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Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z, h2a.z + AtHTA11 RNA-Seq)

ABSTRACT: To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. Furthermore, H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84 % of misexpressed genes. Finally, our hypothesis that the N-terminal tail of Arabidopsis H2A.Z is not crucial for its overall function was supported by the ability of N-terminal end truncations of Arabidopsis HTA11 to largely rescue the defects of h2a.z mutants.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE263310 | GEO | 2024/05/13

REPOSITORIES: GEO

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Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z + HsH2A.Z. RNA-Seq)

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2020-05-18 | PXD019248 | Pride

Methyl-CpG-binding domain 9 (MBD9) is required for H2A.Z incorporation into chromatin at a subset of H2A.Z-enriched regions in the Arabidopsis genome

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Effect of modified H2A.Z protein to gene expression in DT40 cells.

Project description:H2A.Z-nucleosomes participate in both euchromatin and heterochromatin and it has proven difficult to reveal how the disparate roles and stability features imparted by H2A.Z are connected. Using an in situ assay of nucleosome stability in nuclei of DT40 cells expressing engineered forms of the variant we show that H2A.Z is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations, compared to cells expressing C-terminally truncated H2A.Z. Binding of the tail-peptide (C9) to reconstituted nucleosomes, DNA and the nuclear lamina were detected. Upon treatment of HeLa nuclei with C9, the H2A.Z-nucleosomes assumed canonical stability, the peripheral heterochromatin became dispersed and overall nuclease sensitivity increased, recapitulating tail-dependent differences in DT40. When introduced into live cells, C9 elicited chromatin reorganization and transcriptional down-regulation of ~600 genes. Thus, large-scale epigenetic modulation can be achieved by targeting or making advantage of molecular interactions involving the C-terminal tail of H2A.Z.

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NuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis

Project description:Nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, but remains poorly characterized in plants. Here, we describe Arabidopsis homologs of the NuA4 scaffold proteins Enhancer of Polycomb-Like-1 (AtEPL1) and Esa1- Associated Factor 1 (AtEAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors, suggesting that NuA4 activates nuclear plastid genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished genome-wide in Atepl1, while another active chromatin mark, H3K9 acetylation (H3K9ac), is locally enhanced. Expression of many chloroplast-related genes depends on NuA4, as they are downregulated with loss of H4ac and H2A.Zac. Finally, we demonstrate that NuA4 promotes H2A.Z deposition and by doing so prevents spurious activation of stress response genes.

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Project description:In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved in plants. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.

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Project description:Craniofacial disorder Floating-Harbor Syndrome (FHS) is caused by heterozygous truncating mutations in SRCAP, a gene encoding a chromatin remodeler mediating incorporation of histone variant H2A.Z. Here, we demonstrate that FHS-associated mutations result in loss of SRCAP nuclear localization, alter neural crest gene programs in human in vitro models and Xenopus embryos, and cause craniofacial defects. These defects are mediated by one of two H2A.Z subtypes, H2A.Z.2, whose knockdown mimics and whose overexpression rescues the FHS phenotype. Selective rescue by H2A.Z.2 is conferred by one of the three amino acid differences between the H2A.Z subtypes, S38/T38. We further show that H2A.Z.1 and H2A.Z.2 genomic occupancy patterns are qualitatively similar, but quantitatively distinct, and that H2A.Z.2 incorporation at AT-rich enhancers and expression of their associated genes are both sensitized to SRCAP truncations. Altogether, our results illuminate the mechanism underlying a human syndrome and uncover selective functions of H2A.Z subtypes during development.

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Project description:The nucleosomal acetyltransferase of H4 (NuA4) is an essential transcriptional coactivator in eukaryotes, though it remains poorly characterized in plants. Here, we describe Arabidopsis homologues of the NuA4 scaffold proteins Enhancer of Polycomb-Like1 (EPL1) and Esa1-Associated Factor1 (EAF1). Loss of AtEAF1 results in inhibition of growth and chloroplast development. These effects are stronger in the Atepl1 mutant and are further enhanced by loss of Golden2-Like (GLK) transcription factors suggesting that NuA4 activates nuclear plastidic genes alongside GLK. We demonstrate that AtEPL1 is necessary for nucleosomal acetylation of histones H4 and H2A.Z by NuA4 in vitro. These chromatin marks are diminished in Atepl1 genome-wide while another active chromatin mark H3K9ac is locally enhanced. Many chloroplast-related genes depend on NuA4 as they are downregulated with loss of H4ac and H2A.Z alone. Finally, we demonstrate that NuA4 promotes deposition of H2A.Z and by doing so prevents spurious activation of stress response genes.

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