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

Lena A Street¹, Katherine L Rothamel², Kristopher W Brannan³, Wenhao Jin⁴, Benjamin J Bokor¹, Kevin Dong⁴, Kevin Rhine⁴, Assael Madrigal⁴, Norah Al-Azzam⁴, Jenny Kim Kim¹, Yanzhe Ma¹, Darvesh Gorhe¹, Ahmed Abdou¹, Erica Wolin¹, Orel Mizrahi⁵, Joshua Ahdout⁴, Mayuresh Mujumdar⁴, Ella Doron-Mandel¹, Marko Jovanovic⁶, Gene W Yeo⁷

Affiliations

¹ Department of Biological Sciences, Columbia University, New York, NY, USA.
² Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA.
³ Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA; Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
⁴ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
⁵ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
⁶ Department of Biological Sciences, Columbia University, New York, NY, USA. Electronic address: mj2794@columbia.edu.
⁷ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Laboratories for Innovative Medicines, San Diego, CA, USA; Sanford Stem Cell Institute, Innovation Center, San Diego, CA, USA. Electronic address: geneyeo@ucsd.edu.

PMID: 39303721
PMCID: PMC11530141 (available on 2025-10-03)
DOI: 10.1016/j.molcel.2024.08.030

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

Lena A Street et al. Mol Cell. 2024.

. 2024 Oct 3;84(19):3790-3809.e8.

doi: 10.1016/j.molcel.2024.08.030. Epub 2024 Sep 19.

Authors

Affiliations

¹ Department of Biological Sciences, Columbia University, New York, NY, USA.
² Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA.
³ Center for RNA Therapeutics, Houston Methodist Research Institute, Houston, TX, USA; Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
⁴ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
⁵ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
⁶ Department of Biological Sciences, Columbia University, New York, NY, USA. Electronic address: mj2794@columbia.edu.
⁷ Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Center for RNA Technologies and Therapeutics, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA; Sanford Laboratories for Innovative Medicines, San Diego, CA, USA; Sanford Stem Cell Institute, Innovation Center, San Diego, CA, USA. Electronic address: geneyeo@ucsd.edu.

PMID: 39303721
PMCID: PMC11530141 (available on 2025-10-03)
DOI: 10.1016/j.molcel.2024.08.030

Abstract

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.

Keywords: ERH; IP-MS; RBP; RNA-binding proteins; RNA-dependent protein interactions; SEC-MS; SNRNP200; interactome; mRNA life-cycle; protein-protein interactions.

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Conflict of interest statement

Declaration of interests G.W.Y. is a co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Eclipse BioInnovations. G.W.Y.’s interests have been reviewed and approved by the University of California, San Diego, in accordance with its conflict-of-interest policies.

Update of

Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.
Street L, Rothamel K, Brannan K, Jin W, Bokor B, Dong K, Rhine K, Madrigal A, Al-Azzam N, Kim JK, Ma Y, Abdou A, Wolin E, Doron-Mandel E, Ahdout J, Mujumdar M, Jovanovic M, Yeo GW. Street L, et al. bioRxiv [Preprint]. 2023 Jun 8:2023.06.08.544225. doi: 10.1101/2023.06.08.544225. bioRxiv. 2023. Update in: Mol Cell. 2024 Oct 3;84(19):3790-3809.e8. doi: 10.1016/j.molcel.2024.08.030. PMID: 37333282 Free PMC article. Updated. Preprint.

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

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

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