Large-scale map of RNA-binding protein interactomes across the mRNA life cycle
mRNAs interact with RNA-binding proteins (RBPs) throughout their processing and maturation. While efforts have assigned RBPs to RNA substrates, less exploration has leveraged protein-protein interactions (PPIs) to study proteins in mRNA life-cycle stages. We generated an RNA-aware, RBP-centric PPI map across the mRNA life cycle in human cells by immunopurification-mass spectrometry (IP-MS) of ∼100 endogenous RBPs with and without RNase, augmented by size exclusion chromatography-mass spectrometry (SEC-MS). We identify 8,742 known and 20,802 unreported interactions between 1,125 proteins and determine that 73% of the IP-MS-identified interactions are RNA regulated. Our interactome links many proteins, some with unknown functions, to specific mRNA life-cycle stages, with nearly half associated with multiple stages. We demonstrate the value of this resource by characterizing the splicing and export functions of enhancer of rudimentary homolog (ERH), and by showing that small nuclear ribonucleoprotein U5 subunit 200 (SNRNP200) interacts with stress granule proteins and binds cytoplasmic RNA differently during stress.
Authors
- Ella Doron‐Mandel (ORCID: https://orcid.org/0000-0002-2519-5938)
- Katherine Rothamel (ORCID: https://orcid.org/0000-0001-9896-485X)
- Jenny Kim Kim
- Ahmed Abdou
- Lena Annika Street (ORCID: https://orcid.org/0000-0002-5473-6713)
- Erica Wolin
- Benjamin J. Bokor (ORCID: https://orcid.org/0000-0001-9167-7794)
- Kevin Dong (ORCID: https://orcid.org/0000-0002-2341-8472)
- Assael A. Madrigal (ORCID: https://orcid.org/0000-0002-3311-5256)
- Kristopher W. Brannan (ORCID: https://orcid.org/0000-0002-0316-898X)
- Wenhao Jin (ORCID: https://orcid.org/0000-0002-7885-3527)
- Norah Al-Azzam (ORCID: https://orcid.org/0000-0002-8960-8236)
- Kevin Rhine (ORCID: https://orcid.org/0000-0003-1355-2405)
- Joshua Ahdout
- Marko Jovanović (ORCID: https://orcid.org/0000-0001-9707-3377)
- Orel Mizrahi (ORCID: https://orcid.org/0000-0003-2189-5731)
- Mayuresh Mujumdar
- Yanzhe Ma
- Darvesh Gorhe (ORCID: https://orcid.org/0009-0003-5825-6455)
- Gene W. Yeo
Institutions
- University of California San Diego (US)
- Columbia University (US)
Publication Details
- Journal
- Molecular Cell
- Published
- 2024-09-19
- DOI
- https://doi.org/10.1016/j.molcel.2024.08.030
- Citations
- 32
- Primary Topic
- RNA Research and Splicing
- Type
- article
- Field-Weighted Citation Impact
- 7.48
Funders
- National Science Foundation
- Cancer Prevention and Research Institute of Texas
- Coalition for Epidemic Preparedness Innovations
- National Institutes of Health