H3C1 Gene

Name H3 clustered histone 1
Description Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. This structure consists of approximately 146 bp of DNA wrapped around a nucleosome, an 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 found in the large 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 H3C1 is one of the replication‐dependent “canonical” H3 variants that, together with other members of its family, plays a central role in packaging DNA into chromatin and in maintaining epigenetic states during cell division. In several pediatric brain tumors—most notably diffuse intrinsic pontine gliomas (DIPG) and other midline high‐grade gliomas—molecular analyses have uncovered distinct mutation patterns in histone H3 variants. In these tumors, oncogenic mutations that substitute lysine 27 with methionine (K27M) occur either in the replication‐independent H3.3 (encoded by H3F3A) or in the canonical H3.1 variants that include genes such as HIST1H3B and HIST1H3C. Notably, tumors harboring H3.1 K27M aberrations show a divergent molecular and clinical profile relative to their H3.3 counterparts; for instance, H3.1‐mutated tumors tend to exhibit a mesenchymal/astrocytic phenotype with pro‐angiogenic/hypoxic signatures, and they may respond differently to radiotherapy."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In addition to mutation‐driven changes, epigenetic alterations of H3C1 itself can have prognostic significance. For example, aberrant methylation of the HIST1H3C promoter has been associated with established risk factors—such as patient age, disease stage, or MYCN status—in neuroblastoma, and increased HIST1H3C methylation correlates with poorer overall and event‐free survival. This supports a functional role for the epigenetic state of canonical H3 variants in regulating gene expression programs relevant to tumor behavior."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Together, these findings underscore the dual role of H3C1: as an essential structural component of chromatin that ensures proper replication‐dependent nucleosome assembly, and as a modifiable substrate whose alterations—whether by somatic mutation or by epigenetic mechanisms—can drive distinct oncogenic programs and serve as biomarkers for stratifying patient risk.\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": "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": 3, "children": [{"type": "t", "text": "Adam M Fontebasso, Simon Papillon-Cavanagh, Jeremy Schwartzentruber, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Recurrent somatic mutations in ACVR1 in pediatric midline high-grade astrocytoma."}]}, {"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.2950"}], "href": "https://doi.org/10.1038/ng.2950"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24705250"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24705250"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genome Biol (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/gb-2012-13-10-r95"}], "href": "https://doi.org/10.1186/gb-2012-13-10-r95"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23034519"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23034519"}]}]}]}
NCBI Gene ID 8350
API
Download Associations
Predicted Functions View H3C1's ARCHS4 Predicted Functions.
Co-expressed Genes View H3C1's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View H3C1's ARCHS4 Predicted Functions.

Functional Associations

H3C1 has 1,468 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 21 datasets.

Click the + buttons to view associations for H3C1 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 H3C1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
CCLE Cell Line Proteomics Cell lines associated with H3C1 protein from the CCLE Cell Line Proteomics dataset.
CellMarker Gene-Cell Type Associations cell types associated with H3C1 gene from the CellMarker Gene-Cell Type Associations dataset.
ChEA Transcription Factor Targets 2022 transcription factors binding the promoter of H3C1 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 H3C1 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
DeepCoverMOA Drug Mechanisms of Action small molecule perturbations with high or low expression of H3C1 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
DepMap CRISPR Gene Dependency cell lines with fitness changed by H3C1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
DISEASES Experimental Gene-Disease Association Evidence Scores 2025 diseases associated with H3C1 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 H3C1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
GlyGen Glycosylated Proteins ligands (chemical) binding H3C1 protein from the GlyGen Glycosylated Proteins dataset.
GO Biological Process Annotations 2023 biological processes involving H3C1 gene from the curated GO Biological Process Annotations 2023 dataset.
GO Cellular Component Annotations 2023 cellular components containing H3C1 protein from the curated GO Cellular Component Annotations 2023 dataset.
GO Molecular Function Annotations 2023 molecular functions performed by H3C1 gene from the curated GO Molecular Function Annotations 2023 dataset.
Kinase Library Tyrosine Kinome Atlas kinases that phosphorylate H3C1 protein from the Kinase Library Tyrosine Kinome Atlas dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of H3C1 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
PFOCR Pathway Figure Associations 2023 pathways involving H3C1 protein from the PFOCR Pathway Figure Associations 2023 dataset.
PFOCR Pathway Figure Associations 2024 pathways involving H3C1 protein from the Wikipathways PFOCR 2024 dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of H3C1 gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of H3C1 gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of H3C1 gene from the RummaGEO Gene Perturbation Signatures dataset.
WikiPathways Pathways 2024 pathways involving H3C1 protein from the WikiPathways Pathways 2024 dataset.