RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex

Cell Rep. 2022 Apr 26;39(4):110732. doi: 10.1016/j.celrep.2022.110732.


RNA polymerase II (Pol II)-mediated transcription in metazoans requires precise regulation. RNA Pol II-associated protein 2 (RPAP2) was previously identified to transport Pol II from cytoplasm to nucleus and dephosphorylates Pol II C-terminal domain (CTD). Here, we show that RPAP2 binds hypo-/hyper-phosphorylated Pol II with undetectable phosphatase activity. The structure of RPAP2-Pol II shows mutually exclusive assembly of RPAP2-Pol II and pre-initiation complex (PIC) due to three steric clashes. RPAP2 prevents and disrupts Pol II-TFIIF interaction and impairs in vitro transcription initiation, suggesting a function in inhibiting PIC assembly. Loss of RPAP2 in cells leads to global accumulation of TFIIF and Pol II at promoters, indicating a critical role of RPAP2 in inhibiting PIC assembly independent of its putative phosphatase activity. Our study indicates that RPAP2 functions as a gatekeeper to inhibit PIC assembly and transcription initiation and suggests a transcription checkpoint.

Keywords: CP: Molecular biology; Pol II; RPAP2; pre-initiation complex; transcription initiation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus* / metabolism
  • Phosphoric Monoester Hydrolases / metabolism
  • Promoter Regions, Genetic / genetics
  • RNA Polymerase II* / metabolism


  • RNA Polymerase II
  • Phosphoric Monoester Hydrolases