HNRNPU Gene

Name	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)
Description	This gene encodes a member of a family of proteins that bind nucleic acids and function in the formation of ribonucleoprotein complexes in the nucleus with heterogeneous nuclear RNA (hnRNA). The encoded protein has affinity for both RNA and DNA, and binds scaffold-attached region (SAR) DNA. Mutations in this gene have been associated with epileptic encephalopathy, early infantile, 54. A pseudogene of this gene has been identified on chromosome 14. [provided by RefSeq, Jun 2017]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Heterogeneous nuclear ribonucleoprotein U (HNRNPU), also known as scaffold attachment factor A (SAF‐A), is a multifunctional nuclear protein that serves as a central hub in coordinating diverse aspects of gene regulation. Evidence from multiple studies indicates that HNRNPU participates in both chromatin organization and RNA metabolism. For example, HNRNPU forms part of lncRNA–protein complexes: it associates with the long noncoding RNA H19 to facilitate histone acetylation and activation of the miR‐200 family, thereby influencing epithelial–mesenchymal transition, and with the lncRNA FIRRE to regulate the stability of inflammatory mRNAs."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n In addition, HNRNPU directly binds to AU‐rich sequences in the 3′‐untranslated region of transcripts such as that of COX‑2, contributing to RNA binding complexes that govern mRNA export and stability."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Its interaction with components of the transcription elongation machinery – including the histone acetyltransferase PCAF and nuclear actin – further supports a role in modulating RNA polymerase II–dependent transcription."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n HNRNPU is also implicated in higher-order chromatin organization. Its binding to scaffold/matrix attachment regions and interaction with the coactivator p300 help position chromatin in a transcription‐poised state."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " Moreover, by regulating U2 small nuclear ribonucleoprotein maturation and Cajal body morphology, HNRNPU is essential for proper alternative pre‐mRNA splicing; indeed, cardiac‐specific loss of HNRNPU causes widespread splicing defects and lethal dilated cardiomyopathy."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Additional layers of HNRNPU function are highlighted by its involvement in protein homeostasis. It acts as a pseudosubstrate for the SCF(β‑TrCP) ubiquitin ligase, modulating nuclear localization and stability of key regulatory proteins."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "9"}]}, {"type": "t", "text": " Finally, studies in the context of viral infection demonstrate that a hnRNP U–related factor (E1B‑AP5) contributes to adenovirus RNA transport and influences viral oncogenic transformation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "10"}]}, {"type": "t", "text": " \n "}]}, {"type": "t", "text": "\n "}, {"type": "p", "children": [{"type": "t", "text": "\n Collectively, these findings establish HNRNPU as an indispensable multifunctional regulator that integrates RNA processing, chromatin dynamics, transcriptional control, and protein turnover across a broad range of cellular contexts."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}, {"type": "fg_f", "ref": "11"}, {"type": "fg_f", "ref": "5"}, {"type": "fg_f", "ref": "7"}, {"type": "fg_f", "ref": "3"}, {"type": "fg_f", "ref": "9"}, {"type": "fg_f", "ref": "2"}, {"type": "fg_f", "ref": "8"}, {"type": "fg_f", "ref": "10"}, {"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Ling Zhang, Fu Yang, Ji-hang Yuan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Carcinogenesis (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/carcin/bgs381"}], "href": "https://doi.org/10.1093/carcin/bgs381"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23222811"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23222811"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Yajing Lu, Xu Liu, Minghong Xie, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The NF-κB-Responsive Long Noncoding RNA FIRRE Regulates Posttranscriptional Regulation of Inflammatory Gene Expression through Interacting with hnRNPU."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Immunol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.4049/jimmunol.1700091"}], "href": "https://doi.org/10.4049/jimmunol.1700091"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28993514"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28993514"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Steven J Cok, Stephen J Acton, Aubrey R Morrison "}, {"type": "b", "children": [{"type": "t", "text": "The proximal region of the 3'-untranslated region of cyclooxygenase-2 is recognized by a multimeric protein complex containing HuR, TIA-1, TIAR, and the heterogeneous nuclear ribonucleoprotein U."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M302547200"}], "href": "https://doi.org/10.1074/jbc.M302547200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12855701"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12855701"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Ales Obrdlik, Alexander Kukalev, Emilie Louvet, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The histone acetyltransferase PCAF associates with actin and hnRNP U for RNA polymerase II transcription."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.00766-08"}], "href": "https://doi.org/10.1128/MCB.00766-08"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18710935"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18710935"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Ryu-Suke Nozawa, Lora Boteva, Dinesh C Soares, et al. "}, {"type": "b", "children": [{"type": "t", "text": "SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cell.2017.05.029"}], "href": "https://doi.org/10.1016/j.cell.2017.05.029"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28622508"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28622508"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Joost H A Martens, Matty Verlaan, Eric Kalkhoven, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.22.8.2598-2606.2002"}], "href": "https://doi.org/10.1128/MCB.22.8.2598-2606.2002"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11909954"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11909954"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Rui Xiao, Peng Tang, Bo Yang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell (2012)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.molcel.2012.01.009"}], "href": "https://doi.org/10.1016/j.molcel.2012.01.009"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22325991"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22325991"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Junqiang Ye, Nadine Beetz, Sean O'Keeffe, et al. "}, {"type": "b", "children": [{"type": "t", "text": "hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1508461112"}], "href": "https://doi.org/10.1073/pnas.1508461112"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26039991"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26039991"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Matti Davis, Ada Hatzubai, Jens S Andersen, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Pseudosubstrate regulation of the SCF(beta-TrCP) ubiquitin ligase by hnRNP-U."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Genes Dev (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1101/gad.218702"}], "href": "https://doi.org/10.1101/gad.218702"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11850407"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11850407"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "S Gabler, H Schütt, P Groitl, et al. "}, {"type": "b", "children": [{"type": "t", "text": "E1B 55-kilodalton-associated protein: a cellular protein with RNA-binding activity implicated in nucleocytoplasmic transport of adenovirus and cellular mRNAs."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Virol (1998)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/JVI.72.10.7960-7971.1998"}], "href": "https://doi.org/10.1128/JVI.72.10.7960-7971.1998"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "9733834"}], "href": "https://pubmed.ncbi.nlm.nih.gov/9733834"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Ruo-Kai Lin, Yi-Shuan Hsieh, Pinpin Lin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The tobacco-specific carcinogen NNK induces DNA methyltransferase 1 accumulation and tumor suppressor gene hypermethylation in mice and lung cancer patients."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Clin Invest (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1172/JCI40706"}], "href": "https://doi.org/10.1172/JCI40706"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20093774"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20093774"}]}]}]}
Synonyms	HNRNPU-AS1, pp120, EIEE54, GRIP120, HNRNP U, HNRPU, SAF-A, SAFA, U21.1
Proteins	HNRPU_HUMAN
NCBI Gene ID	3192
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

HNRNPU has 20,692 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 131 datasets.

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

If available, associations are ranked by standardized value

Harmonizome 3.0

HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU 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 HNRNPU gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of HNRNPU 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 HNRNPU gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with HNRNPU protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with HNRNPU 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 HNRNPU gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of HNRNPU 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 HNRNPU 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 HNRNPU gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing HNRNPU protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of HNRNPU gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing HNRNPU protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing HNRNPU protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing HNRNPU 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	cellular components co-occuring with HNRNPU 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 HNRNPU protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing HNRNPU protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of HNRNPU gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with HNRNPU gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with HNRNPU gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with HNRNPU gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of HNRNPU protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving HNRNPU gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with HNRNPU 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 HNRNPU 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 HNRNPU gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with HNRNPU 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 HNRNPU 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 HNRNPU gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of HNRNPU gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.