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

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) ana...

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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
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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. [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.
AbstractList	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. 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. 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. 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.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.
Author	Gingras, Anne-Claude Hong, Seo Jung Rathod, Bhavisha Fabian, Marc Knight, James D.R. Eng, Simon W.M. Côté, Jean-François Bagci, Halil Angers, Stéphane Morris, Quaid Dunham, Wade H. MacLeod, Graham Youn, Ji-Young Chen, Ginny I. Bashkurov, Mikhail
Author_xml	– sequence: 1 givenname: Ji-Young surname: Youn fullname: Youn, Ji-Young organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 2 givenname: Wade H. surname: Dunham fullname: Dunham, Wade H. organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 3 givenname: Seo Jung surname: Hong fullname: Hong, Seo Jung organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 4 givenname: James D.R. surname: Knight fullname: Knight, James D.R. organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 5 givenname: Mikhail surname: Bashkurov fullname: Bashkurov, Mikhail organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 6 givenname: Ginny I. surname: Chen fullname: Chen, Ginny I. organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 7 givenname: Halil surname: Bagci fullname: Bagci, Halil organization: Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada – sequence: 8 givenname: Bhavisha surname: Rathod fullname: Rathod, Bhavisha organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada – sequence: 9 givenname: Graham surname: MacLeod fullname: MacLeod, Graham organization: Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada – sequence: 10 givenname: Simon W.M. surname: Eng fullname: Eng, Simon W.M. organization: Department of Immunology, University of Toronto, Toronto, ON, Canada – sequence: 11 givenname: Stéphane surname: Angers fullname: Angers, Stéphane organization: Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada – sequence: 12 givenname: Quaid surname: Morris fullname: Morris, Quaid organization: Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada – sequence: 13 givenname: Marc surname: Fabian fullname: Fabian, Marc organization: Department of Oncology, McGill University, Montréal, QC, Canada – sequence: 14 givenname: Jean-François surname: Côté fullname: Côté, Jean-François organization: Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada – sequence: 15 givenname: Anne-Claude surname: Gingras fullname: Gingras, Anne-Claude email: gingras@lunenfeld.ca organization: Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/29395067$$D View this record in MEDLINE/PubMed
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Snippet	mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless...
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SubjectTerms	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
Title	High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies
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