| Name | H3 clustered histone 3 |
| 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 is intronless and encodes a replication-dependent histone that is a member of the histone H3 family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015] |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Histone H3.3, a replication‐independent variant of canonical H3, plays multifaceted roles in the regulation of chromatin structure and gene expression. In normal cells its deposition at actively transcribed regions is mediated by dedicated chaperones—such as DAXX, HIRA, and even factors associated with the replicative helicase—that facilitate nucleosome assembly and maintain local chromatin dynamics."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "5"}]}, {"type": "t", "text": "\n A variety of posttranslational modifications on H3.3—notably methylation at specific lysine residues—affect its function. For example, trimethylation of lysine 36 on H3.3 (H3.3K36me3) is read by specialized “reader” proteins such as ZMYND11 and BS69 that modulate RNA polymerase II elongation and influence alternative splicing programs, thereby contributing to proper gene regulation and tumor suppression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In the context of development, H3.3 is essential for establishing proper chromatin states. Its lysine 27 residue is critical for the formation of heterochromatin in early embryos by promoting the silencing of pericentromeric repeats via RNA‐interference pathways"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": ", and H3.3 deposition contributes to the dynamic chromatin organization observed in embryonic stem cells as developmental programs are initiated."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Conversely, somatic mutations in H3.3—most notably the K27M and G34 alterations—have been implicated as key drivers in pediatric high‐grade gliomas and diffuse intrinsic pontine gliomas. These mutations perturb normal histone modifications by, for example, inhibiting the activity of the Polycomb repressive complex 2 (PRC2) and inducing a genome‐wide reduction in H3K27 trimethylation. As a consequence, the epigenetic landscape is dramatically reprogrammed to favor oncogenic pathways and a distinct, aggressive tumor phenotype."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "10", "end_ref": "16"}]}, {"type": "t", "text": "\n Furthermore, tumor type specificity is evident with H3.3 alterations: while certain malignancies (such as chondroblastomas) predominantly harbor specific H3.3 mutations, others (for instance, giant cell tumors of bone) show alternative variant–specific changes, emphasizing that even subtle sequence differences and deposition patterns impart unique functional outputs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "17"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, histone H3.3 is not merely a structural component of nucleosomes but a central regulator of transcription, chromatin remodeling, and developmental programming. Its deposition, specific posttranslational modifications, and mutation-driven misregulation are intimately linked to both normal cellular function and the pathogenesis of aggressive pediatric cancers.\n Additional studies addressing alteration of H3.3-associated marks further emphasize its pivotal role in maintaining genome integrity and directing cell fate decisions."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "19"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Pascal Drané, Khalid Ouararhni, Arnaud Depaux, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.566910"}], "href": "https://doi.org/10.1101/gad.566910"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20504901"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20504901"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Alejandra Loyola, Tiziana Bonaldi, Danièle Roche, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2006.08.019"}], "href": "https://doi.org/10.1016/j.molcel.2006.08.019"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17052464"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17052464"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Dominique Ray-Gallet, Adam Woolfe, Isabelle Vassias, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Dynamics of histone H3 deposition in vivo reveal a nucleosome gap-filling mechanism for H3.3 to maintain chromatin integrity."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2011.12.006"}], "href": "https://doi.org/10.1016/j.molcel.2011.12.006"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22195966"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22195966"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Simon J Elsässer, Hongda Huang, Peter W Lewis, et al. "}, {"type": "b", "children": [{"type": "t", "text": "DAXX envelops a histone H3.3-H4 dimer for H3.3-specific recognition."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature11608"}], "href": "https://doi.org/10.1038/nature11608"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23075851"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23075851"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Hongda Huang, Caroline B Strømme, Giulia Saredi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Struct Mol Biol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nsmb.3055"}], "href": "https://doi.org/10.1038/nsmb.3055"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26167883"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26167883"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Hong Wen, Yuanyuan Li, Yuanxin Xi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature13045"}], "href": "https://doi.org/10.1038/nature13045"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24590075"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24590075"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Rui Guo, Lijuan Zheng, Juw Won Park, et al. "}, {"type": "b", "children": [{"type": "t", "text": "BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2014.08.022"}], "href": "https://doi.org/10.1016/j.molcel.2014.08.022"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25263594"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25263594"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Angèle Santenard, Céline Ziegler-Birling, Marc Koch, et al. 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"}, {"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": 13, "children": [{"type": "t", "text": "David Castel, Cathy Philippe, Raphaël Calmon, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Integrated analysis of pediatric glioblastoma reveals a subset of biologically favorable tumors with associated molecular prognostic markers."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Acta Neuropathol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00401-015-1405-4"}], "href": "https://doi.org/10.1007/s00401-015-1405-4"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25752754"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25752754"}]}]}]}
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| NCBI Gene ID | 8352 |
| 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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H3C3 has 825 functional associations with biological entities spanning 4 categories (disease, phenotype or trait, functional term, phrase or reference, cell line, cell type or tissue, gene, protein or microRNA) extracted from 6 datasets.
Click the + buttons to view associations for H3C3 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 H3C3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset. | |
| CM4AI KOLF21J CRISPRi Gene Perturbation Atlas | gene perturbations changing expression of H3C3 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset. | |
| DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 | diseases co-occuring with H3C3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset. | |
| GTEx Tissue Gene Expression Profiles 2023 | tissues with high or low expression of H3C3 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset. | |
| Rummagene Transcription Factor Associations 2026 | transcription factors regulating expression of H3C3 gene from the Rummagene Transcription Factor Associations 2026 dataset. | |
| WikiPathways Pathways 2024 | pathways involving H3C3 protein from the WikiPathways Pathways 2024 dataset. | |