TY - JOUR
T1 - SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes
AU - Brannan, Kristopher W.
AU - Jin, Wenhao
AU - Huelga, Stephanie C.
AU - Banks, Charles A.S.
AU - Gilmore, Joshua M.
AU - Florens, Laurence
AU - Washburn, Michael P.
AU - Van Nostrand, Eric L.
AU - Pratt, Gabriel A.
AU - Schwinn, Marie K.
AU - Daniels, Danette L.
AU - Yeo, Gene W.
N1 - Funding Information:
The authors would like to thank members of the Yeo lab, especially Olga Botvinnik and Katannya Kapeli for critical reading of the manuscript. This work was supported by grants from the NIH (HG004659, U54HG007005, and NS075449 to G.W.Y.). C.A.S.B., J.M.G., L.F., and M.P.W. are supported by the Stowers Institute for Medical Research. E.L.V.N. is a Merck Fellow of the Damon Runyon Cancer Research Foundation (DRG-2172-13). G.W.Y. is an Alfred P. Sloan Research Fellow. G.A.P. is a National Science Foundation Graduate Fellow and was partially supported by the University of California, San Diego, Genetics Training Program through an institutional training grant from the National Institute of General Medical Sciences, T32 GM008666. K.W.B. is a University of California President’s Postdoctoral Fellow and was partially supported by the California Institute for Regenerative Medicine Training Program (CIRM).
Publisher Copyright:
© 2016 Elsevier Inc.
PY - 2016/10/20
Y1 - 2016/10/20
N2 - RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.
AB - RNA metabolism is controlled by an expanding, yet incomplete, catalog of RNA-binding proteins (RBPs), many of which lack characterized RNA binding domains. Approaches to expand the RBP repertoire to discover non-canonical RBPs are currently needed. Here, HaloTag fusion pull down of 12 nuclear and cytoplasmic RBPs followed by quantitative mass spectrometry (MS) demonstrates that proteins interacting with multiple RBPs in an RNA-dependent manner are enriched for RBPs. This motivated SONAR, a computational approach that predicts RNA binding activity by analyzing large-scale affinity precipitation-MS protein-protein interactomes. Without relying on sequence or structure information, SONAR identifies 1,923 human, 489 fly, and 745 yeast RBPs, including over 100 human candidate RBPs that contain zinc finger domains. Enhanced CLIP confirms RNA binding activity and identifies transcriptome-wide RNA binding sites for SONAR-predicted RBPs, revealing unexpected RNA binding activity for disease-relevant proteins and DNA binding proteins.
KW - machine-learning
KW - protein-protein interaction networks
KW - RNA-binding proteins
KW - support vector machine
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U2 - 10.1016/j.molcel.2016.09.003
DO - 10.1016/j.molcel.2016.09.003
M3 - Article
C2 - 27720645
AN - SCOPUS:84992157070
VL - 64
SP - 282
EP - 293
JO - Molecular Cell
JF - Molecular Cell
SN - 1097-2765
IS - 2
ER -