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CXXC1 CXXC finger protein 1 [ Homo sapiens (human) ]

Gene ID: 30827, updated on 27-Nov-2024

Summary

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Official Symbol
CXXC1provided by HGNC
Official Full Name
CXXC finger protein 1provided by HGNC
Primary source
HGNC:HGNC:24343
See related
Ensembl:ENSG00000154832 MIM:609150; AllianceGenome:HGNC:24343
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
CFP1; CGBP; SPP1; PCCX1; PHF18; hCGBP; ZCGPC1; HsT2645; 2410002I16Rik; 5830420C16Rik
Summary
This gene encodes a protein that functions as a transcriptional activator that binds specifically to non-methylated CpG motifs through its CXXC domain. The protein is a component of the SETD1 complex, regulates gene expression and is essential for vertebrate development. [provided by RefSeq, Sep 2015]
Expression
Ubiquitous expression in bone marrow (RPKM 16.4), lymph node (RPKM 14.4) and 25 other tissues See more
Orthologs
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Genomic context

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See CXXC1 in Genome Data Viewer
Location:
18q21.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (50282347..50287692, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (50484088..50489433, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (47808717..47814062, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene cilia and flagella associated protein 53 Neighboring gene uncharacterized LOC124904300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:47792269-47793114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13316 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:47801678-47802178 Neighboring gene methyl-CpG binding domain protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9457 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:47807971-47808551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:47808552-47809132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13320 Neighboring gene uncharacterized LOC124904301 Neighboring gene RNA, 5S ribosomal pseudogene 458

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
  • 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. PCCX1, a novel DNA-binding protein with PHD finger and CXXC domain, is regulated by proteolysis. Fujino T, et al. Biochem Biophys Res Commun, 2000 May 10. PMID 10799292
  2. Identification and characterization of the DNA binding domain of CpG-binding protein. Lee JH, et al. J Biol Chem, 2001 Nov 30. PMID 11572867
  3. Analyzing the impact of CFP1 mutational landscape on epigenetic signaling. Yang Y, et al. FASEB J, 2021 Aug. PMID 34320252
  4. The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain. Xu C, et al. Nat Commun, 2011. PMID 21407193, Free PMC Article
  5. CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands. van de Lagemaat LN, et al. Epigenetics Chromatin, 2018 Oct 6. PMID 30292235, Free PMC Article

See all (78) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Cfp1 Controls Cardiomyocyte Maturation by Modifying Histone H3K4me3 of Structural, Metabolic, and Contractile Related Genes.
    Title: Cfp1 Controls Cardiomyocyte Maturation by Modifying Histone H3K4me3 of Structural, Metabolic, and Contractile Related Genes.
  2. CFP1 governs uterine epigenetic landscapes to intervene in progesterone responses for uterine physiology and suppression of endometriosis.
    Title: CFP1 governs uterine epigenetic landscapes to intervene in progesterone responses for uterine physiology and suppression of endometriosis.
  3. CpG-binding protein CFP1 promotes ovarian cancer cell proliferation by regulating BST2 transcription.
    Title: CpG-binding protein CFP1 promotes ovarian cancer cell proliferation by regulating BST2 transcription.
  4. Analyzing the impact of CFP1 mutational landscape on epigenetic signaling.
    Title: Analyzing the impact of CFP1 mutational landscape on epigenetic signaling.
  5. Associations of site-specific CD4(+)-T-cell hypomethylation within CD40-ligand promotor and enhancer regions with disease activity of women with systemic lupus erythematosus.
    Title: Associations of site-specific CD4(+)-T-cell hypomethylation within CD40-ligand promotor and enhancer regions with disease activity of women with systemic lupus erythematosus.
  6. CFP1 binds open chromatin regions of active genes, including enhancers and non-CpG islands.
    Title: CpG binding protein (CFP1) occupies open chromatin regions of active genes, including enhancers and non-CpG islands.
  7. directly controls the expression of key genes important for thymocyte survival, such as RORgammat, and for T-cell receptor signaling, including Zap70 and CD8, through maintaining the appropriate H3K4me3 on their promoters
    Title: CXXC finger protein 1 is critical for T-cell intrathymic development through regulating H3K4 trimethylation.
  8. NF-kappaB recruitment enhanced the occupancy of the CpG island within the 14-3-3gamma promoter by CFP1.14-3-3gamma induction in CSR is enabled by the CFP1-mediated H3K4me3 enrichment in the promoter, dependent on NF-kappaB and sustained by E2A.
    Title: Induction of activation-induced cytidine deaminase-targeting adaptor 14-3-3γ is mediated by NF-κB-dependent recruitment of CFP1 to the 5'-CpG-3'-rich 14-3-3γ promoter and is sustained by E2A.
  9. The crescent-shaped CFP1 CXXC domain is wedged into the major groove of the CpG DNA, distorting the B-form DNA, and interacts extensively with the major groove of the DNA.
    Title: The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain.
  10. expression of either the amino half of Cfp1 (amino acids 1 to 367 [Cfp1(1-367)]) or the carboxyl half of Cfp1 (Cfp1(361-656)) is sufficient to correct all of the defects observed with embryonic stem cells that lack Cfp1
    Title: CXXC finger protein 1 contains redundant functional domains that support embryonic stem cell cytosine methylation, histone methylation, and differentiation.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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
Tat tat Three components (Setd1A, CXXC1, WDR5) of the Set1 histone methyltransferase complex are identified to interact with HIV-1 Tat in Jurkat cell PubMed

Go to the HIV-1, Human Interaction Database

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 cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables methylated histone binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables methylated histone binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables unmethylated CpG binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in positive regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of Set1C/COMPASS complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Set1C/COMPASS complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Set1C/COMPASS complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
part_of histone methyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear matrix IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck 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 

General protein information

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Preferred Names
CXXC-type zinc finger protein 1
Names
CXXC finger 1 (PHD domain)
CpG binding protein
DNA-binding protein with PHD finger and CXXC domain
PHD finger and CXXC domain-containing protein 1
cpG-binding protein
zinc finger, CpG binding-type containing 1

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_001101654.2 → NP_001095124.1  CXXC-type zinc finger protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001095124.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB031069, BC015733
    Consensus CDS
    CCDS45866.1
    UniProtKB/Swiss-Prot
    Q9P0U4
    Related
    ENSP00000390475.1, ENST00000412036.6
    Conserved Domains (3) summary
    cd15553
    Location:28 → 73
    PHD_Cfp1; PHD finger found in CXXC-type zinc finger protein 1 (Cfp1)
    pfam02008
    Location:162 → 208
    zf-CXXC; CXXC zinc finger domain
    pfam12269
    Location:406 → 640
    zf-CpG_bind_C; CpG binding protein zinc finger C terminal domain

  2. NM_014593.4 → NP_055408.2  CXXC-type zinc finger protein 1 isoform 2

    See identical proteins and their annotated locations for NP_055408.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the mid-coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AB031069
    Consensus CDS
    CCDS11945.1
    UniProtKB/Swiss-Prot
    B2RC03, Q8N2W4, Q96BC8, Q9P0U4, Q9P2V7
    UniProtKB/TrEMBL
    K7EQ21
    Related
    ENSP00000285106.6, ENST00000285106.11
    Conserved Domains (3) summary
    pfam02008
    Location:162 → 208
    zf-CXXC; CXXC zinc finger domain
    cd15553
    Location:28 → 73
    PHD_Cfp1; PHD finger found in CXXC-type zinc finger protein 1 (Cfp1)
    pfam12269
    Location:402 → 636
    zf-CpG_bind_C; CpG binding protein zinc finger C terminal domain

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    50282347..50287692 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017025718.3 → XP_016881207.1  CXXC-type zinc finger protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B2RC03, Q8N2W4, Q96BC8, Q9P0U4, Q9P2V7
    UniProtKB/TrEMBL
    K7EQ21
    Conserved Domains (3) summary
    pfam02008
    Location:162 → 208
    zf-CXXC; CXXC zinc finger domain
    cd15553
    Location:28 → 73
    PHD_Cfp1; PHD finger found in CXXC-type zinc finger protein 1 (Cfp1)
    pfam12269
    Location:402 → 636
    zf-CpG_bind_C; CpG binding protein zinc finger C terminal domain

  2. XM_011525940.3 → XP_011524242.1  CXXC-type zinc finger protein 1 isoform X1

    See identical proteins and their annotated locations for XP_011524242.1

    UniProtKB/Swiss-Prot
    Q9P0U4
    Conserved Domains (3) summary
    cd15553
    Location:28 → 73
    PHD_Cfp1; PHD finger found in CXXC-type zinc finger protein 1 (Cfp1)
    pfam02008
    Location:162 → 208
    zf-CXXC; CXXC zinc finger domain
    pfam12269
    Location:406 → 640
    zf-CpG_bind_C; CpG binding protein zinc finger C terminal domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    50484088..50489433 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054318553.1 → XP_054174528.1  CXXC-type zinc finger protein 1 isoform X2

    UniProtKB/Swiss-Prot
    B2RC03, Q8N2W4, Q96BC8, Q9P0U4, Q9P2V7

  2. XM_054318552.1 → XP_054174527.1  CXXC-type zinc finger protein 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P0U4.2 GenPept UniProtKB/Swiss-Prot:Q9P0U4

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