H3C11 Gene

Name H3 clustered histone 11
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 small 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 variants—including the replication‐dependent form (H3.1, encoded by genes within the HIST1 cluster, sometimes referred to using nomenclature such as “H3C11”) and the replication‐independent form H3.3—are essential components of nucleosomes that not only package DNA but also impart regulatory information to the chromatin. Several of the abstracts demonstrate that these variants play distinct roles in cellular function. For instance, H3.3 is deposited independent of DNA replication by specialized chaperones such as DAXX and ATRX, and it marks transcriptionally active chromatin; mutations in H3.3 (for example, K27M or G34V) lead to widespread disruption of epigenetic marks, notably inhibiting polycomb repressive complex 2 (PRC2)–mediated trimethylation of lysine 27, thereby reprogramming gene expression in pediatric high‐grade gliomas and diffuse intrinsic pontine gliomas (DIPG)."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": " \n In contrast, histone H3.1—typically incorporated during S phase—is associated with different chaperone complexes and, when mutated (as seen with K27M substitutions in certain tumors), defines a separate molecular subgroup with a mesenchymal/astrocytic phenotype and distinct clinical outcomes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Beyond their deposition and incorporation into chromatin, these histone H3 variants serve as platforms for post‐translational modifications that regulate gene expression, cell identity, and genome stability. In the context of oncogenesis, mutant forms of H3 disrupt normal epigenetic programming by altering the balance between activating and repressive marks. For example, the K27M mutation directly impairs the activity of EZH2—the catalytic subunit of PRC2—resulting in a global reduction of the repressive H3K27me3 mark while allowing focal retention at specific loci that may silence tumor suppressor genes."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Moreover, tumor type specificity has been observed with different H3 variant mutations: chondroblastomas predominantly harbor H3.3 mutations encoded by H3F3B, whereas giant cell tumors of bone display alterations in H3F3A."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Together with the findings that proper deposition of H3.3 by the DAXX/ATRX complex is integral to maintaining active chromatin states"}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": ", these studies underline that histone H3 variants are not merely structural components but dynamic regulators of chromatin state whose mutation drives distinct, clinically relevant oncogenic programs.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "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": 2, "children": [{"type": "t", "text": "Sriram Venneti, Mihir T Garimella, Lisa M Sullivan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Evaluation of histone 3 lysine 27 trimethylation (H3K27me3) and enhancer of Zest 2 (EZH2) in pediatric glial and glioneuronal tumors shows decreased H3K27me3 in H3F3A K27M mutant glioblastomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Brain Pathol (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/bpa.12042"}], "href": "https://doi.org/10.1111/bpa.12042"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23414300"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23414300"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Sriram Venneti, Mariarita Santi, Michelle Madden Felicella, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A sensitive and specific histopathologic prognostic marker for H3F3A K27M mutant pediatric glioblastomas."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Acta Neuropathol (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00401-014-1338-3"}], "href": "https://doi.org/10.1007/s00401-014-1338-3"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "25200322"}], "href": "https://pubmed.ncbi.nlm.nih.gov/25200322"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "David Castel, Cathy Philippe, Raphaël Calmon, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis and phenotypes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Acta Neuropathol (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00401-015-1478-0"}], "href": "https://doi.org/10.1007/s00401-015-1478-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26399631"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26399631"}]}, {"type": "r", "ref": 5, "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": 6, "children": [{"type": "t", "text": "Dong Fang, Haiyun Gan, Liang Cheng, et al. "}, {"type": "b", "children": [{"type": "t", "text": "H3.3K27M mutant proteins reprogram epigenome by sequestering the PRC2 complex to poised enhancers."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Elife (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.7554/eLife.36696"}], "href": "https://doi.org/10.7554/eLife.36696"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29932419"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29932419"}]}, {"type": "r", "ref": 7, "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"}]}, {"type": "r", "ref": 8, "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"}]}]}]}
NCBI Gene ID 8354
API
Download Associations
Predicted Functions View H3C11's ARCHS4 Predicted Functions.
Co-expressed Genes View H3C11's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View H3C11's ARCHS4 Predicted Functions.

Functional Associations

H3C11 has 324 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 7 datasets.

Click the + buttons to view associations for H3C11 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 H3C11 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 H3C11 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores 2025 diseases associated with H3C11 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 H3C11 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 H3C11 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of H3C11 gene from the Rummagene Transcription Factor Associations 2026 dataset.
WikiPathways Pathways 2024 pathways involving H3C11 protein from the WikiPathways Pathways 2024 dataset.