Special Biochemistry Seminar

Gene regulation in metazoans involves promoter-proximal pausing of RNA polymerase II (Pol II). The elongation factor complexes DSIF and NELF bind Pol II to orchestrate promoter-proximal pausing after the synthesis of a 20-60nt pre-mRNA. While the paused Pol II can proceed into productive transcription elongation, it can also be prematurely terminated by the ~1.6 MDa Integrator-PP2A complex which cleaves the nascent RNA and dephosphorylates Pol II and associated pausing factors. The Integrator-PP2A complex is highly conserved and regulates Pol II transcription genome wide.

However, the structural basis for Integrator-dependent promoter-proximal regulation of Pol II is not known.

I will present our recent cryo-EM structures of the Integrator-PP2A complex in different functional states. First, the structure of the free complex reveals a closed and inactive state. Second, a pretermination complex of Integrator-PP2A bound to the paused Pol II-DSIF-NELF complex shows how Integrator undergoes dramatic conformational changes to bind Pol II, and the pausing factors and occludes binding of SPT6 and PAF1c that activate transcription elongation. Integrator optimally positions its nuclease and PP2A phosphatase close to their respective substrates, the exiting RNA and the Pol II C-terminal repeat domain. Unexpectedly, we find that, the Integrator nuclease not only cuts nascent RNA but degrades it to unravel the DNA-RNA hybrid bound inside the Pol II cleft to trigger transcription termination. Finally, a structure of Integrator-PP2A bound to Pol II in the post-termination state explains how Pol II is removed from Integrator after termination.

Together, these findings lead to a three-step comprehensive model for how Integrator terminates Pol II transcription during promoter-proximal pausing.