Comprehensive in vivo identification of the c-Myc mRNA interactome using HyPR-MS
- Michele Spiniello1,
- Maisie I. Steinbrink2,
- Anthony J. Cesnik2,
- Rachel M. Miller2,
- Mark Scalf2,
- Michael R. Shortreed2 and
- Lloyd M. Smith2,3
- 1 University of Wisconsin - Madison, Department of Chemistry; University of Studi della Campania Luigi Vanvitelli, Department of Medicine of Precision; Cardarelli Hospital, Division of Immuno-Hematology and Transfusion Medicine;
- 2 University of Wisconsin - Madison, Department of Chemistry
- ↵* Corresponding author; email: smith{at}chem.wisc.edu
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 analyze 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.
Keywords
- Received May 26, 2019.
- Accepted June 27, 2019.
- Published by Cold Spring Harbor Laboratory Press for the RNA Society
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/.
