Key Takeaways & Executive Findings
- •• Proximity labeling enables efficient isolation and purification of RNA from specific subcellular compartments, overcoming limitations of traditional methods. • RNA localization is critical for cellular functions such as localized translation, development, and synaptic plasticity, with examples like gurken and β-actin mRNAs. • The review highlights RNA-related proximity labeling tools and their applications in mapping spatiotemporal RNA dynamics. • This approach provides a powerful strategy to dissect the subcellular transcriptome, advancing understanding of gene regulation and disease mechanisms.
Abstract
The subcellular localization of RNA is critical to a variety of physiological and pathological processes. Dissecting the spatiotemporal regulation of the transcriptome is key to understanding cell function and fate. However, it remains challenging to effectively enrich and catalogue RNAs from various subcellular structures using traditional approaches. In recent years, proximity labeling has emerged as an alternative strategy for efficient isolation and purification of RNA from these intricate subcellular compartments. This review focuses on examining RNA-related proximity labeling tools and exploring their application in elucidating the spatiotemporal regulation of RNA at the subcellular level.
1. Introduction
In eukaryotic cells, biomolecules are intricately organized and localized to specific cellular compartments, essential for their functional roles. Localized mRNA can be translated to produce many copies of proteins in response to local stimuli, providing an effective means to regulate gene expression with high spatial and temporal control. RNA localization represents a critical post-transcriptional regulatory mechanism that affects a multitude of RNA-associated biochemical processes, including folding, editing, splicing, degradation, translation, and interactions with protein binding partners [1]. These processes subsequently influence the functionality and destiny of the proteins encoded by the RNA.
The subcellular localization of RNA is fundamentally connected to its functional roles. Asymmetric RNA distribution facilitates localized protein translation [2], and the three-dimensional structuring of chromatin [3], and development [4,5]. The intracellular positioning of RNA crucially influences its storage, processing, translation, and degradation.
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Jiapeng Liu, Binglin Zhong, Shuojun Li, Shuo Han (2026). Mapping subcellular RNA localization with proximity labeling. Acta Biochimica et Biophysica Sinica. https://doi.org/10.3724/abbs.2024147
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Frequently Asked Questions
What is proximity labeling and how is it used to study RNA localization?
Proximity labeling is a technique that uses enzymes to tag biomolecules in close proximity to a protein of interest. In the context of RNA, it allows for the selective enrichment and purification of RNAs that are localized to specific subcellular compartments, enabling the study of their spatial distribution and dynamics.
Why is RNA localization important for cellular function?
RNA localization is crucial for localized protein synthesis, allowing cells to respond rapidly to local stimuli. It plays key roles in development, neuronal function, and cell polarity, and its dysregulation is linked to various diseases.
What are the limitations of traditional methods for studying RNA localization?
Traditional methods like FISH and biochemical fractionation often lack the resolution to capture RNA from specific subcellular structures or are limited by low throughput and the need for cell lysis, which can disrupt spatial information.
What are some examples of localized mRNAs mentioned in the article?
Examples include gurken mRNA in Drosophila oocytes, which is involved in axis formation, and β-actin mRNA, which localizes to the leading edge of cells via a 'zip code' sequence in its 3' UTR.
How does proximity labeling compare to FISH for studying RNA localization?
While FISH provides direct visualization of RNA in fixed cells, proximity labeling offers a more unbiased and high-throughput approach to identify RNAs in specific compartments, especially in living cells, and can be coupled with sequencing for comprehensive analysis.
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