H3-4 Gene

Name H3.4 histone, cluster member
Description Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin 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; instead, they contain a palindromic termination element. This gene is located separately from the other H3 genes that are in the histone gene cluster on chromosome 6p22-p21.3. [provided by RefSeq, Aug 2015]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Histone H3 and its variants—including H3.3, the testis‐specific H3t, and the primate‐restricted H3.X/H3.Y isoforms—play multifaceted roles in regulating chromatin structure and function. In cancer cells, for example, altered methylation of histone H3 and point mutations in H3.3 disrupt normal epigenetic modifications, thereby perturbing gene expression programs and contributing to tumorigenesis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": " In addition, mitochondrial dysfunction can lead to increased H3 methylation at regulatory promoters, providing a potential epigenetic signature in certain tumors."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n Tissue‐ and developmental stage–specific variants further extend the functional diversity of H3. The testis‐specific variant H3t is critical for early spermatogenesis, enabling distinct nucleosome assembly through selective chaperone pathways and influencing chromatin organization via its unique post‐translational modification patterns."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "6"}]}, {"type": "t", "text": " Similarly, structural studies of primate-specific H3.Y reveal that its nucleosomes exhibit increased DNA end flexibility—with consequent effects on accessibility by regulatory factors—while DUX4-induced H3.X/H3.Y incorporation fosters a relaxed chromatin state that enhances reactivation of target genes during development."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "7", "end_ref": "9"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n Furthermore, specific modifications on these variants are functionally important. For instance, trimethylation at lysine 27 on H3t (H3tK27me3) is recognized by chromatin regulators such as PHF1, linking the variant to Polycomb-mediated gene silencing mechanisms."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": " Studies on plant H3 variants also underscore how subtle amino acid changes can dictate deposition patterns and epigenetic landscapes during development."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, these studies collectively demonstrate that histone H3 variants are not merely structural components of nucleosomes but are dynamic regulators of chromatin. Their diverse incorporation, modification, and interaction profiles enable them to orchestrate gene expression programs critical for processes ranging from development and cellular differentiation to responses in metabolic stress and tumorigenesis.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Ana M Cervera, Jean-Pierre Bayley, Peter Devilee, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Inhibition of succinate dehydrogenase dysregulates histone modification in mammalian cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/1476-4598-8-89"}], "href": "https://doi.org/10.1186/1476-4598-8-89"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19849834"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19849834"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Benjamin T K Yuen, Paul S Knoepfler "}, {"type": "b", "children": [{"type": "t", "text": "Histone H3.3 mutations: a variant path to cancer."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Cell (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ccr.2013.09.015"}], "href": "https://doi.org/10.1016/j.ccr.2013.09.015"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24229707"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24229707"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Leilei Shi, Hong Wen, Xiaobing Shi "}, {"type": "b", "children": [{"type": "t", "text": "The Histone Variant H3.3 in Transcriptional Regulation and Human Disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Biol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jmb.2016.11.019"}], "href": "https://doi.org/10.1016/j.jmb.2016.11.019"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27894815"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27894815"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Hiroaki Tachiwana, Akihisa Osakabe, Hiroshi Kimura, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nucleosome formation with the testis-specific histone H3 variant, H3t, by human nucleosome assembly proteins in vitro."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkn060"}], "href": "https://doi.org/10.1093/nar/gkn060"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18281699"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18281699"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Ho-Geun Kwak, Naoshi Dohmae "}, {"type": "b", "children": [{"type": "t", "text": "Proteomic characterization of histone variants in the mouse testis by mass spectrometry-based top-down analysis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biosci Trends (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.5582/bst.2016.01090"}], "href": "https://doi.org/10.5582/bst.2016.01090"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27545216"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27545216"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Jun Ueda, Akihito Harada, Takashi Urahama, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2016.12.065"}], "href": "https://doi.org/10.1016/j.celrep.2016.12.065"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28099840"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28099840"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Yasuhiro Arimura, Kazuyoshi Shirayama, Naoki Horikoshi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/srep07115"}], "href": "https://doi.org/10.1038/srep07115"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25408271"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25408271"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Tomoya Kujirai, Naoki Horikoshi, Koichi Sato, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Structure and function of human histone H3.Y nucleosome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkw202"}], "href": "https://doi.org/10.1093/nar/gkw202"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27016736"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27016736"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Rebecca Resnick, Chao-Jen Wong, Danielle C Hamm, et al. "}, {"type": "b", "children": [{"type": "t", "text": "DUX4-Induced Histone Variants H3.X and H3.Y Mark DUX4 Target Genes for Expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2019.10.025"}], "href": "https://doi.org/10.1016/j.celrep.2019.10.025"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31722199"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31722199"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Ina Kycia, Srikanth Kudithipudi, Raluca Tamas, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Tudor domain of the PHD finger protein 1 is a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Mol Biol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jmb.2013.08.009"}], "href": "https://doi.org/10.1016/j.jmb.2013.08.009"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23954330"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23954330"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Li Lu, Xiangsong Chen, Shuiming Qian, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The plant-specific histone residue Phe41 is important for genome-wide H3.1 distribution."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-018-02976-9"}], "href": "https://doi.org/10.1038/s41467-018-02976-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29434220"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29434220"}]}]}]}
NCBI Gene ID 8290
API
Download Associations
Predicted Functions View H3-4's ARCHS4 Predicted Functions.
Co-expressed Genes View H3-4's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View H3-4's ARCHS4 Predicted Functions.

Functional Associations

H3-4 has 5,910 functional associations with biological entities spanning 5 categories (chemical, functional term, phrase or reference, disease, phenotype or trait, cell line, cell type or tissue, gene, protein or microRNA) extracted from 23 datasets.

Click the + buttons to view associations for H3-4 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 H3-4 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 H3-4 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CM4AI KOLF21J CRISPRi Gene Perturbation Atlas gene perturbations changing expression of H3-4 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing H3-4 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 cellular components containing H3-4 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 H3-4 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
DISEASES Text-mining Gene-Disease Association Evidence Scores 2025 diseases co-occuring with H3-4 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 H3-4 gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2025 cellular components containing H3-4 protein from the curated GO Cellular Component Annotations 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of H3-4 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with H3-4 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of H3-4 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
JASPAR Predicted Mouse Transcription Factor Targets 2025 transcription factors regulating expression of H3-4 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
KEGG Pathways 2026 pathways involving H3-4 protein from the KEGG Pathways 2026 dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of H3-4 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
Reactome Pathways 2024 pathways involving H3-4 protein from the Reactome Pathways 2024 dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of H3-4 gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of H3-4 gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of H3-4 gene from the RummaGEO Gene Perturbation Signatures dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of H3-4 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 H3-4 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 H3-4 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.
WikiPathways Pathways 2024 pathways involving H3-4 protein from the WikiPathways Pathways 2024 dataset.