Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP

Regulation of RNA polymerase II (Pol II) elongation is a critical step in gene regulation. Here, we report that U1 snRNP recognition and transcription pausing at stable nucleosomes are linked through premature polyadenylation signal (PAS) termination. By generating RNA exosome conditional deletion mouse embryonic stem cells, we identified a large class of polyadenylated short transcripts in the sense direction destabilized by the RNA exosome. These PAS termination events are enriched at the first few stable nucleosomes flanking CpG islands and suppressed by U1 snRNP. Thus, promoter-proximal Pol II pausing consists of two processes: TSS-proximal and +1 stable nucleosome pausing, with PAS termination coinciding with the latter. While pausing factors NELF/DSIF only function in the former step, flavopiridol-sensitive mechanism(s) and Myc modulate both steps. We propose that premature PAS termination near the nucleosome-associated pause site represents a common transcriptional elongation checkpoint regulated by U1 snRNP recognition, nucleosome stability, and Myc activity. [Display omitted] •Promoter-proximal PAS termination in the sense direction, a checkpoint for elongation•Prematurely PAS-terminated RNA is targeted by the RNA exosome•U1 snRNP suppresses PAS termination at first stable nucleosomes flanking CpG islands•Pol II pause at +1 stable nucleosomes is associated with premature PAS termination Chiu and Suzuki et al. report promoter-proximal premature polyadenylation signal (PAS) termination events in the sense direction, targeted by the RNA exosome, for a large class of mammalian promoters. Premature PAS termination coincides with RNA polymerase II pause sites associated with +1 stable nucleosomes and represents a common transcriptional elongation checkpoint regulated by U1 snRNP and Myc.