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bioRxiv · 10.64898/2026.09.29.755375

Programmable sequence-resolved in situ profiling of glycoRNA-protein interactomes by GlycoRNA-Map

Zhang, X.·Zhu, Y.·Baumer, K.·Lu, Y.·Fu, Y.·Liao, J.·Shao, X.·Chang, Y.·Qiao, E.·Dong, H.·Valverde, A. S.·Yeh, H.-C.·Chen, S.-H.·Renata, H.·Ma, Y.
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Abstract

Cell-surface glycoRNAs participate in diverse biological processes, but they were investigated as pooled populations and the protein interactome of individual glycoRNA species remain unresolved. Here we develop GlycoRNA-Map, a programmable photocatalytic proximity-labeling method that maps proteins surrounding sequence-defined endogenous glycoRNAs on living cells. A sialic-acid-binding aptamer and an RNA-hybridization probe jointly recruit a fluorophore-modified oligonucleotide through dual recognition of the glycan and RNA moieties of glycoRNAs. Light-activated biotinylation followed by quantitative mass spectrometry identified 200-418 enriched proteins for each of five glycoRNAs in A549 cells. Comparison of these proteomes revealed limited overlap among different glycoRNA sequences and across cell types, demonstrating that glycoRNA-associated protein environments depend on both RNA identity and cellular context. Transforming growth factor-{beta} receptors 1 and 2 (TGFBR1 and TGFBR2) were identified in the proximal proteomes of multiple glycoRNAs. Removal of cell-surface RNAs enhanced TGF-{beta} receptor signaling and promoted cell migration, demonstrating that glycoRNAs can functionally regulate extracellular signaling by interacting with their protein neighborhoods. GlycoRNA-Map thus provides an accessible strategy for resolving sequence-specific glycoRNA-protein interactome and discovering their roles in membrane signaling.

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Zhang, X., Zhu, Y., Baumer, K., Lu, Y., Fu, Y., Liao, J., Shao, X., Chang, Y., Qiao, E., Dong, H., Valverde, A. S., Yeh, H.-C., Chen, S.-H., Renata, H., Ma, Y.. 2026-09-30. Programmable sequence-resolved in situ profiling of glycoRNA-protein interactomes by GlycoRNA-Map. https://doi.org/10.64898/2026.09.29.755375

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