Elongation rate of RNA polymerase II affects pausing patterns across the 3’ UTR

Yeast mRNAs are polyadenylated at multiple sites in their 3’ untranslated regions (3’UTRs), and poly(A) site usage is regulated by the rate of transcriptional elongation by RNA polymerase II (Pol II). Slow Pol II derivatives favor upstream poly(A) sites and fast Pol II derivatives favor downstream poly(A) sites. Transcriptional elongation and polyadenylation are linked at the nucleotide level, presumably reflecting Pol II dwell time at each residue that influences the level of polyadenylation. Here, we investigate the relationship between Pol II pause sites and poly(A) sites within 3’UTRs. Elongation behavior of RPO21 variants bearing point mutations that affect RNA polymerase II elongation speed were assayed by NET-seq in biological duplicate. Polyadenylation patterns in ubp8Δ and rpb4Δ deletion strains were profiled using 3'READS in biological duplicate.