Elongation rate of RNA polymerase II affects pausing patterns across 3' UTRs

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Yeast messenger RNAs (mRNAs) undergo polyadenylation at multiple sites within their 3' untranslated regions (3' UTRs).
• Polyadenylation site (PAS) selection is intrinsically linked to the elongation rate of RNA polymerase II (Pol II).
• Slower Pol II elongation favors upstream PAS, while faster elongation favors downstream PAS.

Purpose of the Study:

• To investigate how Pol II elongation rate affects Pol II pausing patterns within 3' UTRs.
• To explore the relationship between Pol II pause sites and PAS.
• To understand how sequence preferences at pause sites are modulated by Pol II speed.

Main Methods:

• Analysis of Pol II pausing patterns in wild-type and mutant yeast strains with altered Pol II elongation rates.
• Sequence analysis of regions flanking Pol II pause sites.
• Utilizing a random forest classifier to predict Pol II pause sites based on genomic features.

Main Results:

• Mutations affecting Pol II elongation rate alter sequence preferences at pause sites within 3' UTRs, with distinct preferences compared to coding regions.
• The proximity of PAS to Pol II pause sites is reduced in Pol II speed mutants.
• Pol II pause sites are better predicted by the chromatin landscape than by distance to PAS in Pol II speed derivatives.

Conclusions:

• Pol II pausing and polyadenylation are intricately linked, with Pol II elongation rate playing a significant regulatory role.
• The spatial relationship between Pol II pause sites and PAS is modulated by Pol II speed.
• Chromatin landscape and transcriptional regulatory proteins contribute to the complex interplay between Pol II pausing and polyadenylation.