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

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.

Automated summary

This study identified a novel protein, RPAP2, which plays an important regulatory role in transcription initiation and DNA replication. RPAP2 inhibits the assembly of the pre-initiation complex (PIC) by preventing the interaction between Pol II and TFIIF, thereby limiting the transcription initiation of genes. Loss of RPAP2 leads to the accumulation of TFIIF and Pol II at the promoter regions, affecting gene expression.