Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination

The pervasive nature of RNA polymerase II (Pol II) transcription requires efficient termination. A key player in this process is the cleavage and polyadenylation (CPA) factor PCF11, which directly binds to the Pol II C-terminal domain and dismantles elongating Pol II from DNA in vitro. We demonstrate that PCF11-mediated termination is essential for vertebrate development. A range of genomic analyses, including mNET-seq, 3′ mRNA-seq, chromatin RNA-seq, and ChIP-seq, reveals that PCF11 enhances transcription termination and stimulates early polyadenylation genome-wide. PCF11 binds preferentially between closely spaced genes, where it prevents transcriptional interference and consequent gene downregulation. Notably, PCF11 is sub-stoichiometric to the CPA complex. Low levels of PCF11 are maintained by an auto-regulatory mechanism involving premature termination of its own transcript and are important for normal development. Both in human cell culture and during zebrafish development, PCF11 selectively attenuates the expression of other transcriptional regulators by premature CPA and termination. [Display omitted] •Human PCF11 enhances transcription termination and 3′ end processing, genome-wide•PCF11 is substoichiometric to CPA complex due to autoregulation of its transcription•PCF11 stimulates expression of closely spaced genes but attenuates other genes•PCF11-mediated functions are conserved in vertebrates and essential in development Kamieniarz-Gdula and colleagues demonstrate that vertebrate PCF11 plays selective roles in regulating transcriptional termination and RNA 3′ end processing. It is important for efficient expression of closely spaced genes but in some cases promotes premature termination and gene downregulation. Especially PCF11 transcript levels are kept low by this attenuation mechanism.