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RNA Proximity Labeling: A New Detection Tool for RNA–Protein Interactions

Interfaculty Institute for Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany
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Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Inmaculada Segura and Sandra M. Fernandez-Moya
Molecules 2021, 26(8), 2270; https://doi.org/10.3390/molecules26082270
Received: 15 March 2021 / Revised: 9 April 2021 / Accepted: 10 April 2021 / Published: 14 April 2021
(This article belongs to the Special Issue Neurochemistry of RNA in Health and Disease)
Multiple cellular functions are controlled by the interaction of RNAs and proteins. Together with the RNAs they control, RNA interacting proteins form RNA protein complexes, which are considered to serve as the true regulatory units for post-transcriptional gene expression. To understand how RNAs are modified, transported, and regulated therefore requires specific knowledge of their interaction partners. To this end, multiple techniques have been developed to characterize the interaction between RNAs and proteins. In this review, we briefly summarize the common methods to study RNA–protein interaction including crosslinking and immunoprecipitation (CLIP), and aptamer- or antisense oligonucleotide-based RNA affinity purification. Following this, we focus on in vivo proximity labeling to study RNA–protein interactions. In proximity labeling, a labeling enzyme like ascorbate peroxidase or biotin ligase is targeted to specific RNAs, RNA-binding proteins, or even cellular compartments and uses biotin to label the proteins and RNAs in its vicinity. The tagged molecules are then enriched and analyzed by mass spectrometry or RNA-Seq. We highlight the latest studies that exemplify the strength of this approach for the characterization of RNA protein complexes and distribution of RNAs in vivo. View Full-Text
Keywords: RNA–protein complex; proximity labeling; biotin ligase; ascorbate peroxidase; RNA-binding protein; subcellular transcriptomics RNA–protein complex; proximity labeling; biotin ligase; ascorbate peroxidase; RNA-binding protein; subcellular transcriptomics
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MDPI and ACS Style

Weissinger, R.; Heinold, L.; Akram, S.; Jansen, R.-P.; Hermesh, O. RNA Proximity Labeling: A New Detection Tool for RNA–Protein Interactions. Molecules 2021, 26, 2270. https://doi.org/10.3390/molecules26082270

AMA Style

Weissinger R, Heinold L, Akram S, Jansen R-P, Hermesh O. RNA Proximity Labeling: A New Detection Tool for RNA–Protein Interactions. Molecules. 2021; 26(8):2270. https://doi.org/10.3390/molecules26082270

Chicago/Turabian Style

Weissinger, Ronja, Lisa Heinold, Saira Akram, Ralf-Peter Jansen, and Orit Hermesh. 2021. "RNA Proximity Labeling: A New Detection Tool for RNA–Protein Interactions" Molecules 26, no. 8: 2270. https://doi.org/10.3390/molecules26082270

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