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

• Published in: Molecular cell Vol. 69; no. 3; pp. 517 - 532.e11
• Main Authors: Youn, Ji-Young, Dunham, Wade H., Hong, Seo Jung, Knight, James D.R., Bashkurov, Mikhail, Chen, Ginny I., Bagci, Halil, Rathod, Bhavisha, MacLeod, Graham, Eng, Simon W.M., Angers, Stéphane, Morris, Quaid, Fabian, Marc, Côté, Jean-François, Gingras, Anne-Claude
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.02.2018
• Subjects: BioID; biotinylation; cytoplasmic granules; granules; humans; mass spectrometry; membraneless organelle; messenger RNA; PP4 complex; processing body; proteins; proximity-based labeling; PRRC2C; ribonucleases; ribonucleoprotein complex; stress granule; transcription (genetics); translation (genetics); UBAP2L; BioID; membraneless organelle; ribonucleoprotein complex; proximity-based labeling; stress granule; processing body; mass spectrometry; PRRC2C; PP4 complex; UBAP2L
• ISSN: 1097-2765; 1097-4164; 1097-4164
• DOI: 10.1016/j.molcel.2017.12.020

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. [Display omitted] •We performed BioID on 119 human proteins involved in various facets of mRNA biology•Proximal relationships reveal the spatial organization of RNA regulatory structures•Prey-based analysis identifies 144 protein components of cytosolic RNA granules•UBAP2L, CSDE1, and PRRC2C are required for efficient formation of stress granules Youn et al. performed proximity-based proteomics on 119 human proteins involved in the mRNA life cycle, focusing on cytosolic RNA granule components that are important for mRNA regulation. Systematic analysis of the proximal interactome revealed 144 core components of cytosolic RNA granules and illuminated the spatial organization of RNA regulatory structures.