CBX1 chromobox 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CBX1provided by HGNC
Official Full Name: chromobox 1provided by HGNC
Primary source: HGNC:HGNC:1551
See related: Ensembl:ENSG00000108468 MIM:604511; AllianceGenome:HGNC:1551
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: CBX; M31; MOD1; Hp1beta; p25beta; HP1-BETA; HP1Hsbeta; HP1Hs-beta
Summary: This gene encodes a highly conserved nonhistone protein, which is a member of the heterochromatin protein family . The protein is enriched in the heterochromatin and associated with centromeres. The protein has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow-domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated nonhistone proteins. The protein may play an important role in the epigenetic control of chromatin structure and gene expression. Several related pseudogenes are located on chromosomes 1, 3, and X. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 37.6), brain (RPKM 33.7) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.32

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (48070059..48101478, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (48931877..48964812, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (46147421..46178840, complement)

Chromosome 17 - NC_000017.11 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

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

N[6] -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation.
Title: N(6) -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation.
HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
Title: HP1 proteins compact DNA into mechanically and positionally stable phase separated domains.
Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure.
Title: Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure.
The gamma-irradiation-induced hyperphosphorylation of the HP1beta protein; thus, HP1beta-S88ph could be considered as an important marker of DNA damage.
Title: DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1β-Ser88.
the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1beta CSD-PXVXL complexes.
Title: Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1.
Data show that heterochromatin protein 1-beta (HP1beta) is a prototypic HP1 protein exemplifying most basal chromatin binding and effects.
Title: Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin.
increased HP1beta expression is associated with the poor prognosis in breast cancer
Title: HP1β is a biomarker for breast cancer prognosis and PARP inhibitor therapy.
In this review, we summarize the current knowledge about targeting and functional mechanisms of PRCs, emphasizing the recent breakthroughs related to CBX proteins under a number of physiological and pathological conditions.
Title: Epigenetic regulation by polycomb group complexes: focus on roles of CBX proteins.
Data suggest the reduction of Heterochromatin Protein 1 isoforms HP1beta followed by a decrease in HP1alpha contributes to the pathogenesis of thyroid carcinomas, and their loss is a potential marker of thyroid malignancy and metastatic potential, respectively.
Title: Heterochromatin protein 1 expression is reduced in human thyroid malignancy.
Phosphorylation at Ser89 and Ser175 results in localized conformational changes in HP1beta that do not compromise the ability of the protein to bind chromatin.
Title: Characterization of the effects of phosphorylation by CK2 on the structure and binding properties of human HP1β.

Submit: New GeneRIF Correction See all GeneRIFs (33)

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

EBI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32 EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone methyltransferase binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in chromocenter	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome, telomeric region	HDA more info	PubMed
colocalizes_with chromosome, telomeric region	IDA Inferred from Direct Assay more info	PubMed
located_in female pronucleus	IEA Inferred from Electronic Annotation more info
located_in heterochromatin	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in male pronucleus	IEA Inferred from Electronic Annotation more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in pericentric heterochromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in site of DNA damage	IMP Inferred from Mutant Phenotype more info	PubMed
located_in spindle	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: chromobox protein homolog 1

Names: HP1 beta homolog; chromobox homolog 1 (HP1 beta homolog Drosophila ); heterochromatin protein 1 homolog beta; heterochromatin protein 1-beta; heterochromatin protein p25 beta; modifier 1 protein

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.

mRNA and Protein(s)

NM_001127228.2 → NP_001120700.1 chromobox protein homolog 1

See identical proteins and their annotated locations for NP_001120700.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

BC002609, BC021302, DA020204, DB026977

Consensus CDS

CCDS11525.1

UniProtKB/Swiss-Prot

P23197, P83916

UniProtKB/TrEMBL

J3KS05, Q6IBN6

Related

ENSP00000225603.4, ENST00000225603.9

Conserved Domains (2) summary

cd18650
Location:20 → 69

CD_HP1beta_Cbx1; chromodomain of heterochromatin protein 1 homolog beta

cd18654
Location:112 → 169

CSD_HP1beta_Cbx1; chromo shadow domain of heterochromatin protein 1 homolog beta
NM_006807.5 → NP_006798.1 chromobox protein homolog 1

See identical proteins and their annotated locations for NP_006798.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

BC002609, BC021302, CB053834, DA689514

Consensus CDS

CCDS11525.1

UniProtKB/Swiss-Prot

P23197, P83916

UniProtKB/TrEMBL

J3KS05, Q6IBN6

Related

ENSP00000377060.3, ENST00000393408.7

Conserved Domains (2) summary

cd18650
Location:20 → 69

CD_HP1beta_Cbx1; chromodomain of heterochromatin protein 1 homolog beta

cd18654
Location:112 → 169

CSD_HP1beta_Cbx1; chromo shadow domain of heterochromatin protein 1 homolog beta