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

• Published in: Cell reports (Cambridge) Vol. 39; no. 4; p. 110732
• Main Authors: Wang, Xinxin, Qi, Yilun, Wang, Zhenning, Wang, Li, Song, Aixia, Tao, Bolin, Li, Jiabei, Zhao, Dan, Zhang, Hongwei, Jin, Qianwei, Jiang, Yi-Zhou, Chen, Fei Xavier, Xu, Yanhui, Chen, Xizi
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 26.04.2022
• Subjects: Cell Nucleus - metabolism; Phosphoric Monoester Hydrolases - metabolism; Pol II; pre-initiation complex; Promoter Regions, Genetic - genetics; RNA Polymerase II - metabolism; RPAP2; transcription initiation; CP: Molecular biology; Pol II; pre-initiation complex; transcription initiation; RPAP2
• ISSN: 2211-1247; 2211-1247
• 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. [Display omitted] •RPAP2 binds Pol II and exhibits undetectable phosphatase activity•RPAP2 prevents Pol II-TFIIF interaction and inhibits in vitro transcription initiation•Depletion of RPAP2 in cells increases the levels of Pol II and TFIIF at promoters•Rapid degradation of RPAP2 induces enhanced transcription initiation Using structural, biochemical, and sequencing analyses, Wang et al. demonstrate that RPAP2 stably associates with Pol II, disrupts Pol II-TFIIF interaction, and inhibits transcription initiation. This study suggests a transcription pre-initiation checkpoint, in which RPAP2 functions as a gatekeeper to inhibit pre-initiation complex (PIC) assembly and transcription initiation.