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The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE259416 | GEO | 2024/10/25

REPOSITORIES: GEO

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The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (ChIP-Seq)

Project description:Although the conserved type B histone acetyltransferase is known to regulate both cytoplasmic histone acetylation and nuclear nucleosome assembly, the coordination between the dual functions remains poorly understood. Our study revealed that the Arabidopsis thaliana type B histone acetyltransferase HAG2 interactions with the histone chaperones MSI2, MSI3, and NASP, as well as histones H3 and H4, resulting in the formation of a conserved NuB4 complex. Within this complex, HAG2, MSI2, and MSI3 constitute a histone acetylation module that acetylates newly synthesized histone H4 at lysine 5 and 12 sites in the cytoplasm. This module collaborates with NASP to maintain the abundance of H3 and H4 proteins in the cytoplasm, but it is not necessary for nucleosome assembly in the nucleus, which differs from the role of NuB4 complexes in other eukaryotes. Furthermore, we found that, within the nucleus, the collaborative actions of the histone acetylation module and NASP enhance chromatin accessibility near the transcription start sites of protein-coding genes, while showing a negative impact on chromatin accessibility near the transcription termination sites. This suggests that the Arabidopsis NuB4 complex is responsible for modulating chromatin accessibility across the entire genome, highlighting a plant-specific function of the NuB4 complex.

2024-10-25 | GSE259414 | GEO

The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (ATAC-Seq)

2024-10-25 | GSE259413 | GEO

The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (RNA-Seq)

2024-10-25 | GSE259415 | GEO

The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility

Project description:The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility

| PRJNA1081443 | ENA

The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (RNA-Seq)

Project description:The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (RNA-Seq)

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The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (ChIP-Seq)

Project description:The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (ChIP-Seq)

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The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (ATAC-Seq)

Project description:The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility (ATAC-Seq)

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Structure of the Rtt109-AcCoA/Vps75 complex and implications for chaperone-mediated histone acetylation.

Project description:Yeast Rtt109 promotes nucleosome assembly and genome stability by acetylating K9, K27, and K56 of histone H3 through interaction with either of two distinct histone chaperones, Vps75 or Asf1. We report the crystal structure of an Rtt109-AcCoA/Vps75 complex revealing an elongated Vps75 homodimer bound to two globular Rtt109 molecules to form a symmetrical holoenzyme with a ?12 Å diameter central hole. Vps75 and Rtt109 residues that mediate complex formation in the crystals are also important for Rtt109-Vps75 interaction and H3K9/K27 acetylation both in vitro and in yeast cells. The same Rtt109 residues do not participate in Asf1-mediated Rtt109 acetylation in vitro or H3K56 acetylation in yeast cells, demonstrating that Asf1 and Vps75 dictate Rtt109 substrate specificity through distinct mechanisms. These studies also suggest that Vps75 binding stimulates Rtt109 catalytic activity by appropriately presenting the H3-H4 substrate within the central cavity of the holoenzyme to promote H3K9/K27 acetylation of new histones before deposition.

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Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes.

Project description:Acetylation of histone H3 on lysine 56 occurs during mitotic and meiotic S phase in fungal species. This acetylation blocks a direct electrostatic interaction between histone H3 and nucleosomal DNA, and the absence of this modification is associated with extreme sensitivity to genotoxic agents. We show here that H3-K56 acetylation is catalyzed when Rtt109, a protein that lacks significant homology to known acetyltransferases, forms an active complex with either of two histone binding proteins, Asf1 or Vps75. Rtt109 binds to both these cofactors, but not to histones alone, forming enzyme complexes with kinetic parameters similar to those of known histone acetyltransferase (HAT) enzymes. Therefore, H3-K56 acetylation is catalyzed by a previously unknown mechanism that requires a complex of two proteins: Rtt109 and a histone chaperone. Additionally, these complexes are functionally distinct, with the Rtt109/Asf1 complex, but not the Rtt109/Vps75 complex, being critical for resistance to genotoxic agents.

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Histone chaperone exploits intrinsic disorder to switch acetylation specificity.

Project description:Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.

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