Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint [RNA-Seq]

NELF and Integrator are key regulators of promoter-proximal pausing and premature termination. Integrator subunit 12 (INTS12) contains a PHD domain within a flexible linker. While PHDs generally bind histones, we identify an interaction between the INTS12 PHD and a domain in the flexible C-terminal tentacle of NELF-A. Mutation of either domain disrupts the interaction, and although RNAPII-associated pausing complexes form, they are dysfunctional. Importantly, upon NELF-A mutation, interactions of the Integrator-containing pausing complex with transcriptional activators become apparent that correlate with increased pause-escape. Indeed, while INTS12 PHD loss functionally mimics Integrator loss, NELF-A mutation mimics loss of NELF, although the RNAPII pause position does not change. This supports a model in which Integrator is an integral component of the promoter-proximal pausing complex, and where INTS12’s PHD either interacts with NELF-A to pause/terminate transcription or enables interaction with activators and positive transcription regulators to allow pause-escape.