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

Blears, D.; Bech, P.; Martinez, D. L.; Dai, P.; Shah, R. A.; Fong, N.; Han, Z.; Mitter, R.; Sheridan, R.; Johansen, J. V.; Dirac-Svejstrup, A. B.; Bentley, D.; Svejstrup, J. Q.

doi:10.64898/2026.06.30.735463

bioRxiv · 10.64898/2026.06.30.735463

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

Blears, D.·Bech, P.·Martinez, D. L.·Dai, P.·Shah, R. A.·Fong, N.·Han, Z.·Mitter, R.·Sheridan, R.·Johansen, J. V.·Dirac-Svejstrup, A. B.·Bentley, D.·Svejstrup, J. Q.

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Abstract

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.

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Blears, D., Bech, P., Martinez, D. L., Dai, P., Shah, R. A., Fong, N., Han, Z., Mitter, R., Sheridan, R., Johansen, J. V., Dirac-Svejstrup, A. B., Bentley, D., Svejstrup, J. Q.. 2026-07-01. Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint. https://doi.org/10.64898/2026.06.30.735463

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