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

    Gene ID: 30827, updated on 28-Oct-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
    mouse all
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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

    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)

    Genotypes

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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