title: Serial interactome capture of the human cell nucleus.
abstract: Novel RNA-guided cellular functions are paralleled by an increasing number of RNA-binding proteins (RBPs). Here we present 'serial RNA interactome capture' (serIC), a multiple purification procedure of ultraviolet-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with high specificity. We apply serIC to the nuclei of proliferating K562 cells to obtain the first human nuclear RNA interactome. The domain composition of the 382 identified nuclear RBPs markedly differs from previous IC experiments, including few factors without known RNA-binding domains that are in good agreement with computationally predicted RNA binding. serIC extends the number of DNA-RNA-binding proteins (DRBPs), and reveals a network of RBPs involved in p53 signalling and double-strand break repair. serIC is an effective tool to couple global RBP capture with additional selection or labelling steps for specific detection of highly purified RBPs.
authors.affiliation: Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Conrad
authors.affiliation: Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany.|Department of Biochemistry, Free University of Berlin, 14195 Berlin, Germany.
authors.forename: Anne-Susann
authors.initials: AS
authors.lastname: Albrecht
authors.affiliation: Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany.|Department of Informatics, Free University of Berlin, 14195 Berlin, Germany.
authors.forename: Veronica Rodrigues
authors.initials: VR
authors.lastname: de Melo Costa
authors.affiliation: Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany.|CU Systems Medicine, 97080 Würzburg 14195, Germany.
authors.forename: Sascha
authors.initials: S
authors.lastname: Sauer
authors.affiliation: Max Planck Institute for Molecular Genetics, Mass Spectrometry Core Facility, 14195 Berlin, Germany.
authors.forename: David
authors.identifier: http://orcid.org/0000-0002-0170-868X
authors.initials: D
authors.lastname: Meierhofer
authors.affiliation: Max Planck Institute for Molecular Genetics, Otto Warburg Laboratories, 14195 Berlin, Germany.
authors.forename: Ulf Andersson
authors.initials: UA
authors.lastname: Ørom
mesh_terms: D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism* / Q000528:radiation effects; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D020014:K562 Cells; D025941:Protein Interaction Mapping; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014466:Ultraviolet Rays; D000094704:RNA, Guide, CRISPR-Cas Systems
chemical_list: D004247:DNA; D004268:DNA-Binding Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D000094704:RNA, Guide, CRISPR-Cas Systems