title: In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.
abstract: Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. Here, we introduce an in vivo proximity labeling (IPL) technology that employs an affinity tag combined with a photoactivatable probe to label polypeptides and RNAs in the vicinity of a protein of interest in vivo. Using quantitative mass spectrometry and deep sequencing, we show that IPL correctly identifies known protein-protein and protein-RNA interactions in the nucleus of mammalian cells. Thus, IPL provides additional temporal and spatial information for the characterization of biological interactions in vivo.
authors.affiliation: Howard Hughes Medical Institute and Department of Biochemistry, New York University School of Medicine , 522 First Avenue, New York, New York 10016, United States.
authors.forename: David B
authors.initials: DB
authors.lastname: Beck
authors.forename: Varun
authors.initials: V
authors.lastname: Narendra
authors.forename: William J
authors.initials: WJ
authors.lastname: Drury
authors.forename: Ryan
authors.initials: R
authors.lastname: Casey
authors.forename: Pascal W T C
authors.initials: PW
authors.lastname: Jansen
authors.forename: Zuo-Fei
authors.initials: ZF
authors.lastname: Yuan
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Garcia
authors.forename: Michiel
authors.initials: M
authors.lastname: Vermeulen
authors.forename: Roberto
authors.initials: R
authors.lastname: Bonasio
mesh_terms: D001710:Biotin / Q000737:chemistry / Q000378:metabolism; D002853:Chromatography, Liquid; D000071221:Enhancer of Zeste Homolog 2 Protein; D057809:HEK293 Cells; D006801:Humans; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D063151:Polycomb Repressive Complex 2 / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods; D013194:Staining and Labeling / Q000379:methods*; D019809:Streptavidin / Q000737:chemistry / Q000378:metabolism; D053719:Tandem Mass Spectrometry
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA; D001710:Biotin; D019809:Streptavidin; C498409:EZH2 protein, human; D000071221:Enhancer of Zeste Homolog 2 Protein; D063151:Polycomb Repressive Complex 2
keywords: Proximity labeling; RNA-seq; biotinylation; covalent tag; protein−RNA interactions; protein−protein interactions