ArticleMolecular cell2024
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.
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Article in Molecular cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- ARID5A RNA-binding coordinates microglial defense and ferroptosis in iPSC-derived models.Nature communications · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- PROTAC-mediated regulation of programmed cell death: From molecular mechanisms to therapeutic breakthroughs.Innovation (Cambridge (Mass.)) · 2026Review
- Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased manner.PLoS genetics · 2026Article
- DNA recognition, cleavage, and toxic metal ion interaction of an artificial zinc finger protein inside E. coli cells.Protein science : a publication of the Protein Society · 2026Article
- ZNF469 drives TGF-β1/SMAD3-mediated extracellular matrix regulation in pulmonary fibrosis.Biomolecules & biomedicine · 2026Article
- Article
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- BRAF inhibitor resistance in melanoma: from resistance mechanisms to therapeutic innovations.Molecular biomedicine · 2026Review
- Zinc finger proteins (ZFPs) in health and disease.Molecular biomedicine · 2026Review
- Identification and structural characterization of anthrax toxin receptor 2 as the Clostridium perfringens NetF receptor.Nature communications · 2026Article
- RNA-coupled CRISPR screens reveal ZNF207 as a regulator of LMNA aberrant splicing in progeria.Molecular cell · 2026Article
- ZNF473 as a biomarker and potential therapeutic target in cancer: integrated bioinformatics and experimental evidence with a focus on hepatocellular carcinoma.Frontiers in oncology · 2026Article
- Genome-Wide Association Study on the Estimated Breeding Values for Udder and Longevity and the Candidate Genes in Holstein-Friesian Cows in Hungary.Animals : an open access journal from MDPI · 2025Article
- ZAD mediates chromatin binding and insulator activity of Drosophila Pita and can be replaced with the human ZFP276 ZAD-like domain.Epigenetics & chromatin · 2025Article
- Cytoplasmic PXR regulates glucose metabolism by binding mRNAs and modulating their stability.Nature structural & molecular biology · 2025Article
- Pleiotropic Effects on Tachyzoite and Host Cell Proteomes in Knock-Out Clones of the Open Reading Frames 297720 and 319730 Constitutively Expressed inInternational journal of molecular sciences · 2025Article
- diPaRIS: Dynamic and Interpretable Protein-RNA Interactions Prediction With U-Shaped Network and Novel Structure Encoding.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- TEAMwork: Interplay of Post-Transcriptional Mechanisms, Epigenetics and Metabolism in (Auto-)Immunity.European journal of immunology · 2025Review
- The dual role of RNA-binding proteins: promotion of tumorigenesis, drug resistance, and emerging therapeutic targets.Acta biochimica et biophysica Sinica · 2025Article
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Authors and funding
23 authors.
Maya L GosztylaDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Lijun ZhanDepartment of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
Sara OlsonDepartment of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
Xintao WeiDepartment of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
Jack NaritomiDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Grady NguyenDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Lena StreetDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Grant A GodaDepartment of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
Francisco F CavazosDepartment of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
Jonathan C SchmokDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Manya JainDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Easin Uddin SyedInstitut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; School of Pharmacy, Brac University, Dhaka 1212, Bangladesh.
Eunjeong KwonInstitut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada.
Wenhao JinSanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA.
Eric KofmanDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Alexandra T TankkaDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Allison LiDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Valerie GonzalezDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Eric LécuyerInstitut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3T 1J4, Canada; Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada.
Daniel DominguezDepartment of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA.
Marko JovanovicDepartment of Biological Sciences, Columbia University, New York, NY 10027, USA.
Brenton R GraveleyDepartment of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
Gene W YeoDepartment of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA 92037, USA. Electronic address: geneyeo@ucsd.edu.
Funding
TR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3MFunctional RNA elements in the human genomeR01HG004659 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Kevin Daniel Corbett, Eugene Wei-Ming Yeo · 2008 to 2026
$12.4MUsing Networks to Seed Hierarchical Whole-cell Models of CancerU54CA209891 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KROGAN, NEVAN J · 2017 to 2021
$10.9MA Comprehensive Functional Map of Human Protein-RNA InteractionsU41HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R. · 2018 to 2021
$9.4MTechnology Development Coordinating CenterU24HG011735 · NHGRI · JACKSON LABORATORY · PI Mark D ADAMS · 2021 to 2026
$8.1MPredoctoral and Postdoctoral Training in Cancer Cell BiologyT32CA067754 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEAN Y.J. WANG · 1995 to 2026
$6.5MA comprehensive binding and functional map of human RNA-binding proteinsU24HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R., YEO, EUGENE WEI-MING · 2022 to 2025
$5.5MSTAMP technology to enable single-cell and isoform-sensitive detection of RBP sitesR01HG011864 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI YEO, EUGENE WEI-MING · 2021 to 2024
$4.0MExtensive multiplexing of protein nucleic-acid interactions to comprehensively study gene expression regulation from chromatin to mRNA degradationR01HG012216 · NHGRI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI GUTTMAN, MITCHELL, JOVANOVIC, MARKO · 2022 to 2025
$3.1MDefining the programmed proteome rejuvenation underlying gametogenesisR01AG071869 · NIA · UNIVERSITY OF CALIFORNIA BERKELEY · PI BRAR, GLORIA ANN, JOVANOVIC, MARKO · 2021 to 2025
$2.9MProtein Disorder as a Modifier of RNA Binding and RegulationR35GM142864 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Daniel Issac Dominguez · 2021 to 2026
$2.5MRibo-STAMPEDE: novel tools for molecular profiling of brain cell typesRF1MH126719 · NIMH · SCRIPPS RESEARCH INSTITUTE, THE · PI LIPPI, GIORDANO, YEO, EUGENE WEI-MING · 2022 to 2022
$2.3MNational Science Foundation (NSF) 2224211NCI NIH HHS T32 CA067754NCI NIH HHS U54 CA209891NHGRI NIH HHS R01 HG004659NHGRI NIH HHS R01 HG011864NHGRI NIH HHS R01 HG012216NHGRI NIH HHS U24 HG009889NHGRI NIH HHS U24 HG011735NHGRI NIH HHS U41 HG009889NIA NIH HHS R01 AG071869NIGMS NIH HHS P41 GM103504NIGMS NIH HHS R35 GM142864NIH HHS S10 OD025052NIH HHS S10 OD026929NIMH NIH HHS RF1 MH126719
Abstract
RNA interactome studies have revealed that hundreds of zinc-finger proteins (ZFPs) are candidate RNA-binding proteins (RBPs), yet their RNA substrates and functional significance remain largely uncharacterized. Here, we present a systematic multi-omics analysis of the DNA- and RNA-binding targets and regulatory roles of more than 100 ZFPs representing 37 zinc-finger families. We show that multiple ZFPs are previously unknown regulators of RNA splicing, alternative polyadenylation, stability, or translation. The examined ZFPs show widespread sequence-specific RNA binding and preferentially bind proximal to transcription start sites. Additionally, several ZFPs associate with their targets at both the DNA and RNA levels. We highlight ZNF277, a C2H2 ZFP that binds thousands of RNA targets and acts as a multi-functional RBP. We also show that ZNF473 is a DNA/RNA-associated protein that regulates the expression and splicing of cell cycle genes. Our results reveal diverse roles for ZFPs in transcriptional and post-transcriptional gene regulation.
Indexed as
RNA-Binding ProteinsRNA SplicingZinc FingersAlternative SplicingBinding SitesDNA-Binding ProteinsGene Expression RegulationHEK293 CellsHeLa CellsHumansMultiomicsProtein BindingRNADNA-Binding ProteinsRNARNA-Binding ProteinsCut&RuneCLIPmulti-omicsRibo-STAMPRNA binding proteinRNA-seqSLAM-seqzinc fingerZNF277ZNF473
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