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Super-resolved imaging of mRNA ultrastructure in cells

Passera, A.; Welzl, P.; Gomez-Segalas, A.; Plaschka, C.; Balzarotti, F.

2026-01-23 biophysics
10.64898/2026.01.23.701081 bioRxiv
Show abstract

Messenger RNA (mRNA) is a central polymer of gene expression, whose ultrastructure and defining regulatory rules remain unclear. To visualize the ultrastructure of mRNA, we here develop Combi-PAINT, a powerful and generalizable method for combinatorial super-resolved DNA-PAINT multiplexing, which we combine with high-efficiency RNA labelling and MINFLUX microscopy. This approach enables the nanometer-precision tracing of mRNA in three dimensions in cells. We use Combi-PAINT to visualize multiple distinct mRNA species inside the human cell nucleus and cytoplasm, revealing their quantitative ultrastructures and transcript-specific molecular patterns. By bridging sequence specificity with nanometer resolution, we provide a new lens for studying the cellular life of mRNA.

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