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

Negative Elongation Factor (NELF) and Integrator are general regulators of transcriptional pausing and premature termination at the beginning of protein-coding genes. While NELF is a key pausing factor, Integrator triggers premature termination of dysfunctional RNAPII complexes. Here, we identify a direct interaction between the plant homeodomain (PHD) finger of Integrator subunit 12 (INTS12) and a previously unrecognized C-terminal domain (CTD) in the flexible tentacle of NELF-A. Mutation of either domain disrupts the interaction, and although RNAPII-associated pausing complexes still form, they are dysfunctional. Importantly, while deletion of the INTS12 PHD finger functionally mimics Integrator loss, a single point mutation in NELF-A CTD instead mimics loss of NELF, suggesting the presence of competitive interactions. Together, our findings uncover a novel mode of PHD finger binding and outline how an interaction between Integrator and NELF regulates transcriptional pausing and premature termination.