CNBP Gene

HGNC Family	Zinc fingers
Name	CCHC-type zinc finger, nucleic acid binding protein
Description	This gene encodes a nucleic-acid binding protein with seven zinc-finger domains. The protein has a preference for binding single stranded DNA and RNA. The protein functions in cap-independent translation of ornithine decarboxylase mRNA, and may also function in sterol-mediated transcriptional regulation. A CCTG expansion from <30 repeats to 75-11000 repeats in the first intron of this gene results in myotonic dystrophy type 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2016]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Cellular nucleic acid binding protein (CNBP), also known as ZNF9, is emerging as a multifunctional regulator of gene expression that operates through its interactions with G‐rich sequences and the formation or resolution of G‐quadruplex (G4) structures. CNBP has been shown to facilitate oncogenic and developmental transcription programs by modulating G4 structures in key promoter regions. For instance, in gastric cancer cells a circular RNA derived from HuR (“circ‐HuR”) interacts with CNBP and restrains its binding to the HuR promoter, thereby down‐regulating HuR expression and suppressing tumor progression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n In addition, CNBP contributes to metabolic and proliferative control in cancer: in Hedgehog‐dependent medulloblastoma, CNBP becomes phosphorylated and associates with Sufu to stabilize its own levels, promoting ornithine decarboxylase translation and polyamine biosynthesis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " Equally important is its role in mRNA metabolism where CNBP binds preferentially to G‐rich elements that are prone to adopting stable G4 structures, thereby increasing the translational efficiency of these mRNAs by preventing or resolving such inhibitory secondary structures."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n CNBP is also crucial for proper embryonic development. Genetic studies in mouse models demonstrate that loss of CNBP leads to impaired forebrain induction and anterior patterning, a defect that can be efficiently rescued by CNBP transgene expression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": " In a transcriptional context, CNBP has been implicated in the regulation of the oncogene c‐myc; it specifically binds to the G‐rich nuclease hypersensitive element (NHE) III_1 of c‐myc and promotes G4 formation, cooperating with other factors such as NM23‐H2 to ultimately stimulate transcription."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " Conversely, CNBP’s unfolding activity on G4 motifs in promoters – as observed in genes like KRAS and the developmental regulator NOGGIN – relieves transcriptional repression, thereby fine‐tuning gene expression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n \n "}, {"type": "p", "children": [{"type": "t", "text": "\n Finally, aberrant expression of CNBP/ZNF9 is linked to myotonic dystrophy type 2, highlighting its importance in normal cellular function and disease."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": " Together, these studies underscore a dual role for CNBP as a facilitator of mRNA translation and as a modulator of transcription via its dynamic interactions with G-quadruplex structures and diverse protein partners.\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Feng Yang, Anpei Hu, Dan Li, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circ-HuR suppresses HuR expression and gastric cancer progression by inhibiting CNBP transactivation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cancer (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1186/s12943-019-1094-z"}], "href": "https://doi.org/10.1186/s12943-019-1094-z"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31718709"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31718709"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Davide D'Amico, Laura Antonucci, Laura Di Magno, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Non-canonical Hedgehog/AMPK-Mediated Control of Polyamine Metabolism Supports Neuronal and Medulloblastoma Cell Growth."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Dev Cell (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.devcel.2015.09.008"}], "href": "https://doi.org/10.1016/j.devcel.2015.09.008"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26460945"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26460945"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Daniel Benhalevy, Sanjay K Gupta, Charles H Danan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Rep (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.celrep.2017.02.080"}], "href": "https://doi.org/10.1016/j.celrep.2017.02.080"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28329689"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28329689"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Wei Chen, Yuqiong Liang, Wenjie Deng, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The zinc-finger protein CNBP is required for forebrain formation in the mouse."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Development (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/dev.00349"}], "href": "https://doi.org/10.1242/dev.00349"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12588852"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12588852"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Siqi Chen, Lijuan Su, Jun Qiu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mechanistic studies for the role of cellular nucleic-acid-binding protein (CNBP) in regulation of c-myc transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochim Biophys Acta (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbagen.2013.06.007"}], "href": "https://doi.org/10.1016/j.bbagen.2013.06.007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23774591"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23774591"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Aldana P David, Angélique Pipier, Federico Pascutti, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CNBP controls transcription by unfolding DNA G-quadruplex structures."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkz527"}], "href": "https://doi.org/10.1093/nar/gkz527"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31219592"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31219592"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Olayinka Raheem, Shodimu-Emmanuel Olufemi, Linda L Bachinski, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutant (CCTG)n expansion causes abnormal expression of zinc finger protein 9 (ZNF9) in myotonic dystrophy type 2."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Pathol (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.2353/ajpath.2010.100179"}], "href": "https://doi.org/10.2353/ajpath.2010.100179"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20971734"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20971734"}]}]}]}
Synonyms	RNF163, CNBP1, DM2, PROMM, ZCCHC22, ZNF9
Proteins	CNBP_HUMAN
NCBI Gene ID	7555
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

CNBP has 9,141 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 120 datasets.

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

If available, associations are ranked by standardized value

Harmonizome 3.0

CNBP Gene

Functional Associations

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

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by CNBP gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of CNBP 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 CNBP 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 CNBP 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 CNBP 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 CNBP 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 CNBP 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 CNBP 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 CNBP 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 CNBP gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of CNBP gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of CNBP 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 CNBP gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Gene Mutation Profiles	cell lines with CNBP gene mutations from the CCLE Cell Line Gene Mutation Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with CNBP protein from the CCLE Cell Line Proteomics dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of CNBP gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of CNBP 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 CNBP gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with CNBP gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of CNBP gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing CNBP protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with CNBP 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 CNBP 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 CNBP gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with CNBP gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with CNBP gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with CNBP gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of CNBP protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by CNBP gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving CNBP gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving CNBP gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with CNBP 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 CNBP 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 CNBP gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with CNBP 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 CNBP 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 CNBP gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of CNBP 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 CNBP from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with CNBP gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.