H1-3 H1.3 linker histone, cluster member [Homo sapiens (human)] - Gene

Summary

Official Symbol: H1-3provided by HGNC
Official Full Name: H1.3 linker histone, cluster memberprovided by HGNC
Primary source: HGNC:HGNC:4717
See related: Ensembl:ENSG00000124575 MIM:142210; AllianceGenome:HGNC:4717
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: H1D; H1.3; H1F3; H1s-2; HIST1H1D
Summary: Histones are basic nuclear proteins responsible for 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 H1 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]
Orthologs: all
NEW: Try the new Gene table
Try the new Transcript table

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 (26234212..26234987, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (26102677..26103452, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (26234440..26235215, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data suggest that NPM1mut AML prognosis depends on the epigenetic silencing of the HIST1 cluster and that, among the H3K27me3 silenced histone genes, HIST1H1D plays a role in AML blast differentiation.
Title: Epigenetic down-regulation of the HIST1 locus predicts better prognosis in acute myeloid leukemia with NPM1 mutation.
Results show that histone H1.3, was identified only in non-neoplastic MCF-10A breast cells but not in metastatic MDA-MB-231 breast cancer cells .
Title: Quantitative Mass Spectrometry Reveals that Intact Histone H1 Phosphorylations are Variant Specific and Exhibit Single Molecule Hierarchical Dependence.
Histone H1 organizes and maintains an extensive protein-protein interaction network in the nucleolus required for nucleolar structure and integrity.
Title: Proteomic characterization of the nucleolar linker histone H1 interaction network.
Integration with apoptotic intermediates (via C-terminal tail interactions) may constitute a more generalized function of linker histone isoforms in apoptotic cascades.
Title: The C-terminal domain (CTD) in linker histones antagonizes anti-apoptotic proteins to modulate apoptotic outcomes at the mitochondrion.
Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma.
Title: Mutations in linker histone genes HIST1H1 B, C, D, and E; OCT2 (POU2F2); IRF8; and ARID1A underlying the pathogenesis of follicular lymphoma.
overexpression of histone cluster 1 is associated with recurrence in meningiomas.
Title: Differential expression profiling analyses identifies downregulation of 1p, 6q, and 14q genes and overexpression of 6p histone cluster 1 genes as markers of recurrence in meningiomas.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Identification of 15 loci influencing height in a Korean population.
Observational study of gene-disease association. (HuGE Navigator)
Title: Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study.
confirmed N-terminal acetylation on all isoforms plus a single internal acetylation site; phosphorylation sites were located on peptides containing the cyclin dependent kinase (CDK) consensus motif
Title: Characterization of phosphorylation sites on histone H1 isoforms by tandem mass spectrometry.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

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

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Identification of ten loci associated with height highlights new biological pathways in human growth. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

Go to the top of the page Help

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify H1d associated HIV-1 Gag in 293T cells	PubMed
Tat	tat	Overexpression of NPM1 enhances HIV-1 Tat-mediated transactivation by reducing the histone H1 occupancy on the chromatinized template of HIV-1 LTR	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH79903 (e-PCR)
- UniSTS:84005

PMC111054P3 (e-PCR)
- UniSTS:270219

NoName (e-PCR)
- UniSTS:483214

NoName (e-PCR)
- UniSTS:481723

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleosomal DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural constituent of chromatin	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromosome condensation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA recombination	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in nucleosome assembly	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in euchromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
part_of nucleosome	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: histone H1.3

Names: H1 histone family, member 3; histone 1, H1d; histone H1c; histone H1s-2; histone cluster 1 H1 family member d; histone cluster 1, H1d

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.