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Programmable control of spatial transcriptome in live cells and neurons.
Mengting Han1, Maylin L Fu1, Yanyu Zhu1
1Department of Bioengineering, Stanford University, Stanford, CA, USA.
Nature
|May 21, 2025
Summary
Scientists developed CRISPR-mediated transcriptome organization (CRISPR-TO) to control RNA location in cells. This tool allows researchers to study how RNA positioning affects cell functions and diseases in real-time.
Area of Science:
- Cell Biology
- Molecular Biology
- Genetics
Background:
- Spatial RNA organization is crucial for cellular functions and disease pathogenesis.
- Current technologies are limited in perturbing endogenous RNA within specific subcellular regions, hindering functional studies.
- Understanding the spatial transcriptome is essential for deciphering cellular processes.
Purpose of the Study:
- To develop a novel system for programmable control of endogenous RNA localization in live cells.
- To enable functional interrogation of the spatial transcriptome by perturbing RNA localization.
- To investigate the role of RNA localization in neuronal development and function.
Main Methods:
- CRISPR-mediated transcriptome organization (CRISPR-TO) system utilizing nuclease-dead dCas13.
- Targeted localization of endogenous RNAs to various subcellular compartments (mitochondria, p-bodies, stress granules, etc.).
- Inducible and reversible RNA transport along microtubules using motor proteins.
Main Results:
- CRISPR-TO successfully targeted RNAs to diverse subcellular locations in multiple cell types.
- Demonstrated inducible and reversible RNA transport along microtubules in living cells.
- Repositioned mRNAs were translated locally in neurons, influencing filopodial protrusion and axonal regeneration.
- CRISPR-TO screening identified Stmn2 mRNA localization as a key regulator of neurite outgrowth.
Conclusions:
- CRISPR-TO provides a versatile platform for manipulating and studying RNA localization dynamics in live cells.
- This system bridges a gap in technologies for functional interrogation of the spatial transcriptome.
- CRISPR-TO enables high-throughput screening of RNA localization effects in biological processes and disease models.
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