β-Actin mRNA interactome mapping by proximity biotinylation

Joyita Mukherjee, Orit Hermesh, Carolina Eliscovich, Nicolas Nalpas, Mirita Franz-Wachtel, Boris Maček, Ralf Peter Jansen

Research output: Contribution to journalArticle

Abstract

The molecular function and fate of mRNAs are controlled by RNA-binding proteins (RBPs). Identification of the interacting proteome of a specific mRNA in vivo remains very challenging, however. Based on the widely used technique of RNA tagging with MS2 aptamers for RNA visualization, we developed a RNA proximity biotinylation (RNA-BioID) technique by tethering biotin ligase (BirA*) via MS2 coat protein at the 3′ UTR of endogenous MS2-tagged β-actin mRNA in mouse embryonic fibroblasts. We demonstrate the dynamics of the β-actin mRNA interactome by characterizing its changes on serum-induced localization of the mRNA. Apart from the previously known interactors, we identified more than 60 additional β-actin–associated RBPs by RNA-BioID. Among these, the KH domain-containing protein FUBP3/ MARTA2 has been shown to be required for β-actin mRNA localization. We found that FUBP3 binds to the 3′ UTR of β-actin mRNA and is essential for β-actin mRNA localization, but does not interact with the characterized β-actin zipcode element. RNA-BioID provides a tool for identifying new mRNA interactors and studying the dynamic view of the interacting proteome of endogenous mRNAs in space and time.

Original languageEnglish (US)
Pages (from-to)12863-12872
Number of pages10
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number26
DOIs
StatePublished - Jan 1 2019

Fingerprint

Biotinylation
Actins
Messenger RNA
RNA
RNA-Binding Proteins
3' Untranslated Regions
Proteome
Nucleotide Aptamers
Capsid Proteins
Ligases
Biotin
Fibroblasts

Keywords

  • FUBP3
  • mRNA localization
  • RNA-binding protein
  • RNA-BioID

ASJC Scopus subject areas

  • General

Cite this

β-Actin mRNA interactome mapping by proximity biotinylation. / Mukherjee, Joyita; Hermesh, Orit; Eliscovich, Carolina; Nalpas, Nicolas; Franz-Wachtel, Mirita; Maček, Boris; Jansen, Ralf Peter.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 116, No. 26, 01.01.2019, p. 12863-12872.

Research output: Contribution to journalArticle

Mukherjee, Joyita ; Hermesh, Orit ; Eliscovich, Carolina ; Nalpas, Nicolas ; Franz-Wachtel, Mirita ; Maček, Boris ; Jansen, Ralf Peter. / β-Actin mRNA interactome mapping by proximity biotinylation. In: Proceedings of the National Academy of Sciences of the United States of America. 2019 ; Vol. 116, No. 26. pp. 12863-12872.
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