bioRxiv preprint doi: https://doi.org/10.1101/405589; this version posted December 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. β-actin mRNA interactome mapping by proximity biotinylation Joyita Mukherjee1, Orit Hermesh1, Nicolas Nalpas2, Mirita Franz-Wachtel2, Boris Maček2, Ralf-Peter Jansen1,3 1 Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany. 2 Proteome Center Tübingen, University of Tübingen, Tübingen, Germany. 3 Corresponding author: Ralf-Peter Jansen University of Tübingen Interfaculty Institute of Biochemistry Hoppe-Seyler-Strasse 4 72076 Tübingen, Germany Phone: +49-7071-2974161 Email:
[email protected] KEYWORDS: RNA-BioID, mRNA localization, FUBP3, RNA binding protein, protein−RNA interaction, object-based co-localization, Label free quantification. RUNNING TITLE: RNA-BioID identifies β-actin mRNA-associated proteins 1 bioRxiv preprint doi: https://doi.org/10.1101/405589; this version posted December 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT The molecular function and fate of mRNAs are controlled by RNA binding proteins (RBPs). However, identification of the interacting proteome of a specific mRNA in vivo is still very challenging. Based on the widely-used RNA tagging with MS2 aptamers for RNA visualization, we developed a novel RNA proximity biotinylation (RNA-BioID) method by tethering biotin ligase (BirA*) via MS2 coat protein (MCP) at the 3’UTR of endogenously MS2 tagged β-actin mRNA in mouse embryonic fibroblasts (MEFs).