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Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci. 2018;5:90doi: 10.3389/fmolb.2018.00090.
Giambruno, R., Mihailovich, M., & Bonaldi, T. (2018). Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Frontiers in molecular biosciences, 590. https://doi.org/10.3389/fmolb.2018.00090
Giambruno, Roberto, et al. "Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World." Frontiers in molecular biosciences vol. 5 (2018): 90. doi: https://doi.org/10.3389/fmolb.2018.00090
Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci. 2018 Nov 08;5:90. doi: 10.3389/fmolb.2018.00090. eCollection 2018. PMID: 30467545; PMCID: PMC6236024.
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Front Mol Biosci. 2018 Nov 08;5:90. doi: 10.3389/fmolb.2018.00090. eCollection 2018.

Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World.

Frontiers in molecular biosciences

Roberto Giambruno, Marija Mihailovich, Tiziana Bonaldi

Affiliations

  1. Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.

PMID: 30467545 PMCID: PMC6236024 DOI: 10.3389/fmolb.2018.00090

Abstract

The interaction between non-coding RNAs (ncRNAs) and proteins is crucial for the stability, localization and function of the different classes of ncRNAs. Although ncRNAs, when embedded in various ribonucleoprotein (RNP) complexes, control the fundamental processes of gene expression, their biological functions and mechanisms of action are still largely unexplored. Mass Spectrometry (MS)-based proteomics has emerged as powerful tool to study the ncRNA world: on the one hand, by identifying the proteins interacting with distinct ncRNAs; on the other hand, by measuring the impact of ncRNAs on global protein levels. Here, we will first provide a concise overview on the basic principles of MS-based proteomics for systematic protein identification and quantification; then, we will recapitulate the main approaches that have been implemented for the screening of ncRNA interactors and the dissection of ncRNA-protein complex composition. Finally, we will describe examples of various proteomics strategies developed to characterize the effect of ncRNAs on gene expression, with a focus on the systematic identification of microRNA (miRNA) targets.

Keywords: RNA-affinity purifications; SILAC; gene expression; mass spectrometry; miRNA; ncRNA; proteome

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