High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

Ji-Young Youn; Wade H Dunham; Seo Jung Hong; James D R Knight; Mikhail Bashkurov; Ginny I Chen; Halil Bagci; Bhavisha Rathod; Graham MacLeod; Simon W M Eng; Stéphane Angers; Quaid Morris; Marc Fabian; Jean-François Côté; Anne-Claude Gingras

doi:10.1016/j.molcel.2017.12.020

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

Mol Cell. 2018 Feb 1;69(3):517-532.e11. doi: 10.1016/j.molcel.2017.12.020. Epub 2018 Jan 25.

Authors

Affiliations

¹ Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
² Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
³ Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.
⁴ Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
⁵ Department of Immunology, University of Toronto, Toronto, ON, Canada; Division of Rheumatology, The Hospital for Sick Children (SickKids), Toronto, ON, Canada.
⁶ Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
⁷ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto, ON, Canada.
⁸ Department of Oncology, McGill University, Montréal, QC, Canada; Segal Cancer Centre, Jewish General Hospital, Lady Davis Institute for Medical Research, Montréal, QC, Canada.
⁹ Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada; Département de Biochimie, Université de Montréal, Montréal, QC, Canada; Département de Médecine (Programmes de Biologie Moléculaire), Université de Montréal, Montréal, QC, Canada.
¹⁰ Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. Electronic address: gingras@lunenfeld.ca.

PMID: 29395067
DOI: 10.1016/j.molcel.2017.12.020

Abstract

mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless structures such as stress granules (SGs) and processing bodies (PBs). Here, systematic in vivo proximity-dependent biotinylation (BioID) analysis of 119 human proteins associated with different aspects of mRNA biology uncovers 7424 unique proximity interactions with 1,792 proteins. Classical bait-prey analysis reveals connections of hundreds of proteins to distinct mRNA-associated processes or complexes, including the splicing and transcriptional elongation machineries (protein phosphatase 4) and the CCR4-NOT deadenylase complex (CEP85, RNF219, and KIAA0355). Analysis of correlated patterns between endogenous preys uncovers the spatial organization of RNA regulatory structures and enables the definition of 144 core components of SGs and PBs. We report preexisting contacts between most core SG proteins under normal growth conditions and demonstrate that several core SG proteins (UBAP2L, CSDE1, and PRRC2C) are critical for the formation of microscopically visible SGs.

Keywords: BioID; PP4 complex; PRRC2C; UBAP2L; mass spectrometry; membraneless organelle; processing body; proximity-based labeling; ribonucleoprotein complex; stress granule.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Carrier Proteins / metabolism
Cytoplasm / metabolism
Cytoplasm / ultrastructure*
Cytoplasmic Granules / metabolism*
DNA-Binding Proteins / metabolism
Humans
Intracellular Space
Proteins / metabolism
RNA / metabolism
RNA, Messenger / metabolism*
RNA-Binding Proteins / metabolism
Stress, Physiological

Substances

CSDE1 protein, human
Carrier Proteins
DNA-Binding Proteins
Proteins
RNA, Messenger
RNA-Binding Proteins
Ubap2L protein, human
PRRC2A protein, human
RNA

Grants and funding

FDN 143301/CIHR/Canada