title: Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.
abstract: The RNA-binding protein Roquin is required to prevent autoimmunity. Roquin controls T-helper cell activation and differentiation by limiting the induced expression of costimulatory receptors such as tumor necrosis factor receptor superfamily 4 (Tnfrs4 or Ox40). A constitutive decay element (CDE) with a characteristic triloop hairpin was previously shown to be recognized by Roquin. Here we use SELEX assays to identify a novel U-rich hexaloop motif, representing an alternative decay element (ADE). Crystal structures and NMR data show that the Roquin-1 ROQ domain recognizes hexaloops in the SELEX-derived ADE and in an ADE-like variant present in the Ox40 3'-UTR with identical binding modes. In cells, ADE-like and CDE-like motifs cooperate in the repression of Ox40 by Roquin. Our data reveal an unexpected recognition of hexaloop cis elements for the posttranscriptional regulation of target messenger RNAs by Roquin.
authors.affiliation: Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg DE-85764, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Janowski
authors.affiliation: Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, München DE-81377, Germany.|Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, Planegg-Martinsried DE-82152, Germany.
authors.forename: Gitta A
authors.initials: GA
authors.lastname: Heinz
authors.affiliation: Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg DE-85764, Germany.|Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching DE-85747, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schlundt
authors.affiliation: Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, München DE-81377, Germany.|Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, Planegg-Martinsried DE-82152, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Wommelsdorf
authors.affiliation: Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, München DE-81377, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Brenner
authors.affiliation: Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, Basel CH-4056, Switzerland.
authors.forename: Andreas R
authors.initials: AR
authors.lastname: Gruber
authors.affiliation: AptaIT GmbH, Goethestrasse 52, München 80336, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Blank
authors.affiliation: Institute of Laboratory Animal Science, University of Zurich, Wagistrasse 12, Schlieren 8952, Switzerland.
authors.forename: Thorsten
authors.initials: T
authors.lastname: Buch
authors.affiliation: AptaIT GmbH, Goethestrasse 52, München 80336, Germany.|Department of Medicine III and Transfusion Medicine, University Hospital Grosshadern, LMU, Marchioninistrasse 15, München 81377, Germany.
authors.forename: Raymund
authors.initials: R
authors.lastname: Buhmann
authors.affiliation: Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, Basel CH-4056, Switzerland.
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.affiliation: Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg DE-85764, Germany.|Department of Cell Biology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, Planegg-Martinsried DE-82152, Germany.
authors.forename: Dierk
authors.initials: D
authors.lastname: Niessing
authors.affiliation: Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Marchioninistrasse 25, München DE-81377, Germany.|Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 9, Planegg-Martinsried DE-82152, Germany.
authors.forename: Vigo
authors.initials: V
authors.lastname: Heissmeyer
authors.affiliation: Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg DE-85764, Germany.|Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, Garching DE-85747, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Sattler
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics*; D000818:Animals; D001483:Base Sequence; D018360:Crystallography, X-Ray; D004252:DNA Mutational Analysis; D024202:Electrophoretic Mobility Shift Assay; D008024:Ligands; D051379:Mice; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D066244:Proton Magnetic Resonance Spectroscopy; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D053262:Receptors, OX40 / Q000235:genetics*; D052156:SELEX Aptamer Technique; D044767:Ubiquitin-Protein Ligases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D008024:Ligands; D053262:Receptors, OX40; D012313:RNA; C501406:Rc3h1 protein, mouse; D044767:Ubiquitin-Protein Ligases