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Directed evolution of a genetically encoded photocatalyst for temporally resolved proximity labeling of subcellular RNAs and proteins

ABSTRACT: In eukaryotic cells, the precise spatial localization of RNAs and proteins is essential for proper cellular function. Genetically encoded photocatalytic proximity labeling techniques have expanded our ability to map subcellular proteomes and transcriptomes, but their temporal resolution remains limited. Here, we introduce Lantern, an engineered flavoprotein optimized via directed evolution, which enables sub‑minute, spatially resolved labeling of cellular biomolecules. Lantern is targetable to diverse subcellular compartments, including the endoplasmic reticulum, mitochondria, and stress granules (SGs), to map local transcriptomes (CAP-seq) and proteomes (CAP-MS). Using Lantern, we observed that m6A‑enriched RNAs are recruited to SGs within five minutes of stress induction, while ER‑proximal RNAs associate with the SG scaffold protein G3BP1 during early SG assembly. Additionally, Lantern was adapted for cell-surface tagging (CAP-CELL), enabling spatially resolved cell typing and the analysis of cell-cell interactions. Collectively, this study establishes Lantern as a powerful tool that offers unprecedented temporal resolution for investigating the dynamic organization of subcellular molecular networks.

ORGANISM(S): Mus musculus Rattus norvegicus Homo sapiens

PROVIDER: GSE292673 | GEO | 2026/03/27

REPOSITORIES: GEO

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	GSE292673_ERM_all_counts.xlsx	Xlsx
	GSE292673_GLORI2_As_ratio0.1.xlsx	Xlsx
	GSE292673_GLORI2_basal_ratio0.1.xlsx	Xlsx
	GSE292673_HEK293T_SG_all_counts.xlsx	Xlsx

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