Fig. 3: PHOTON captures transcriptome information within subcellular compartments.

A Representative images of photocleaving cDNA molecules within nucleoli (white outlines). Scale bar, 2 µm. n = 2 independent experiments. B Heatmap showing the top-enriched RNA species in the nucleolus identified using the PHOTON data. C Representative images of photocleaving cDNA molecules (cyan) in sodium arsenite-induced SGs (magenta). SGs with white dashed outlines were targeted for photocleavage. Scale bar, 1 µm. n = 3 independent experiments. D HCR-FISH images showing the spatial distribution of ZMIZ1, EP400, AHNAK2, and ZACN mRNAs (green) in relation to sodium arsenite-induced SGs (red) in HeLa cells. Line graphs on the right show the intensity profiles of both the mRNA signal (green line) and the SG signal (red line) along the yellow line in the inserts. Scale bar, 2 µm. n = 1 experiment.