Datasets

Title	Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics
Organism
Number of Samples	6
Release Date	2015/05/19 00:00
Sequencing Types
Protocol Details

Title
Authors	Liu TY, Huang HH, Wheeler D, Xu Y, Wells JA, Song YS, Wiita AP
Journal	Cell systems
Publication Date	2017 Jun 28
Abstract	Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multiple myeloma cells exposed to bortezomib, a first-line chemotherapy and proteasome inhibitor. In the absence of drug effects, we found that direct measurement of protein synthesis by pSILAC correlated well with indirect measurement of synthesis from ribosome footprint density. This correlation, however, broke down under bortezomib-induced stress. By developing a statistical model integrating longitudinal proteomic and mRNA-sequencing measurements, we found that proteomics could directly detect global alterations in translational rate caused by bortezomib; these changes are not detectable by ribosomal profiling alone. Further, by incorporating pSILAC data into a gene expression model, we predict cell-stress specific proteome remodeling events. These results demonstrate that pSILAC provides an important complement to ribosome profiling in measuring proteome dynamics. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
PMC	PMC5546878
PMID	28578850
DOI

Liu et al. 2017 (PRJNA284399)