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

Rina Hirano,Rintaro Inoue,Mikihiro Shibata,Tomoya Kujirai,Ken Morishima,Masaaki Sugiyama,Hitoshi Kurumizaka,Yasuhiro Arimura,Aya Okuda

doi:10.1038/s42003-021-01707-z

Abstract

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.

Highlights

H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes
We previously reported that the crystal of the heterotypic nucleosome core particle (NCP) with the histone variant, CENP-A, which forms an NCP with flexible DNA ends, diffracted better than that of the homotypic NCP19,44
We found that 49.4% of the H2A.B NCP existed as the open conformation, in which two small histone complexes are bound to the DNA and detached from the large histone complex at the initial stage of the HS-AFM analysis (Fig. 3a, c)

Summary

Introduction

H2A.B is an evolutionarily distant histone H2A variant that accumulates on DNA repair sites, DNA replication sites, and actively transcribing regions in genomes. We found that 49.4% of the H2A.B NCP existed as the open conformation, in which two small histone complexes (probably H2A.B-H2B dimers) are bound to the DNA and detached from the large histone complex (probably H3-H4 tetramer) at the initial stage of the HS-AFM analysis (Fig. 3a, c).

Results

Conclusion