title: Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions.
abstract: Systematic analysis of the RNA-protein interactome requires robust and scalable methods. We here show the combination of two completely orthogonal, generic techniques to identify RNA-protein interactions: PAR-CLIP reveals a collection of RNAs bound to a protein whereas SILAC-based RNA pull-downs identify a group of proteins bound to an RNA. We investigated binding sites for five different proteins (IGF2BP1-3, QKI and PUM2) exhibiting different binding patterns. We report near perfect agreement between the two approaches. Nevertheless, they are non-redundant, and ideally complement each other to map the RNA-protein interaction network.
authors.affiliation: Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Marion
authors.initials: M
authors.lastname: Scheibe
authors.forename: Falk
authors.initials: F
authors.lastname: Butter
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Matthias
authors.initials: M
authors.lastname: Mann
mesh_terms: D001665:Binding Sites; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*
chemical_list: C498779:IGF2BP2 protein, human; C471243:PUM2 protein, human; C490832:QKI protein, human; D012333:RNA, Messenger; D016601:RNA-Binding Proteins