Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS

Michele Spiniello; Maisie I. Steinbrink; Anthony J. Cesnik; Rachel M. Miller; Mark Scalf; Michael R. Shortreed; Lloyd M. Smith

doi:10.1261/rna.072157.119

Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS

¹Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
²Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Naples 80138, Italy
³Division of Immuno-Hematology and Transfusion Medicine, Cardarelli Hospital, Naples 80131, Italy

Corresponding author: smith{at}chem.wisc.edu

↵4 These authors contributed equally to this work.

Abstract

Proteins bind mRNA through their entire life cycle from transcription to degradation. We analyzed c-Myc mRNA protein interactors in vivo using the HyPR-MS method to capture the crosslinked mRNA by hybridization and then analyzed the bound proteins using mass spectrometry proteomics. Using HyPR-MS, 229 c-Myc mRNA-binding proteins were identified, confirming previously proposed interactors, suggesting new interactors, and providing information related to the roles and pathways known to involve c-Myc. We performed structural and functional analysis of these proteins and validated our findings with a combination of RIP-qPCR experiments, in vitro results released in past studies, publicly available RIP- and eCLIP-seq data, and results from software tools for predicting RNA–protein interactions.

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Footnotes

Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.072157.119.
Freely available online through the RNA Open Access option.

Received May 26, 2019.
Accepted June 27, 2019.

This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.