Anp32e, a higher eukaryotic histone chaperone directs preferential recognition for H2A.Z

Abstract

H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is preferentially recognized by non-histone proteins remains elusive. Here we identified Anp32e, a novel higher eukaryote-specific histone chaperone for H2A.Z. Anp32e preferentially associates with H2A.Z-H2B dimers rather than H2A-H2B dimers in vitro and in vivo and dissociates non-nucleosomal aggregates formed by DNA and H2A-H2B. We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change. Genome-wide profiling of Anp32e revealed a remarkable co-occupancy between Anp32e and H2A.Z. Cells overexpressing Anp32e displayed a strong global H2A.Z loss at the +1 nucleosomes, whereas cells depleted of Anp32e displayed a moderate global H2A.Z increase at the +1 nucleosomes. This suggests that Anp32e may help to resolve the non-nucleosomal H2A.Z aggregates and also facilitate the removal of H2A.Z at the +1 nucleosomes, and the latter may help RNA polymerase II to pass the first nucleosomal barrier.

Histone chaperone Anp32e removes H2A.Z from DNA double-strand breaks and promotes nucleosome reorganization and DNA repair

“…The crystal structure of Anp32e bound to H2A.Z indicates that Anp32e makes multiple contacts with H2A.Z, including T103/I104 in the C-terminal docking domain (20,21) (Fig. 2A).…”

“…Although the Anp32e interacting residues are conserved in H2A, the extra glycine residue in H2A (blue circle; Fig. 2A) disrupts Anp32e-H2A interaction (20,21), so that Anp32e only binds H2A.Z. We therefore replaced the Anp32e binding region of H2A.Z with the equivalent region from H2A, including the extra glycine, creating the chimeric H2A.Z protein H2A.Z NG ( Fig.…”

“…The observation that the LANA protein, which binds the acidic domain (30), can rescue H4 acetylation in the absence of Anp32e supports this finding. However, Anp32e, in common with many histone exchange reactions, actually removes the entire H2A.Z-H2B dimer (20,21), potentially creating tetrasomes (containing only H3-H4 dimers). Studies indicate that H2B is lost from the chromatin at DSBs (43), suggesting that removal of H2A.Z-H2B by Anp32e may create chromatin regions containing tetrasomes or possibly lacking any nucleosomes.…”

“…H2A.Z contains a specific binding site for Anp32e (20,21), which partially overlaps with the acidic domain to which the H4 tail binds (24)(25)(26)(27). Anp32e binding to H2A.Z may displace the H4 tail, promoting H4 acetylation.…”

Differential deposition of H2A.Z in rice seedling tissue during the day-night cycle

“…1 Genome wide analysis has widely characterized H2A.Z deposition in S. cerevisiae, 2-4 Drosophila,. 5,6 mammals, [7][8][9][10] Arabidopsis, 1,[11][12][13] and rice. 14 H2A.Z deposition is probably involved in diverse genomic processes, such as gene transcription, meiotic recombination, chromosome segregation, DNA repair, and genome stability.…”