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

Summary

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

Location:: 18q21.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_03	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (50282347..50287692, complement)
RS_2023_03	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (50484088..50489433, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (47808717..47814062, complement)

Chromosome 18 - NC_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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.
Analyzing the impact of CFP1 mutational landscape on epigenetic signaling.
Title: Analyzing the impact of CFP1 mutational landscape on epigenetic signaling.
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.
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.
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.
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.
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.
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.
study shows endogenous DNMT1 & CFP1 interact in vivo; CFP1 interaction with Setd1A or Setd1B not required for its interaction with DNMT1; result indicates CFP1 intersects cytosine methylation machinery independently of its association with Setd1 complexes
Title: CFP1 interacts with DNMT1 independently of association with the Setd1 Histone H3K4 methyltransferase complexes.
CGBP interacts with MLL1, MLL2 as well as Set1 H3-Lysine 4 (H3K4) specific methyl-transferases and plays critical roles in regulations of MLL target genes.
Title: Human CpG binding protein interacts with MLL1, MLL2 and hSet1 and regulates Hox gene expression.

Submit: New GeneRIF Correction See all GeneRIFs (12)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_7961-7962:996688184:1 (e-PCR)
- UniSTS:269858

MARC_7961-7962:997213336:1 (e-PCR)
- UniSTS:269858

CGBP (e-PCR), detects polymorphism
- UniSTS:279704

RH91758 (e-PCR)
- UniSTS:84133

D18S1024 (e-PCR)
- UniSTS:758

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	PubMed
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 histone H3-K4 methylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in histone H3-K4 methylation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
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)

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
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

Q9P0U4, Q9P2V7

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_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000018.10 Reference GRCh38.p14 Primary Assembly

Range

50282347..50287692 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q9P0U4, Q9P2V7

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
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

NC_060942.1 Alternate T2T-CHM13v2.0

Range

50484088..50489433 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q9P2V7
XM_054318552.1 → XP_054174527.1 CXXC-type zinc finger protein 1 isoform X1