Extended Data Fig. 2 |. Pol II S5p correlation analysis DAPI vs. nearest neighbor distances.

a. POL II S5p tokPAINT image including DAPI overlay (same as shown in Fig. 2a). The line profiles below the image show the POL II S5p and DAPI signal distribution across the white box indicated in the image. The box first crosses two DAPI-negative regions without POL II S5p signal (presumably nucleoli) followed by a third DAPI-negative region featuring high S5p signal. b Histogram of k-nearest-neighbor distances between POL II S5p localization clusters. c To test the expected anti-correlation between DAPI intensity (as a degree of chromatin compactness) and S5p abundance, which is more associated with open chromatin, we plotted k-nearest neighbor distances (k=1,3,5) vs. normalized DAPI intensity. As expected, localization clusters with small k-nearest neighbor distances, indicating a high local abundance of the antigen, are associated with DAPI weaker regions (k=5, Pearson’s R=0.24, p<6×10⁻⁶⁸). The weak correlation could be explained by nucleoli counteracting it with DAPI weak regions deprived of S5p. d Rendering of the image in a with colors indicating 3^rd-nearest-neighbor distance. This visually confirms that DAPI-weak regions tend to feature higher local abundances of POL II S5p localization clusters^37,38. Scale bars, 3 μm.