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

Lena A. Street; Katherine L. Rothamel; Kristopher W. Brannan; Wenhao Jin; Benjamin J. Bokor; Kevin Dong; Kevin Rhine; Assael Madrigal; Norah Al-Azzam; Jenny Kim Kim; Yanzhe Ma; Darvesh Gorhe; Ahmed Abdou; Erica Wolin; Orel Mizrahi; Joshua Ahdout; Mayuresh Mujumdar; Ella Doron-Mandel; Marko Jovanovic; Gene W. Yeo

doi:10.1016/j.molcel.2024.08.030

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

Lena A. Street, Katherine L. Rothamel, Kristopher W. Brannan, Wenhao Jin, Benjamin J. Bokor, Kevin Dong, Kevin Rhine, Assael Madrigal, Norah Al-Azzam, Jenny Kim Kim, Yanzhe Ma, Darvesh Gorhe, Ahmed Abdou, Erica Wolin, Orel Mizrahi, Joshua Ahdout, Mayuresh Mujumdar, Ella Doron-Mandel, Marko Jovanovic, Gene W. Yeo

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

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.

Original language	English (US)
Pages (from-to)	3790-3809.e8
Journal	Molecular Cell
Volume	84
Issue number	19
DOIs	https://doi.org/10.1016/j.molcel.2024.08.030
State	Published - Oct 3 2024

Keywords

ERH
interactome
IP-MS
mRNA life-cycle
protein-protein interactions
RBP
RNA-binding proteins
RNA-dependent protein interactions
SEC-MS
SNRNP200
Humans
Ribonucleoproteins, Small Nuclear/metabolism
RNA, Messenger/metabolism
Protein Interaction Maps
Protein Interaction Mapping
RNA-Binding Proteins/metabolism
RNA Splicing
Mass Spectrometry
HEK293 Cells
Protein Binding
HeLa Cells

ASJC Scopus subject areas

Molecular Biology
Cell Biology

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10.1016/j.molcel.2024.08.030

Cite this

Street, L. A., Rothamel, K. L., Brannan, K. W., Jin, W., Bokor, B. J., Dong, K., Rhine, K., Madrigal, A., Al-Azzam, N., Kim, J. K., Ma, Y., Gorhe, D., Abdou, A., Wolin, E., Mizrahi, O., Ahdout, J., Mujumdar, M., Doron-Mandel, E., Jovanovic, M., & Yeo, G. W. (2024). Large-scale map of RNA-binding protein interactomes across the mRNA life cycle. Molecular Cell, 84(19), 3790-3809.e8. https://doi.org/10.1016/j.molcel.2024.08.030

Street, LA, Rothamel, KL, Brannan, KW, Jin, W, Bokor, BJ, Dong, K, Rhine, K, Madrigal, A, Al-Azzam, N, Kim, JK, Ma, Y, Gorhe, D, Abdou, A, Wolin, E, Mizrahi, O, Ahdout, J, Mujumdar, M, Doron-Mandel, E, Jovanovic, M & Yeo, GW 2024, 'Large-scale map of RNA-binding protein interactomes across the mRNA life cycle', Molecular Cell, vol. 84, no. 19, pp. 3790-3809.e8. https://doi.org/10.1016/j.molcel.2024.08.030

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title = "Large-scale map of RNA-binding protein interactomes across the mRNA life cycle",

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, interactome, IP-MS, mRNA life-cycle, protein-protein interactions, RBP, RNA-binding proteins, RNA-dependent protein interactions, SEC-MS, SNRNP200, Humans, Ribonucleoproteins, Small Nuclear/metabolism, RNA, Messenger/metabolism, Protein Interaction Maps, Protein Interaction Mapping, RNA-Binding Proteins/metabolism, RNA Splicing, Mass Spectrometry, HEK293 Cells, Protein Binding, HeLa Cells",

author = "Street, {Lena A.} and Rothamel, {Katherine L.} and Brannan, {Kristopher W.} and Wenhao Jin and Bokor, {Benjamin J.} and Kevin Dong and Kevin Rhine and Assael Madrigal and Norah Al-Azzam and Kim, {Jenny Kim} and Yanzhe Ma and Darvesh Gorhe and Ahmed Abdou and Erica Wolin and Orel Mizrahi and Joshua Ahdout and Mayuresh Mujumdar and Ella Doron-Mandel and Marko Jovanovic and Yeo, {Gene W.}",

note = "Publisher Copyright: {\textcopyright} 2024 The Author(s)",

year = "2024",

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doi = "10.1016/j.molcel.2024.08.030",

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T1 - Large-scale map of RNA-binding protein interactomes across the mRNA life cycle

AU - Street, Lena A.

AU - Rothamel, Katherine L.

AU - Brannan, Kristopher W.

AU - Jin, Wenhao

AU - Bokor, Benjamin J.

AU - Dong, Kevin

AU - Rhine, Kevin

AU - Madrigal, Assael

AU - Al-Azzam, Norah

AU - Kim, Jenny Kim

AU - Ma, Yanzhe

AU - Gorhe, Darvesh

AU - Abdou, Ahmed

AU - Wolin, Erica

AU - Mizrahi, Orel

AU - Ahdout, Joshua

AU - Mujumdar, Mayuresh

AU - Doron-Mandel, Ella

AU - Jovanovic, Marko

AU - Yeo, Gene W.

PY - 2024/10/3

Y1 - 2024/10/3

N2 - 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.

AB - 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.

KW - ERH

KW - interactome

KW - IP-MS

KW - mRNA life-cycle

KW - protein-protein interactions

KW - RBP

KW - RNA-binding proteins

KW - RNA-dependent protein interactions

KW - SEC-MS

KW - SNRNP200

KW - Humans

KW - Ribonucleoproteins, Small Nuclear/metabolism

KW - RNA, Messenger/metabolism

KW - Protein Interaction Maps

KW - Protein Interaction Mapping

KW - RNA-Binding Proteins/metabolism

KW - RNA Splicing

KW - Mass Spectrometry

KW - HEK293 Cells

KW - Protein Binding

KW - HeLa Cells

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U2 - 10.1016/j.molcel.2024.08.030

DO - 10.1016/j.molcel.2024.08.030

M3 - Article

C2 - 39303721

AN - SCOPUS:85206018440

SN - 1097-2765

VL - 84

SP - 3790-3809.e8

JO - Molecular Cell

JF - Molecular Cell

IS - 19

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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