H3-3A Gene

Name H3.3 histone A
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 is a replication-independent member of the histone H3 family. [provided by RefSeq, Jul 2008]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n The H3‐3A gene (commonly referred to as H3F3A) encodes the replication‐independent histone variant H3.3, which plays a central role in maintaining chromatin structure and dynamics. In normal cells, H3.3 is deposited at active genes, telomeres, centromeres, and pericentric heterochromatin—contributing to the regulation of transcription, chromatin accessibility, and genomic stability (see."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n A number of studies have revealed that somatic mutations in H3F3A, notably the lysine‐to‐methionine (K27M) and glycine‐to‐arginine/valine (G34R/V) substitutions, are frequent in pediatric and young adult gliomas. These mutations disrupt key post‐translational modifications—such as the trimethylation of lysine 27 (H3K27me3) or alteration of lysine 36 methylation patterns—thereby reprogramming the epigenetic landscape. As a consequence, these aberrations perturb the regulation of gene expression, contribute to distinct transcriptional profiles and cellular identities, and drive oncogenic pathways including the upregulation of potent oncogenes (for instance, MYCN) (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}, {"type": "fg_fs", "start_ref": "4", "end_ref": "10"}]}, {"type": "t", "text": " \n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In addition to its role in transcriptional regulation, H3.3 functions in preserving chromosomal integrity. Its incorporation at telomeric and pericentromeric regions is critical for proper heterochromatin organization; loss or mutation of H3.3 can lead to telomere dysfunction and genomic instability, both of which are frequently observed in tumor cells (see."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n Cumulatively, these studies establish that H3-3A/H3F3A is not only a core component required for normal chromatin architecture and gene regulation, but that mutations in this gene act as key driving events in pediatric high-grade gliomas by impairing normal histone modification landscapes and reprogramming transcription. This dual role—with disruption of both epigenetic signaling and chromatin stability—underlines its importance as a molecular link between developmental chromatin regulation and oncogenic transformation.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "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": 2, "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": 3, "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": 4, "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": 5, "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": 6, "children": [{"type": "t", "text": "Kui-Ming Chan, Dong Fang, Haiyun Gan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.217778.113"}], "href": "https://doi.org/10.1101/gad.217778.113"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23603901"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23603901"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Pawel Buczkowicz, Christine Hoeman, Patricia Rakopoulos, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.2936"}], "href": "https://doi.org/10.1038/ng.2936"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24705254"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24705254"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "David A Solomon, Matthew D Wood, Tarik Tihan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Diffuse Midline Gliomas with Histone H3-K27M Mutation: A Series of 47 Cases Assessing the Spectrum of Morphologic Variation and Associated Genetic Alterations."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Brain Pathol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/bpa.12336"}], "href": "https://doi.org/10.1111/bpa.12336"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26517431"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26517431"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Koki Aihara, Akitake Mukasa, Kengo Gotoh, et al. "}, {"type": "b", "children": [{"type": "t", "text": "H3F3A K27M mutations in thalamic gliomas from young adult patients."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Neuro Oncol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/neuonc/not144"}], "href": "https://doi.org/10.1093/neuonc/not144"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24285547"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24285547"}]}, {"type": "r", "ref": 10, "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"}]}]}]}
NCBI Gene ID 3020
API
Download Associations
Predicted Functions View H3-3A's ARCHS4 Predicted Functions.
Co-expressed Genes View H3-3A's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View H3-3A's ARCHS4 Predicted Functions.

Functional Associations

H3-3A has 2,189 functional associations with biological entities spanning 5 categories (chemical, disease, phenotype or trait, functional term, phrase or reference, cell line, cell type or tissue, gene, protein or microRNA) extracted from 32 datasets.

Click the + buttons to view associations for H3-3A 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 H3-3A 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 H3-3A gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CCLE Cell Line Proteomics Cell lines associated with H3-3A protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with H3-3A gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of H3-3A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
CM4AI KOLF21J CRISPRi Gene Perturbation Atlas gene perturbations changing expression of H3-3A gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
DeepCoverMOA Drug Mechanisms of Action small molecule perturbations with high or low expression of H3-3A protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
DGIdb Drug Targets 2026 interacting drugs for H3-3A protein from the DGIdb Drug Targets 2026 dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores 2025 diseases associated with H3-3A 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 H3-3A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
GO Biological Process Annotations 2023 biological processes involving H3-3A gene from the curated GO Biological Process Annotations 2023 dataset.
GO Cellular Component Annotations 2023 cellular components containing H3-3A protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by H3-3A gene from the curated GO Molecular Function Annotations 2023 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of H3-3A gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GTEx Tissue-Specific Aging Signatures tissue samples with high or low expression of H3-3A gene relative to other tissue samples from the GTEx Tissue-Specific Aging Signatures dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with H3-3A gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
HuBMAP Azimuth Cell Type Annotations cell types associated with H3-3A gene from the HuBMAP Azimuth Cell Type Annotations dataset.
IMPC Knockout Mouse Phenotypes phenotypes of mice caused by H3-3A gene knockout from the IMPC Knockout Mouse Phenotypes dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of H3-3A gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
KEGG Pathways 2026 pathways involving H3-3A protein from the KEGG Pathways 2026 dataset.
MoTrPAC Rat Endurance Exercise Training tissue samples with high or low expression of H3-3A gene relative to other tissue samples from the MoTrPAC Rat Endurance Exercise Training dataset.
PFOCR Pathway Figure Associations 2023 pathways involving H3-3A protein from the PFOCR Pathway Figure Associations 2023 dataset.
PFOCR Pathway Figure Associations 2024 pathways involving H3-3A protein from the Wikipathways PFOCR 2024 dataset.
Reactome Pathways 2024 pathways involving H3-3A protein from the Reactome Pathways 2024 dataset.
Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of H3-3A 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 H3-3A 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 H3-3A 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 H3-3A gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of H3-3A gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of H3-3A gene from the RummaGEO Gene Perturbation Signatures dataset.
Sci-Plex Drug Perturbation Signatures drug perturbations changing expression of H3-3A gene from the Sci-Plex Drug Perturbation Signatures dataset.
WikiPathways Pathways 2024 pathways involving H3-3A protein from the WikiPathways Pathways 2024 dataset.