Elongation rate of RNA polymerase II affects pausing patterns across the 3’ UTR. 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. Overall design: 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.

酵母mRNA的3'非翻译区（3' untranslated regions, 3’UTRs）存在多个多聚腺苷酸化位点，且poly(A)位点的使用情况受RNA聚合酶II（RNA polymerase II, Pol II）的转录延伸速率调控。转录速度较慢的Pol II突变体倾向于选用上游的poly(A)位点，而转录速度较快的Pol II突变体则偏好下游的poly(A)位点。转录延伸与多聚腺苷酸化在核苷酸水平上存在关联，这大概率反映了Pol II在每个核苷酸残基上的停留时间会影响多聚腺苷酸化的水平。本研究旨在探究3’UTRs内Pol II暂停位点与poly(A)位点之间的关联。实验总体设计：通过NET-seq技术对携带可影响RNA聚合酶II延伸速度的点突变的RPO21变体的延伸行为进行检测，设置两次生物学重复；利用3'READS技术对ubp8Δ和rpb4Δ基因缺失菌株的多聚腺苷酸化模式进行分析，同样设置两次生物学重复。