H3C1 H3 clustered histone 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: H3C1provided by HGNC
Official Full Name: H3 clustered histone 1provided by HGNC
Primary source: HGNC:HGNC:4766
See related: Ensembl:ENSG00000275714 MIM:602810; AllianceGenome:HGNC:4766
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: H3/A; H3C2; H3C3; H3C4; H3C6; H3C7; H3C8; H3FA; H3C10; H3C11; H3C12; HIST1H3A
Summary: 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]
Orthologs: mouse all
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Genomic context

Location:: 6p22.2

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (26020451..26020958)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (25886390..25886897)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (26020679..26021186)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Macrophage MCT4 inhibition activates reparative genes and protects from atherosclerosis by histone H3 lysine 18 lactylation.
Title: Macrophage MCT4 inhibition activates reparative genes and protects from atherosclerosis by histone H3 lysine 18 lactylation.
H3K27me3 conditions chemotolerance in triple-negative breast cancer.
Title: H3K27me3 conditions chemotolerance in triple-negative breast cancer.
Histone H3G34 Mutation in Brain and Bone Tumors.
Title: Histone H3G34 Mutation in Brain and Bone Tumors.
CSB reduces H3K9me3 chromatin remodeler SETDB1 and exacerbates cellular aging.
Title: Cockayne syndrome group B deficiency reduces H3K9me3 chromatin remodeler SETDB1 and exacerbates cellular aging.
Enhancer activity requires CBP/P300 bromodomain-dependent histone H3K27 acetylation.
Title: Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation.
the H3 K27M mutation was mainly associated with a poorer prognosis in infratentorial gliomas compared with the corresponding H3 wild-type gliomas
Title: H3 K27M-mutant diffuse midline gliomas in different anatomical locations.
In 2 cases, we identified H3F3A mutation, classically described in pediatric midline gliomas
Title: Cerebellar high-grade gliomas do not present the same molecular alterations as supratentorial high-grade gliomas and may show histone H3 gene mutations.
Data indicate the mechanism for epigenetic regulation in cancer by inducing E3 ubiquitin ligase NEDD4-dependent histone H3 ubiquitination.
Title: H3 ubiquitination by NEDD4 regulates H3 acetylation and tumorigenesis.
the identification of increased expression of H3K27me3 during a patient's clinical course can be helpful for determining whether the tumors are heterochronous
Title: Immunohistochemical evaluation of H3K27 trimethylation in malignant peripheral nerve sheath tumors.
Here, we report that JMJD5, a Jumonji C (JmjC) domain-containing protein, is a Cathepsin L-type protease that mediates histone H3 N-tail proteolytic cleavage under stress conditions that cause a DNA damage response.
Title: JMJD5 cleaves monomethylated histone H3 N-tail under DNA damaging stress.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 is identified to have a physical interaction with histone cluster 1, H3a (HIST1H3A) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed
Tat	tat	HIV-1 Tat peptides bind core histones H2A, H2B, H3 and H4, and Tat protein recruits histone acetyltransferases to the HIV-1 LTR promoter leading to acetylation of histones H3 and H4, derepressing chromatin structure and increasing NFkappaB responsiveness	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:481684

PMC316937P2 (e-PCR)
- UniSTS:273064

STS-Z46261 (e-PCR)
- UniSTS:12211

RH46871 (e-PCR)
- UniSTS:44799

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables cadherin binding	HDA more info	PubMed
enables protein binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IEA Inferred from Electronic Annotation more info
enables structural constituent of chromatin	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin organization	NAS Non-traceable Author Statement more info	PubMed
involved_in epigenetic regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_positive_effect gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleosome assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in nucleosome assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in telomere organization	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of nucleosome	IDA Inferred from Direct Assay more info	PubMed
part_of nucleosome	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleus	HDA more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone H3.1

Names: H3 histone family, member A; histone 1, H3a; histone H3/a; histone cluster 1 H3 family member a; histone cluster 1, H3a

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.