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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
Published on: September 28, 2017
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The search for RNA-binding proteins: a technical and interdisciplinary challenge.
Jeffrey M Smith1,2, Jarrod J Sandow1,2, Andrew I Webb1,2
1Department of Advanced Technology and Biology, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia.
Biochemical Society Transactions
|January 25, 2021
Summary
RNA-binding proteins regulate gene expression and homeostasis. Advanced methods reveal extensive RNA-protein networks, but interpretation challenges remain for researchers studying post-transcriptional regulation.
Area of Science:
- Molecular Biology
- Genetics
- Proteomics
Background:
- RNA-binding proteins (RBPs) are crucial for gene expression.
- RNA-protein interactions increasingly recognized for homeostatic regulation.
- Technological advances have expanded the known repertoire of RBPs.
Purpose of the Study:
- To review the impact of RNA-centric capture methods on understanding post-transcriptional regulation.
- To discuss the challenges in interpreting data generated by these methods for systems biology and target validation.
Main Methods:
- RNA-centric capture methods coupled with mass spectrometry-based proteomics and RNA sequencing.
- Cross-linking of proteins to RNA in native cellular environments.
- Analysis of extracted protein-RNA complexes to map regulatory networks.
Main Results:
- Significant expansion of identified RNA-binding proteins from hundreds to thousands.
- Revelation of extensive regulatory networks mediated by RNA-protein interactions.
- Identification of molecular interfaces involved in these interactions.
Conclusions:
- RNA-centric methods provide powerful snapshots of RNA-protein interactions.
- These methods have reshaped the understanding of post-transcriptional regulation.
- Technical limitations in current methods pose interpretation challenges for systems biologists and experimental researchers.
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