DataSets / Project home (RNA Bodies)
Proximity based map of proteins involved in mRNA life cycle reveals network of protein complexes in RNA-containing bodies
First Author: Jiyoung Youn
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 P-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 1792 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, 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 pre-existing 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.

This dataset is part of a manuscript published in Molecular Cell, alongside a Preview by Simon Alberti and a profile of first author Ji-Young Youn. Also see linked paper in Cell by Gene Yeo's group.

Please contact Anne-Claude Gingras (gingras@lunenfeld.ca) for details.


Navigating this website

• The data included here is by default filtered with AvgP ≥ 0.95, as calculated by SAINTexpress; unselect the "high confidence" buttons to view all data. You can also download a complete interactome table through the Supplementary data section (left).

Select "Explore baits" (left) to view all baits profiled, organized alphabetically (view as a list). Clicking on a bait will retrieve all its interactors (high confidence by default) and indicate which interactions are already deposited in the BioGRID and IntAct databases.

• Selecting multiple baits (or all baits) will enable a download of the SAINT result file that can be opened at ProHits-viz for visualization and further exploration.

• Also see the many links to excellent external resources for the baits and/or preys, including ProteinAtlas, ProteomicsDB, NCBI Gene, GeneCards and UniProt.

• Search for a bait or prey by Official Gene Symbol through the "Search" tab on left (or at the top). You will be able to search across all projects you have access to.

• Please see the Supplementary Data tab for additional figures, tables and input files for Cytoscape and prohits-viz.

Note that the mass spectrometry data has been deposited at MassIVE.


Copyright © 2012 Gingras labs, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital.