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Large-scale map of RNA-binding protein interactomes across the mRNA life cycle

Lena A Street1, Katherine L Rothamel2, Kristopher W Brannan3

  • 1Department of Biological Sciences, Columbia University, New York, NY, USA.

Molecular Cell
|September 20, 2024
PubMed

Insights

This study maps protein-protein interactions (PPIs) of RNA-binding proteins (RBPs) across the mRNA lifecycle. It reveals numerous RNA-regulated interactions, linking proteins to specific mRNA stages and functions.

Area of Science:

  • Molecular Biology
  • Proteomics
  • RNA Biology

Background:

  • Messenger RNAs (mRNAs) interact with RNA-binding proteins (RBPs) during their lifecycle.
  • Previous studies focused on RBP-RNA interactions, with less exploration of RBP-protein interactions (PPIs) in mRNA processing stages.

Purpose of the Study:

  • To construct an RNA-aware, RBP-centric PPI map across the human mRNA lifecycle.
  • To identify novel PPIs and understand their regulation by RNA.
  • To link proteins, including those with unknown functions, to specific mRNA lifecycle stages.

Main Methods:

  • Utilized immunopurification-mass spectrometry (IP-MS) of approximately 100 endogenous RBPs, with and without RNase treatment.
  • Augmented IP-MS data with size exclusion chromatography-mass spectrometry (SEC-MS).
  • Analyzed identified interactions for RNA regulation.

Main Results:

  • Identified 8,742 known and 20,802 novel PPIs among 1,125 proteins.
  • Determined that 73% of identified PPIs are RNA-regulated.
  • Linked numerous proteins to specific mRNA lifecycle stages, with nearly half associated with multiple stages.

Conclusions:

  • The generated interactome provides a valuable resource for studying mRNA processing and RBP functions.
  • Demonstrated the utility of the resource by characterizing enhancer of rudimentary homolog (ERH) functions in splicing and export.
  • Showcased differential cytoplasmic RNA binding of SNRNP200 during stress, linking it to stress granule proteins.
Keywords:
ERHIP-MSRBPRNA-binding proteinsRNA-dependent protein interactionsSEC-MSSNRNP200interactomemRNA life-cycleprotein-protein interactions

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