CXXC1 Gene

HGNC Family	Zinc fingers
Name	CXXC finger protein 1
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n CXXC1 (also known as CFP1) is a CpG‐binding protein that selectively recognizes unmethylated CpG motifs, most notably those concentrated in CpG islands. Through this binding activity, CXXC1 serves as a critical targeting subunit for the SETD1/COMPASS histone H3K4 methyltransferase complex, thereby directing the deposition of H3K4 trimethylation at active promoters. In embryonic stem cells and other contexts, this targeting ensures a proper chromatin state by promoting H3K4me3 at expressed, CpG island–associated genes while preventing ectopic methylation at other regulatory regions; such activity contributes to the fidelity of gene transcription and differentiation programs."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": " Moreover, beyond its role in transcriptional regulation, CXXC1 has been implicated in meiotic processes; specifically, it interacts with factors such as PRDM9 and IHO1 to facilitate the proper localization of recombination hotspots and the formation of DNA double‐strand breaks during gametogenesis, thus linking chromatin modification to genome reorganization in meiosis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "5", "end_ref": "7"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In summary, CXXC1 functions as an essential epigenetic adapter that integrates non‐methylated CpG signals with histone methyltransferase activity to regulate gene expression, maintain chromatin integrity during development and differentiation, and support accurate meiotic recombination.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "John P Thomson, Peter J Skene, Jim Selfridge, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CpG islands influence chromatin structure via the CpG-binding protein Cfp1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature08924"}], "href": "https://doi.org/10.1038/nature08924"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20393567"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20393567"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Jeong-Heon Lee, David G Skalnik "}, {"type": "b", "children": [{"type": "t", "text": "CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M508312200"}], "href": "https://doi.org/10.1074/jbc.M508312200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16253997"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16253997"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Sergei Denissov, Helmut Hofemeister, Hendrik Marks, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mll2 is required for H3K4 trimethylation on bivalent promoters in embryonic stem cells, whereas Mll1 is redundant."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Development (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/dev.102681"}], "href": "https://doi.org/10.1242/dev.102681"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24423662"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24423662"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Thomas Clouaire, Shaun Webb, Pete Skene, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.194209.112"}], "href": "https://doi.org/10.1101/gad.194209.112"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22855832"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22855832"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Chao Xu, Chuanbing Bian, Robert Lam, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ncomms1237"}], "href": "https://doi.org/10.1038/ncomms1237"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21407193"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21407193"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Kenneth Paigen, Petko M Petkov "}, {"type": "b", "children": [{"type": "t", "text": "PRDM9 and Its Role in Genetic Recombination."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Trends Genet (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.tig.2017.12.017"}], "href": "https://doi.org/10.1016/j.tig.2017.12.017"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29366606"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29366606"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Yukiko Imai, Frédéric Baudat, Miguel Taillepierre, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The PRDM9 KRAB domain is required for meiosis and involved in protein interactions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Chromosoma (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00412-017-0631-z"}], "href": "https://doi.org/10.1007/s00412-017-0631-z"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28527011"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28527011"}]}]}]}
Synonyms	ZCGPC1, 5830420C16RIK, SPP1, HCGBP, PHF18, PCCX1, CFP1, 2410002I16RIK, CGBP, HST2645
Proteins	CXXC1_HUMAN
NCBI Gene ID	30827
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

CXXC1 has 8,391 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, functional term, phrase or reference, disease, phenotype or trait, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 116 datasets.

Click the + buttons to view associations for CXXC1 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

CXXC1 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CXXC1 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of CXXC1 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of CXXC1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of CXXC1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of CXXC1 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CXXC1 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of CXXC1 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CXXC1 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of CXXC1 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of CXXC1 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of CXXC1 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with CXXC1 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with CXXC1 gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CXXC1 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of CXXC1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of CXXC1 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of CXXC1 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing CXXC1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing CXXC1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with CXXC1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with CXXC1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of CXXC1 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with CXXC1 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with CXXC1 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with CXXC1 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by CXXC1 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with CXXC1 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with CXXC1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with CXXC1 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with CXXC1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with CXXC1 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at CXXC1 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CXXC1 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of CXXC1 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing CXXC1 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with CXXC1 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of CXXC1 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with CXXC1 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing CXXC1 from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of CXXC1 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.