Single-molecule live imaging of subunit interactions and exchange within cellular regulatory complexes

Cells are built from vast networks of competing molecular interactions, most of which have been impossible to monitor in vivo. We recently devised a new strategy, proximity-assisted photoactivation (PAPA), to detect these interactions at single-molecule resolution in live cells. Here we apply PAPA to visualize the network of interactions that regulate the central transcription elongation factor P-TEFb. PAPA between multiple pairs of endogenous proteins, combined with fast single-molecule tracking (fSMT), revealed that inactive P-TEFb within the 7SK ribonucleoprotein complex is largely unbound to chromatin, that this complex dissociates within minutes of treatment with a P-TEFb kinase inhibitor, and that heterogeneous ribonucleoproteins (hnRNPs) bind 7SK concomitant with P-TEFb release. Unlike 7SK-bound P-TEFb, P-TEFb associated with the coactivator BRD4 exhibited increased binding to chromatin. Our results address longstanding questions about a key transcriptional regulator and demonstrate that PAPA-fSMT can probe subunit interactions and exchange within endogenous regulatory complexes in live cells.