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CBX1 chromobox 1 [ Homo sapiens (human) ]

Gene ID: 10951, updated on 2-Nov-2024

Summary

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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
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Genomic context

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See CBX1 in Genome Data Viewer
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_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:46124493-46125096 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:46125097-46125698 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:46125699-46126300 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46131609-46132468 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46133329-46134186 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46134187-46135046 Neighboring gene NFE2L1 divergent transcript Neighboring gene COPI coat complex subunit zeta 2 Neighboring gene NFE2 like bZIP transcription factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46171341-46171930 Neighboring gene RNA, U6 small nuclear 1201, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:46178573-46179172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8650 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:46186828-46187001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12327 Neighboring gene uncharacterized LOC124904018 Neighboring gene sorting nexin 11 Neighboring gene VISTA enhancer hs697 Neighboring gene src kinase associated phosphoprotein 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Heterochromatin protein HP1Hsbeta (p25beta) and its localization with centromeres in mitosis. Furuta K, et al. Chromosoma, 1997 Jun. PMID 9169582
  2. DNA Damage Changes Distribution Pattern and Levels of HP1 Protein Isoforms in the Nucleolus and Increases Phosphorylation of HP1β-Ser88. Legartová S, et al. Cells, 2019 Sep 17. PMID 31533340, Free PMC Article
  3. Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1. Liu Y, et al. J Biol Chem, 2017 Apr 7. PMID 28223359, Free PMC Article
  4. Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin. Hiragami-Hamada K, et al. Nat Commun, 2016 Apr 19. PMID 27090491, Free PMC Article
  5. HP1β is a biomarker for breast cancer prognosis and PARP inhibitor therapy. Lee YH, et al. PLoS One, 2015. PMID 25769025, Free PMC Article

See all (190) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure.
    Title: Beyond the Nucleosome: Nucleosome-Protein Interactions and Higher Order Chromatin Structure.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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)

  1. 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

  2. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    48070059..48101478 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48931877..48964812 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P83916.1 GenPept UniProtKB/Swiss-Prot:P83916

Gene LinkOut

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