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Single and Combined Methods to Specifically or Bulk-Purify RNA–Protein Complexes

Authors
  • Van Ende, Roosje
  • Balzarini, Sam
  • Geuten, Koen
Type
Published Article
Journal
Biomolecules
Publisher
MDPI AG
Publication Date
Aug 07, 2020
Volume
10
Issue
8
Identifiers
DOI: 10.3390/biom10081160
PMID: 32784769
PMCID: PMC7464009
Source
PubMed Central
Keywords
License
Green

Abstract

The ribonome interconnects the proteome and the transcriptome. Specific biology is situated at this interface, which can be studied in bulk using omics approaches or specifically by targeting an individual protein or RNA species. In this review, we focus on both RNA- and ribonucleoprotein-(RNP) centric methods. These methods can be used to study the dynamics of the ribonome in response to a stimulus or to identify the proteins that interact with a specific RNA species. The purpose of this review is to provide and discuss an overview of strategies to cross-link RNA to proteins and the currently available RNA- and RNP-centric approaches to study RNPs. We elaborate on some major challenges common to most methods, involving RNP yield, purity and experimental cost. We identify the origin of these difficulties and propose to combine existing approaches to overcome these challenges. The solutions provided build on the recently developed organic phase separation protocols, such as Cross-Linked RNA eXtraction (XRNAX), orthogonal organic phase separation (OOPS) and Phenol-Toluol extraction (PTex).

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