H2AFZ Human
Description
Molecular Structure and Biochemical Properties
H2AFZ (also known as H2A.Z.1) is a histone variant belonging to the H2A family, encoded by the H2AFZ gene in humans. Unlike canonical histones that are primarily expressed during S-phase, H2AFZ is expressed throughout the cell cycle .
Protein Structure
H2AFZ Human is a single, non-glycosylated polypeptide chain containing 128 amino acids with a molecular mass of approximately 15.9kDa . The recombinant form often includes additional amino acids (typically a His-tag) for purification purposes, bringing the total to around 151 amino acids.
Table 2: Comparison of H2A.Z Isoforms
Remarkably, a single amino acid difference at position 38 (S38 in H2A.Z.1 vs. T38 in H2A.Z.2) confers distinct functional properties to these isoforms, affecting nucleosomal structural polymorphisms and dynamics .
Functional Roles in Chromatin Regulation
H2AFZ plays critical roles in modulating chromatin structure and dynamics, with significant impacts on gene expression, DNA repair, and chromosome segregation.
Nucleosome Stability and DNA Accessibility
Advanced modeling of human nucleosome stability and dynamics has revealed that incorporation of H2AFZ substantially decreases the energy barrier for DNA unwrapping, leading to:
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Spontaneous DNA unwrapping of approximately forty base pairs from both nucleosome ends
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Increased nucleosome gapping
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Enhanced histone plasticity
Both N- and C-terminal tails of H2AFZ play major roles in facilitating DNA unwrapping, whereas the histone variant H3.3 has minimal impact on this process .
Genomic Distribution and Incorporation Mechanisms
H2AFZ is enriched at specific genomic locations, particularly:
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The -1 and +1 nucleosomes surrounding nucleosome-depleted regions at active promoters
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Enhancer regions
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Sites of DNA damage repair
H2AFZ incorporation into chromatin is mediated by specialized ATP-dependent chromatin remodeling complexes, primarily SRCAP (Snf2-related CREBBP activator protein) and p400, which exchange canonical H2A-H2B dimers with H2A.Z-H2B dimers . Conversely, removal of H2AFZ can be mediated by the ANP32E chaperone protein .
Regulation of Gene Expression
The relationship between H2AFZ and gene expression is complex and context-dependent, with evidence supporting both activating and repressive roles.
Promoter Architecture
H2AFZ plays multiple distinct roles in regulating promoter chromatin architecture. High-depth mapping of H2A.Z-containing nucleosomes across human Pol II promoters has revealed diverse promoter structures that differ in nucleosome organization and sensitivity to MNase digestion .
Key aspects of an active chromatin structure include:
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Positioned H2A.Z MNase-resistant nucleosomes upstream or downstream of the transcription start site (TSS)
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An MNase-sensitive nucleosome at the TSS itself
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Increased accessibility of transcription factor binding sites upon loss of H2A.Z
Context-Dependent Regulation
RNA-Seq analysis in untransformed cells has demonstrated that H2AFZ can regulate both distinct and overlapping sets of genes positively or negatively in a context-dependent manner . Furthermore, H2AFZ can have:
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Similar functions to H2A.Z.2 for many genes (1208 genes regulated in the same way)
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Antagonistic functions compared to H2A.Z.2 for other genes (242 genes regulated in opposite ways)
This complex interplay suggests that the balance between H2A.Z.1 and H2A.Z.2 at promoters is critically important for regulating specific gene expression, providing an additional layer of complexity to the control of gene expression by histone variants .
Role in Development and Cellular Function
The biological significance of H2AFZ extends beyond its molecular functions, with critical roles in development and specialized cellular processes.
Embryonic Development
Studies in mice have demonstrated that H2AFZ is essential for embryonic development, with knockout models showing that lack of functional H2AFZ leads to embryonic lethality . This essential role underscores the non-redundant functions of H2AFZ that cannot be compensated by other histone variants.
Cell Division and Chromosome Segregation
H2AFZ is implicated in the formation of constitutive heterochromatin and is vital for chromosome segregation during cell division . Its proper deposition and maintenance are therefore critical for genomic stability.
DNA Damage Response
Recent research has revealed that H2AFZ is involved in DNA double-strand break (DSB) repair initiation, particularly in post-mitotic cells like muscle fibers . H2AFZ is required to initiate DNA DSB repair by recruiting Ku80 to DNA lesions via specific interactions between Ku80's vWA domain and H2AFZ. This suggests that H2A.Z-containing nucleosomes act as molecular platforms to bring together proteins required for DNA repair .
Roles in Cancer and Disease
Dysregulation of H2AFZ expression and function has been implicated in multiple pathological conditions, particularly in cancer.
H2AFZ in Hepatocellular Carcinoma
H2AFZ is significantly overexpressed in hepatocellular carcinoma (HCC), with high expression levels associated with poor prognosis .
Table 3: H2AFZ Functions in Hepatocellular Carcinoma
Furthermore, H2AFZ overexpression in HCC appears to be regulated by TP53 mutation, a frequently observed event in HCC . Analysis of differential expression genes between H2AFZ-high and H2AFZ-low groups suggests that H2AFZ mainly promotes cell proliferation and associates with resistance to platinum drugs .
H2AFZ in Lung Adenocarcinoma
Immunohistochemical staining has revealed that H2AFZ is primarily localized in the nucleus of LUAD cells but is not recognized in adjacent normal tissues . Expression levels are significantly associated with multiple clinical features:
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Pathological stage (highest in advanced stages)
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T classification (highest in T3)
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N classification (highest in N2)
The association with tumor-infiltrating immune cells suggests that H2AFZ could serve as a prognostic biomarker correlated with immune infiltration in LUAD .
H2AFZ in Other Cancer Types
Analysis of the TIMER 2.0 database indicates that H2AFZ is overexpressed in many cancer types compared to adjacent normal tissues, including:
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Bladder cancer
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Breast cancer
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Cervical cancer
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Colorectal cancer
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Gastric cancer
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Kidney cancer
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Liver cancer
This widespread dysregulation suggests a potential fundamental role for H2AFZ in carcinogenesis across multiple tissues and cell types.
Molecular Mechanisms and Interactions
The functional effects of H2AFZ are mediated through specific molecular interactions and mechanisms that influence chromatin structure and nuclear processes.
Protein Interactions
Mass spectrometry analysis has shown that H2AFZ has specific interactors that differ from those of H2A.Z.2, which can mediate their functional antagonism . In hepatocellular carcinoma, H2AFZ overexpression is associated with a network of kinases including:
These interactions suggest that H2AFZ may influence cell cycle progression and other cellular processes through direct or indirect interactions with key regulatory kinases.
Epigenetic Regulation
H2AFZ deposition patterns are qualitatively similar but quantitatively distinct from H2A.Z.2, with evidence suggesting that H2A.Z.2 is present at a higher ratio to H2A.Z.1 at enhancers versus promoters . This differential distribution may contribute to the isoform-specific functions observed in various cellular contexts.
Current Research and Future Directions
Research on H2AFZ continues to evolve, with several emerging areas of interest that may lead to new therapeutic approaches.
Role in Aging and Degenerative Diseases
Recent studies have shown that depletion of H2AFZ in mouse skeletal muscle causes oxidative stress, protein oxidation, DNA damage accumulation, and lesions in neuromuscular junctions and mitochondria . These effects collectively lead to premature muscle aging and reduced lifespan, highlighting potential roles for H2AFZ in aging and degenerative diseases.
Therapeutic Potential
Given its roles in cancer progression and DNA repair, H2AFZ represents a potential therapeutic target. Strategies that modulate H2AFZ expression or function might prove effective in treating cancers characterized by H2AFZ overexpression, particularly hepatocellular carcinoma and lung adenocarcinoma.
Diagnostic Applications
The consistent overexpression of H2AFZ in multiple cancer types suggests its potential utility as a diagnostic or prognostic biomarker. Future research may focus on developing assays to detect H2AFZ levels or modifications in tissue samples or liquid biopsies.
Product Specs
Q&A
How do H2A.Z.1 (H2AFZ) and H2A.Z.2 (H2AFV) functionally diverge despite high sequence similarity?
Methodological approach:
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Use isoform-specific antibodies (e.g., anti-H2A.Z.1 vs. anti-H2A.Z.2) for ChIP-seq to map genomic occupancy differences .
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Employ CRISPR/Cas9 knockout models to study subtype-specific phenotypes (e.g., H2A.Z.2 knockdown rescues craniofacial defects in Floating-Harbor syndrome models, while H2A.Z.1 does not) .
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Analyze post-translational modifications (e.g., acetylation at N-terminal lysines) via mass spectrometry to identify subtype-specific regulatory mechanisms .
Key finding:
What experimental strategies resolve contradictory reports of H2AFZ as both oncogenic and tumor-suppressive?
Advanced analysis framework:
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Context-dependent validation: Compare H2AFZ expression in TP53 wild-type vs. mutant backgrounds using isogenic cell lines .
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Pathway enrichment: Perform GSEA on RNA-seq data from H2AFZ-high tumors to identify cell cycle (PLK1, CDK1) vs. immune checkpoint (PD-L1, CTLA-4) dominance .
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Single-cell ATAC-seq: Profile chromatin accessibility changes in H2AFZ-overexpressing cells to distinguish direct regulatory effects from bystander phenomena .
Critical data: In HCC, H2AFZ overexpression correlates with TP53 mutations (HR = 2.1, p < 0.001) and platinum resistance (AUC = 0.78) .
How to design studies investigating H2AFZ's dual role in epigenetic regulation and immune modulation?
Integrated workflow:
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Step 1: Use CUT&Tag to map H2AFZ binding near immune checkpoint genes (e.g., PD-L1, CTLA-4) in tumor-infiltrating lymphocytes .
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Step 2: Validate functional links via siRNA knockdown paired with IFN-γ ELISpot assays to measure T-cell activation .
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Step 3: Apply spatial transcriptomics to correlate H2AFZ expression gradients with immune desert/excluded phenotypes in tumor sections.
Contradiction resolution: H2AFZ stabilizes nucleosomes at E2F1-target promoters to drive proliferation , while simultaneously creating permissive chromatin at immune gene loci through H3K4me3 priming .
What controls are essential when studying H2A.Z isoform redundancy in gene regulation?
Rigorous experimental design:
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Include spike-in chromatin (e.g., Drosophila S2 cell chromatin) for ChIP-qPCR normalization to avoid false positives from compensatory isoform binding .
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Use S38A/T38A mutants to isolate functional impacts of the critical H2A.Z.1/H2A.Z.2 divergent residue .
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Pair RNA-seq with Ribo-seq to distinguish transcriptional vs. translational effects of isoform depletion.
Red flag: Overexpression of H2A.Z.2.2 (the primate-specific isoform) alters nucleosome stability by 37% compared to H2A.Z.1 , requiring species-matched model systems.
How to validate H2AFZ as a predictive biomarker for immune checkpoint inhibitor response?
Translational methodology:
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Retrospective cohort analysis: Stratify HCC patients by H2AFZ expression (top 25% vs. bottom 25%) and calculate objective response rates to anti-PD1 therapy .
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Mechanistic testing: Generate H2AFZ-knockout PDX models and track CD8+ T-cell infiltration via multiplex IHC.
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Epigenetic editing: Use dCas9-H2AFZ fusions to site-specifically deposit H2A.Z at PD-L1 promoters, followed by flow cytometry analysis of ligand surface expression.
Prognostic value: H2AFZ-high/TP53-mutant HCC patients show 5.8-month median OS vs. 14.2 months in H2AFZ-low/TP53-wild type (p = 0.007) .
Product Science Overview
H2A.Z, also known as H2AFZ, is a variant of the H2A histone family. Histones are proteins that play a crucial role in the organization and regulation of DNA within the nucleus of eukaryotic cells. H2A.Z is highly conserved across species, from yeast to humans, with about 90% of its primary sequence preserved . This conservation underscores its essential role in various cellular processes.
Histones, including H2A.Z, are integral components of nucleosomes, the basic units of chromatin. A nucleosome consists of approximately 146 base pairs of DNA wrapped around a histone octamer, which includes two copies each of H2A, H2B, H3, and H4 . H2A.Z is distinct from the canonical H2A histone, showing only about 60% homology with it . This difference allows H2A.Z to perform unique functions that are not shared by the canonical H2A.
H2A.Z is involved in several critical processes, including:
- Transcriptional Regulation: H2A.Z plays a role in both the activation and repression of gene transcription. It is incorporated into chromatin in a replication-independent manner, meaning it can be added to chromatin outside of DNA replication .
- DNA Repair: H2A.Z is implicated in the repair of DNA damage, helping to maintain genome stability .
- Chromatin Dynamics: The presence of H2A.Z in nucleosomes affects the stability and structure of chromatin, making it more dynamic and accessible to regulatory proteins .
H2A.Z exists in multiple variants, with H2A.Z.2.2 being one of the notable ones. This variant is alternatively spliced and causes significant nucleosome destabilization, which can impact gene expression and chromatin structure . Post-translational modifications (PTMs) such as acetylation and ubiquitination of H2A.Z also play a crucial role in its function, influencing its interaction with other proteins and its incorporation into chromatin .
The unique properties of H2A.Z make it a key player in various biological processes. Its ability to modulate chromatin structure and function allows it to participate in the fine-tuning of gene expression, DNA repair, and other essential cellular activities. The study of H2A.Z and its variants continues to provide insights into the complex regulation of chromatin and its impact on cellular function and disease.
