title: RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.
abstract: The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFα mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ∼ 3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage-induced mRNAs, indicating a role of this RNA-binding protein in the post-transcriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of the NF-κB pathway regulators such as IκBα and A20. RC3H1 uses ROQ and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with IκB kinase and NF-κB activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-κB pathway.
authors.affiliation: RNA Biology and Posttranscriptional Regulation, Berlin Institute of Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Murakawa
authors.affiliation: Signal Transduction in Tumor Cells, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hinz
authors.affiliation: Mathematical Modelling of Cellular Processes, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Janina
authors.initials: J
authors.lastname: Mothes
authors.affiliation: 1] Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany [2] Helmholtz Protein Sample Production Facility, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Schuetz
authors.affiliation: Department of Computer Science and Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-Universität Freiburg, 79110 Freiburg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Uhl
authors.affiliation: RNA Biology and Posttranscriptional Regulation, Berlin Institute of Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Emanuel
authors.initials: E
authors.lastname: Wyler
authors.affiliation: Immune Regulation and Cancer, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Tomoharu
authors.initials: T
authors.lastname: Yasuda
authors.affiliation: Integrative Proteomics and Metabolomics Platform, Berlin Institute of Medical Systems Biology at the Max-Delbrück Center for Molecular, 13125 Berlin, Germany.
authors.forename: Guido
authors.initials: G
authors.lastname: Mastrobuoni
authors.affiliation: Institut für Informatik, Ludwig-Maximilians-Universität, 80333 München, Germany.
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Friedel
authors.affiliation: Institute for Virology and Immunobiology, University of Würzburg, 97078 Würzburg, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Dölken
authors.affiliation: Integrative Proteomics and Metabolomics Platform, Berlin Institute of Medical Systems Biology at the Max-Delbrück Center for Molecular, 13125 Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Kempa
authors.affiliation: Department of Hematology and Oncology, Technische Universität, 81675 München, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Schmidt-Supprian
authors.affiliation: 1] Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany [2] Integrative Research Institute (IRI) for the Life Sciences and Institute for Theoretical Biology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
authors.forename: Nils
authors.initials: N
authors.lastname: Blüthgen
authors.affiliation: Department of Computer Science and Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-Universität Freiburg, 79110 Freiburg, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.affiliation: 1] Macromolecular Structure and Interaction, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany [2] Chemistry and Biochemistry Institute, Freie Universität Berlin, 14195 Berlin, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Heinemann
authors.affiliation: Mathematical Modelling of Cellular Processes, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Wolf
authors.affiliation: Signal Transduction in Tumor Cells, Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Claus
authors.initials: C
authors.lastname: Scheidereit
authors.affiliation: RNA Biology and Posttranscriptional Regulation, Berlin Institute of Medical Systems Biology at the Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Landthaler
mesh_terms: D001665:Binding Sites; D015153:Blotting, Western; D004249:DNA Damage; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D057809:HEK293 Cells; D006801:Humans; D020672:I-kappa B Proteins / Q000378:metabolism*; D047908:Intracellular Signaling Peptides and Proteins / Q000378:metabolism*; D000072000:NF-KappaB Inhibitor alpha; D016328:NF-kappa B / Q000378:metabolism*; D009687:Nuclear Proteins / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability / Q000235:genetics*; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics*; D015398:Signal Transduction; D000072598:Tumor Necrosis Factor alpha-Induced Protein 3; D044767:Ubiquitin-Protein Ligases / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D020672:I-kappa B Proteins; D047908:Intracellular Signaling Peptides and Proteins; D016328:NF-kappa B; C000606204:NFKBIA protein, human; D009687:Nuclear Proteins; C000592051:RC3H1 protein, human; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D000072000:NF-KappaB Inhibitor alpha; D044767:Ubiquitin-Protein Ligases; C076529:TNFAIP3 protein, human; D000072598:Tumor Necrosis Factor alpha-Induced Protein 3