ZNF609 Gene

HGNC Family	Zinc fingers
Name	zinc finger protein 609
Description	Predicted to enable promoter-specific chromatin binding activity. Involved in regulation of myoblast proliferation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Mar 2025]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nCircular RNA ZNF609 (circ‐ZNF609) has emerged as a multifunctional regulator in a variety of physiological and pathological contexts. In skeletal muscle, circ‐ZNF609 is generated during myoblast differentiation and is capable of being translated into a protein in a cap‐independent manner, thereby specifically controlling myoblast proliferation. In parallel, dysregulation of circ‐ZNF609 has been implicated in developmental abnormalities such as Hirschsprung disease, where its reduced expression is associated with impaired cell proliferation and migration due to its function as a competing endogenous RNA modulating miR-150-5p and AKT3. Moreover, in several cancers including renal carcinoma, nasopharyngeal carcinoma, and gastric cancer, circ‐ZNF609 is aberrantly expressed, promoting malignant behaviors such as increased proliferation, invasion, and angiogenesis through interactions with different miRNAs (e.g., miR-138-5p, miR-145) and downstream effectors such as FOXP4 and STMN1."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn cholangiocarcinoma, circ‐ZNF609 is markedly overexpressed, where its high levels correlate with advanced tumor stage, lymphatic invasion, and poor patient survival. Its oncogenic effect is mediated by functioning as an endogenous sponge for miR-432-5p, which leads to the upregulation of the oncogene LRRC1. Furthermore, transcription factors like YY1 and RNA-binding proteins such as eIF4A3 enhance the biogenesis of circ‐ZNF609, underscoring its complex regulation in tumor progression."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditionally, circ‐ZNF609 plays a significant role in non-cancerous conditions. In ischemic acute kidney injury, circ‐ZNF609 is highly expressed following ischemia/reperfusion injury and encodes a functional 250 amino acid protein (ZNF609-250aa) that activates AKT3/mTOR signaling, leading to impaired autophagy flux and enhanced cell apoptosis. Similarly, in the context of diabetic retinopathy, the upregulation of circZNF609 in retinal microvascular endothelial cells contributes to high glucose-induced cellular damage by sponging miR-150-5p, thereby exacerbating apoptosis, oxidative stress, and disruption of normal vascular function."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "8"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Lei Peng, Guanglin Chen, Zhongxian Zhu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circular RNA ZNF609 functions as a competitive endogenous RNA to regulate AKT3 expression by sponging miR-150-5p in Hirschsprung's disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncotarget (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.18632/oncotarget.13656"}], "href": "https://doi.org/10.18632/oncotarget.13656"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27903978"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27903978"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Ivano Legnini, Gaia Di Timoteo, Francesca Rossi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2017.02.017"}], "href": "https://doi.org/10.1016/j.molcel.2017.02.017"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28344082"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28344082"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Yunhe Xiong, Jiabin Zhang, Chao Song "}, {"type": "b", "children": [{"type": "t", "text": "CircRNA ZNF609 functions as a competitive endogenous RNA to regulate FOXP4 expression by sponging miR-138-5p in renal carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Physiol (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcp.27744"}], "href": "https://doi.org/10.1002/jcp.27744"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30478938"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30478938"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "L Zhu, Y Liu, Y Yang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CircRNA ZNF609 promotes growth and metastasis of nasopharyngeal carcinoma by competing with microRNA-150-5p."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur Rev Med Pharmacol Sci (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.26355/eurrev_201904_17558"}], "href": "https://doi.org/10.26355/eurrev_201904_17558"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31002133"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31002133"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Z Liu, H-M Pan, L Xin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Circ-ZNF609 promotes carcinogenesis of gastric cancer cells by inhibiting miRNA-145-5p expression."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur Rev Med Pharmacol Sci (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.26355/eurrev_201911_19433"}], "href": "https://doi.org/10.26355/eurrev_201911_19433"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31773689"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31773689"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Jin Wang, Yan Lin, Dong-Hui Jiang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CircRNA ZNF609 promotes angiogenesis in nasopharyngeal carcinoma by regulating miR-145/STMN1 axis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Kaohsiung J Med Sci (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/kjm2.12381"}], "href": "https://doi.org/10.1002/kjm2.12381"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33943007"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33943007"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Canghai Guan, Lang Liu, Yuqiao Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "YY1 and eIF4A3 are mediators of the cell proliferation, migration and invasion in cholangiocarcinoma promoted by circ-ZNF609 by targeting miR-432-5p to regulate LRRC1."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Aging (Albany NY) (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.18632/aging.203735"}], "href": "https://doi.org/10.18632/aging.203735"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34898474"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34898474"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Xin Ouyang, Zhimei He, Heng Fang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A protein encoded by circular ZNF609 RNA induces acute kidney injury by activating the AKT/mTOR-autophagy pathway."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Ther (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ymthe.2022.09.007"}], "href": "https://doi.org/10.1016/j.ymthe.2022.09.007"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36110046"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36110046"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Jing Gao, Chenfei Wang, Jie Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CircZNF609 inhibits miR-150-5p to promote high glucose-induced damage to retinal microvascular endothelial cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Endocrinol (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.mce.2024.112261"}], "href": "https://doi.org/10.1016/j.mce.2024.112261"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38679361"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38679361"}]}]}]}
Proteins	ZN609_HUMAN
NCBI Gene ID	23060
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

ZNF609 has 7,049 functional associations with biological entities spanning 8 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) extracted from 108 datasets.

Click the + buttons to view associations for ZNF609 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

ZNF609 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 ZNF609 gene relative to other tissues from the Allen Brain Atlas Adult Human 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 ZNF609 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 RNA-seq	tissue samples with high or low expression of ZNF609 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 ZNF609 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 ZNF609 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 ZNF609 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 ZNF609 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 ZNF609 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of ZNF609 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 ZNF609 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with ZNF609 protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with ZNF609 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 ZNF609 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of ZNF609 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 ZNF609 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of ZNF609 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ZNF609 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing ZNF609 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing ZNF609 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with ZNF609 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 ZNF609 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with ZNF609 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with ZNF609 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with ZNF609 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by ZNF609 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 ZNF609 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with ZNF609 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 ZNF609 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with ZNF609 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 ZNF609 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 ZNF609 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of ZNF609 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 ZNF609 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of ZNF609 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneSigDB Published Gene Signatures	PubMedIDs of publications reporting gene signatures containing ZNF609 from the GeneSigDB Published Gene Signatures dataset.
	GEO Signatures of Differentially Expressed Genes for Diseases	disease perturbations changing expression of ZNF609 gene from the GEO Signatures of Differentially Expressed Genes for Diseases dataset.
	GEO Signatures of Differentially Expressed Genes for Gene Perturbations	gene perturbations changing expression of ZNF609 gene from the GEO Signatures of Differentially Expressed Genes for Gene Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Kinase Perturbations	kinase perturbations changing expression of ZNF609 gene from the GEO Signatures of Differentially Expressed Genes for Kinase Perturbations dataset.
	GEO Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of ZNF609 gene from the GEO Signatures of Differentially Expressed Genes for Small Molecules dataset.
	GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations	transcription factor perturbations changing expression of ZNF609 gene from the GEO Signatures of Differentially Expressed Genes for Transcription Factor Perturbations dataset.