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Reposted by Jorge Trojanowski

Sinem Saka @sinemsaka.bsky.social · 27/04/2026

Cells are not just bags of molecules. Function depends on spatial interactions: RNAs and/or proteins come together with interaction partners to drive regulation and function. In our new preprint, we introduce ProPER, a novel method for in situ proximity detection. Preprint: tinyurl.com/muju86s6

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

7/ Special thanks to all Saka lab members who helped with the clay animation. #proximity #SpatialBiology #RNA #lifecycle

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

6/ This project is a team effort involving multiple members of the Saka lab. Eva-Maria Geissen from the EMBL Data Science Center contributed the kinetic modeling. We’re grateful for funding from the EIPOD4 programme (Marie Skłodowska Curie Actions, Grant agreement number 847543).

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

5/ ProPER integrates naturally with various in situ modalities including protein-, RNA- and metabolic-labeling. We’re excited about its capability to perform logical operations in situ, e.g. to record multivalent proximities by converting and adding barcode sequences to the growing DNA concatemer.

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

4/ We performed multiplex detection of RNA life cycle stages on the same molecule detecting proximity to splicing and translation markers. We traced back differences in the induction kinetics of 2 inflammatory genes to states including transcription site-bound splicing and dispersed splicing.

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

3/ We observed efficient and dense labeling of interaction sites, as exemplified by two microtubule components. The limited size of the DNA product allows to resolve more continuous and compact structures when compared to the proximity ligation assay (PLA) products.

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

2/ ProPER implements in situ proximity extension by leveraging primer exchange reaction. The hairpin extends its cognate primer when they are in physical proximity. Proximity-encoded DNA barcodes are recorded into single stranded DNA concatemers, which are read out by fluorescent oligos @embl.org

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Jorge Trojanowski @jorgetrojanowski.bsky.social · 27/04/2026

1/ ProPER - Our novel ligation-free proximity detection method for efficient multiplexed imaging of molecular interactions in situ. Among other things we use it to image the life cycle of RNA molecules and resolve differential kinetics of gene expression steps. New preprint: doi.org/10.64898/202...

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