| Name | H3.3 histone B |
| Description | Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene contains introns and its mRNA is polyadenylated, unlike most histone genes. The protein encoded by this gene is a replication-independent histone that is a member of the histone H3 family. Pseudogenes of this gene have been identified on the X chromosome, and on chromosomes 5, 13 and 17. [provided by RefSeq, Oct 2015] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Histone H3.3, encoded by nearly identical genes such as H3F3A and H3F3B, is a replication‐independent variant central to chromatin dynamics and genome regulation. In normal development and differentiated cells, H3.3 is deposited at actively transcribed regions as well as at heterochromatic domains (including telomeres and pericentromeric regions), thereby supporting proper chromatin architecture, facilitating the recruitment of chromatin modifiers such as polycomb repressive complexes, and maintaining genome stability."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In several pediatric and young adult tumors—including various high‐grade gliomas and diffuse intrinsic pontine gliomas—recurrent mutations in H3.3 (notably K27M and G34 substitutions) have emerged as key drivers of oncogenesis. These mutations disrupt normal post‐translational modifications such as H3K27 trimethylation and H3K36 methylation, thereby reprogramming gene expression, altering the epigenetic landscape, and establishing distinct molecular and anatomical tumor subgroups."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "8"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Moreover, tumor type–specific mutations—for example, the lysine‐to‐methionine substitution at residue 36 predominantly encoded by H3F3B in chondroblastoma—highlight the nuanced, context‐dependent functions of H3.3 variants in determining cellular identity and driving oncogenic programs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Together, these findings demonstrate that H3.3 is not only critical for the regulation of transcription and maintenance of chromatin structure during normal development but that its mutation in diverse cellular contexts is sufficient to rewire epigenetic states, leading to aberrant gene expression and tumorigenesis.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Laura A Banaszynski, Duancheng Wen, Scott Dewell, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2013.08.061"}], "href": "https://doi.org/10.1016/j.cell.2013.08.061"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24074864"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24074864"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Simon J Elsaesser, Aaron D Goldberg, C David Allis "}, {"type": "b", "children": [{"type": "t", "text": "New functions for an old variant: no substitute for histone H3.3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Curr Opin Genet Dev (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.gde.2010.01.003"}], "href": "https://doi.org/10.1016/j.gde.2010.01.003"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20153629"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20153629"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Chuan-Wei Jang, Yoichiro Shibata, Joshua Starmer, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone H3.3 maintains genome integrity during mammalian development."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.264150.115"}], "href": "https://doi.org/10.1101/gad.264150.115"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26159997"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26159997"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Jeremy Schwartzentruber, Andrey Korshunov, Xiao-Yang Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature10833"}], "href": "https://doi.org/10.1038/nature10833"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22286061"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22286061"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Dominik Sturm, Hendrik Witt, Volker Hovestadt, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Cell (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ccr.2012.08.024"}], "href": "https://doi.org/10.1016/j.ccr.2012.08.024"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23079654"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23079654"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Peter W Lewis, Manuel M Müller, Matthew S Koletsky, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Science (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1126/science.1232245"}], "href": "https://doi.org/10.1126/science.1232245"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23539183"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23539183"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Dong-Anh Khuong-Quang, Pawel Buczkowicz, Patricia Rakopoulos, et al. "}, {"type": "b", "children": [{"type": "t", "text": "K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Acta Neuropathol (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00401-012-0998-0"}], "href": "https://doi.org/10.1007/s00401-012-0998-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22661320"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22661320"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Lynn Bjerke, Alan Mackay, Meera Nandhabalan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone H3.3. mutations drive pediatric glioblastoma through upregulation of MYCN."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Discov (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1158/2159-8290.CD-12-0426"}], "href": "https://doi.org/10.1158/2159-8290.CD-12-0426"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23539269"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23539269"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Sam Behjati, Patrick S Tarpey, Nadège Presneau, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.2814"}], "href": "https://doi.org/10.1038/ng.2814"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24162739"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24162739"}]}]}]}
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| NCBI Gene ID | 3021 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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H3-3B has 9,838 functional associations with biological entities spanning 6 categories (chemical, disease, phenotype or trait, functional term, phrase or reference, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 34 datasets.
Click the + buttons to view associations for H3-3B from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles | tissue samples with high or low expression of H3-3B gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset. | |
| Carcinogenome Chemical Perturbation Carcinogenicity Signatures | small molecule perturbations changing expression of H3-3B gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset. | |
| CellMarker Gene-Cell Type Associations | cell types associated with H3-3B gene from the CellMarker Gene-Cell Type Associations dataset. | |
| ClinVar Gene-Phenotype Associations 2025 | phenotypes associated with H3-3B gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset. | |
| CM4AI KOLF21J CRISPRi Gene Perturbation Atlas | gene perturbations changing expression of H3-3B gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset. | |
| COMPARTMENTS Curated Protein Localization Evidence Scores 2025 | cellular components containing H3-3B protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 | cellular components containing H3-3B protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset. | |
| COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 | cellular components co-occuring with H3-3B protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset. | |
| DISEASES Experimental Gene-Disease Association Evidence Scores 2025 | diseases associated with H3-3B gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 | diseases co-occuring with H3-3B gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset. | |
| GO Biological Process Annotations 2025 | biological processes involving H3-3B gene from the curated GO Biological Process Annotations2025 dataset. | |
| GO Cellular Component Annotations 2025 | cellular components containing H3-3B protein from the curated GO Cellular Component Annotations 2025 dataset. | |
| GO Molecular Function Annotations 2025 | molecular functions performed by H3-3B gene from the curated GO Molecular Function Annotations 2025 dataset. | |
| GTEx eQTL 2025 | SNPs regulating expression of H3-3B gene from the GTEx eQTL 2025 dataset. | |
| GTEx Tissue Gene Expression Profiles 2023 | tissues with high or low expression of H3-3B gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset. | |
| GWAS Catalog SNP-Phenotype Associations 2025 | phenotypes associated with H3-3B gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset. | |
| HuBMAP Azimuth Cell Type Annotations | cell types associated with H3-3B gene from the HuBMAP Azimuth Cell Type Annotations dataset. | |
| JASPAR Predicted Human Transcription Factor Targets 2025 | transcription factors regulating expression of H3-3B gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset. | |
| KEGG Pathways 2026 | pathways involving H3-3B protein from the KEGG Pathways 2026 dataset. | |
| LINCS L1000 CMAP Chemical Perturbation Consensus Signatures | small molecule perturbations changing expression of H3-3B gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset. | |
| MoTrPAC Rat Endurance Exercise Training | tissue samples with high or low expression of H3-3B gene relative to other tissue samples from the MoTrPAC Rat Endurance Exercise Training dataset. | |
| PFOCR Pathway Figure Associations 2024 | pathways involving H3-3B protein from the Wikipathways PFOCR 2024 dataset. | |
| Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures | gene perturbations changing expression of H3-3B gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset. | |
| Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures | gene perturbations changing expression of H3-3B gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset. | |
| Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures | gene perturbations changing expression of H3-3B gene from the Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures dataset. | |
| Rummagene Transcription Factor Associations 2026 | transcription factors regulating expression of H3-3B gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| RummaGEO Drug Perturbation Signatures | drug perturbations changing expression of H3-3B gene from the RummaGEO Drug Perturbation Signatures dataset. | |
| RummaGEO Gene Perturbation Signatures | gene perturbations changing expression of H3-3B gene from the RummaGEO Gene Perturbation Signatures dataset. | |
| Sci-Plex Drug Perturbation Signatures | drug perturbations changing expression of H3-3B gene from the Sci-Plex Drug Perturbation Signatures dataset. | |
| Tahoe Therapeutics Tahoe 100M Perturbation Atlas | drug perturbations changing expression of H3-3B gene from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset. | |
| TISSUES Curated Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of H3-3B protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset. | |
| TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 | tissues with high expression of H3-3B protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset. | |
| TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 | tissues co-occuring with H3-3B protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset. | |
| WikiPathways Pathways 2024 | pathways involving H3-3B protein from the WikiPathways Pathways 2024 dataset. | |