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

Abstract

Summary 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.

Selective roles of vertebrate PCF11 in premature and full-length transcript termination

“…55 genes showed simultaneously decreased CPA and termination ( Figure S7A). Premature termination in the absence of a detectable polyadenylated product most likely reflects the unstable nature of such transcripts (Chiu et al, 2018). In the reverse scenario, decreased intragenic PAS usage without associated changes in termination possibly reflects the uncoupling of CPA and termination as described in Figure 2.…”

The INO80 ATP-dependent chromatin remodelling complex alleviates stalled Polymerase II to promote non-coding RNA transcription termination

“…Promoter-proximal transcriptional pausing has recently been linked to premature termination in metazoans (Chiu et al, 2018;Erickson et al, 2018;Krebs et al, 2017;Steurer et al, 2018).…”

“…Recent studies in metazoans have suggested that RNA polymerases paused proximally to promoters are targeted for premature termination, with the released RNA undergoing degradation (Chiu et al, 2018;Krebs et al, 2017). To test whether promoter-proximal pausing in yeast is associated with premature termination, we calculated and compared the TR WT and TII Mtr4 for the first 200nt after TSS.…”

“…In mammals, short, promoter-associated polyadenylated RNAs have been identified (Kapranov et al, 2007). Here, premature termination and exosome-dependent degradation of mRNA transcripts for a large class of protein-coding genes has been recently described to coincide with promoter-proximal RNAPII pausing sites (Chiu et al, 2018). Experiments with chemical transcriptional inhibitors indicated high rates of turnover and premature termination of promoter-proximal paused RNAPII (Erickson et al, 2018;Krebs et al, 2017;Steurer et al, 2018), suggesting regulation of gene expression by transcriptional attenuation.…”

“…ATP-dependent chromatin remodelling enzymes shape the chromatin landscape and act at almost all stages of RNA production controlling transcription activation and silencing, modulation of transcriptional rates, transcription termination and RNA export from the nucleus (Babour et al, 2016;Boeger et al, 2008;Morillon et al, 2003;Smolle et al, 2012;Whitehouse et al, 2007). In mammals, premature termination of mRNA genes and promoter-proximal transcriptional pausing have been associated with nucleosome organization (Chiu et al, 2018). However, the role of chromatin remodelers in co-transcriptional RNA quality control remains elusive.…”