer A . Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1. Mol Cell. 2017; 66(3):384-397.e8. PMC: 5508712. DOI: 10.1016/j.molcel.2017.04.012. View

Kimura T, Hirai S, Kujirai T, Fujita R, Ogasawara M, Ehara H . Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K. Genes Cells. 2024; 29(9):769-781. PMC: 11448003. DOI: 10.1111/gtc.13143. View

Croll T . ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol. 2018; 74(Pt 6):519-530. PMC: 6096486. DOI: 10.1107/S2059798318002425. View

Bagert J, Mitchener M, Patriotis A, Dul B, Wojcik F, Nacev B . Oncohistone mutations enhance chromatin remodeling and alter cell fates. Nat Chem Biol. 2021; 17(4):403-411. PMC: 8174649. DOI: 10.1038/s41589-021-00738-1. View

10.

Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N . Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome. Nucleic Acids Res. 2018; 46(19):10007-10018. PMC: 6212774. DOI: 10.1093/nar/gky661. View

11.

Williams C, Headd J, Moriarty N, Prisant M, Videau L, Deis L . MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2017; 27(1):293-315. PMC: 5734394. DOI: 10.1002/pro.3330. View

12.

Higo T, Suka N, Ehara H, Wakamori M, Sato S, Maeda H . Development of a hexahistidine-3× FLAG-tandem affinity purification method for endogenous protein complexes in Pichia pastoris. J Struct Funct Genomics. 2014; 15(4):191-9. PMC: 4237914. DOI: 10.1007/s10969-014-9190-1. View

13.

Nacev B, Feng L, Bagert J, Lemiesz A, Gao J, Soshnev A . The expanding landscape of 'oncohistone' mutations in human cancers. Nature. 2019; 567(7749):473-478. PMC: 6512987. DOI: 10.1038/s41586-019-1038-1. View

14.

Yuan W, Wu T, Fu H, Dai C, Wu H, Liu N . Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science. 2012; 337(6097):971-5. DOI: 10.1126/science.1225237. View

15.

Scheres S . Processing of Structurally Heterogeneous Cryo-EM Data in RELION. Methods Enzymol. 2016; 579:125-57. DOI: 10.1016/bs.mie.2016.04.012. View

16.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

17.

Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine S . Structure of the complete elongation complex of RNA polymerase II with basal factors. Science. 2017; 357(6354):921-924. DOI: 10.1126/science.aan8552. View

18.

Muthurajan U, Bao Y, Forsberg L, Edayathumangalam R, Dyer P, White C . Crystal structures of histone Sin mutant nucleosomes reveal altered protein-DNA interactions. EMBO J. 2004; 23(2):260-71. PMC: 1271754. DOI: 10.1038/sj.emboj.7600046. View

19.

Rohou A, Grigorieff N . CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J Struct Biol. 2015; 192(2):216-21. PMC: 6760662. DOI: 10.1016/j.jsb.2015.08.008. View

20.

Kruger W, Herskowitz I . A negative regulator of HO transcription, SIN1 (SPT2), is a nonspecific DNA-binding protein related to HMG1. Mol Cell Biol. 1991; 11(8):4135-46. PMC: 361230. DOI: 10.1128/mcb.11.8.4135-4146.1991. View