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Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome

Hirano, Rina Arimura, Yasuhiro Kujirai, Tomoya Shibata, Mikihiro Okuda, Aya Morishima, Ken Inoue, Rintaro Sugiyama, Masaaki Kurumizaka, Hitoshi 京都大学 DOI:10.1038/s42003-021-01707-z

2021.02.12

概要

H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. In cells, H2A.B exchanges rapidly in chromatin, but the mechanism has remained enigmatic. In the present study, we found that the H2A.B-H2B dimer incorporated within the nucleosome exchanges with the canonical H2A-H2B dimer without assistance from additional factors, such as histone chaperones and nucleosome remodelers. High-speed atomic force microscopy revealed that the H2A.B nucleosome, but not the canonical H2A nucleosome, transiently forms an intermediate “open conformation”, in which two H2A.B-H2B dimers may be detached from the H3-H4 tetramer and bind to the DNA regions near the entry/exit sites. Mutational analyses revealed that the H2A.B C-terminal region is responsible for the adoption of the open conformation and the H2A.B-H2B exchange in the nucleosome. These findings provide mechanistic insights into the histone exchange of the H2A.B nucleosome.

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Acknowledgements

We are grateful to Ms. Y. Iikura (The University of Tokyo) and Ms. Y. Takeda (The

University of Tokyo). We also thank Mr. K. Shirayama (Waseda University), and Mr.

N. Yajima (Waseda University) for their assistance. This work was supported in part by JSPS

KAKENHI Grant Numbers JP15H06691 [to Y. A.], JP18H01836 [to M. Shibata],

JP19H05257 [to M. Shibata], JP18H05229 [to M. Sugiyama], JP18H05534 [to H. K. and M.

Sugiyama] and JP20H00449 [to H. K.]. This work was also partly supported by JST CREST

Grant Number JPMJCR16G1 [to H. K. and T. K.], JST ERATO Grant Number JPMJER1901

[to H. K.], the Platform Project for Supporting Drug Discovery and Life Science Research

(BINDS) from AMED under Grant Number JP20am0101076 [to H. K.], and the project for

Construction of the basis for the advanced materials science and analytical study by the

innovative use of quantum beam and nuclear sciences in KURNS [to M. Sugiyama].

Author contributions

R.H., Y.A. and T.K. performed biochemical analyses, and Y.A. performed X-ray crystallography. A.O., K.M., R.I. and M. Sugiyama performed the SAXS analyses. M. Shibata

ARTICLE

performed the HS-AFM analyses. H.K. conceived, designed, and supervised all of the

work, and R.H., T.K. and H.K. wrote the paper. All of the authors discussed the results

and commented on the manuscript.

Competing interests

The authors declare no competing interests.

Additional information

Supplementary information The online version contains supplementary material

available at https://doi.org/10.1038/s42003-021-01707-z.

Correspondence and requests for materials should be addressed to H.K.

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