Photocatalytic Proximity Labeling Maps RNA and Protein Subcellular Landscapes

ABSTRACT: Cellular function relies on the precise spatiotemporal organization of biomolecules within organelles. Mapping the local proteome and transcriptome of specific compartments is crucial for understanding cellular processes but remains challenging. Existing proximity labeling (PL) methods based on enzymes often require genetic manipulation, can suffer from background activity, or are limited to a single molecule type. Here, we introduce a versatile photocatalytic proximity labeling (PhotoPL) platform using targeted photocatalysts and activatable probes to map both RNA and protein landscapes within defined subcellular regions in living cells. The platform's modular design allows for simple redirection to new targets by chemically conjugating the catalyst to different targeting moieties. Visible light activation of organelle-targeted ruthenium complexes generates localized singlet oxygen or initiates electron transfer, which selectively activates inert phenylselenomethyl phenol probes to generate reactive quinone methide intermediates. These intermediates rapidly crosslink proximal proteins and nucleic acids within nanometers of the catalyst. We demonstrate precise targeting of PhotoPL to mitochondria and the endoplasmic reticulum (ER), enabling high-resolution mapping of their respective proteomes and transcriptomes. Comparative analysis reveals distinct molecular signatures and co-enrichment patterns, providing insights into organelle-specific functions, RNA localization mechanisms, and protein-RNA interplay under basal and stress conditions. This chemically controlled, light-triggered PhotoPL strategy offers a powerful and highly adaptable toolbox for dissecting the molecular organization of living cells with high spatiotemporal resolution.

ORGANISM(S): Homo sapiens

PROVIDER: GSE304177 | GEO | 2026/09/26

REPOSITORIES: GEO