In-cell identification and measurement of RNA-protein interactions

Antoine Graindorge, Inês Pinheiro, Anna Nawrocka, Allison C. Mallory, Peter Tsvetkov, Noa Gil, Carlo Carolis, Frank Buchholz, Igor Ulitsky, Edith Heard, Mikko Taipale and Alena Shkumatava ()
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Antoine Graindorge: Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934
Inês Pinheiro: Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934
Anna Nawrocka: Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934
Allison C. Mallory: Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934
Peter Tsvetkov: Whitehead Institute for Biomedical Research
Noa Gil: Weizmann Institute of Science
Carlo Carolis: The Barcelona Institute of Science and Technology
Frank Buchholz: Medical System Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden
Igor Ulitsky: Weizmann Institute of Science
Edith Heard: Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934
Mikko Taipale: Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics
Alena Shkumatava: Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Regulatory RNAs exert their cellular functions through RNA-binding proteins (RBPs). Identifying RNA-protein interactions is therefore key for a molecular understanding of regulatory RNAs. To date, RNA-bound proteins have been identified primarily through RNA purification followed by mass spectrometry. Here, we develop incPRINT (in cell protein-RNA interaction), a high-throughput method to identify in-cell RNA-protein interactions revealed by quantifiable luminescence. Applying incPRINT to long noncoding RNAs (lncRNAs), we identify RBPs specifically interacting with the lncRNA Firre and three functionally distinct regions of the lncRNA Xist. incPRINT confirms previously known lncRNA-protein interactions and identifies additional interactions that had evaded detection with other approaches. Importantly, the majority of the incPRINT-defined interactions are specific to individual functional regions of the large Xist transcript. Thus, we present an RNA-centric method that enables reliable identification of RNA-region-specific RBPs and is applicable to any RNA of interest.

Date: 2019
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DOI: 10.1038/s41467-019-13235-w

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