Promoter-Terminator Gene Loops Affect Alternative 3'-End Processing in Yeast.

Area of Science:

• Molecular Biology
• Yeast Genetics
• Transcriptional Regulation

Background:

• Eukaryotic genes utilize alternative polyadenylation (APA) to generate transcript variants.
• Gene looping, which brings gene ends near promoters, is implicated in transcriptional memory and initiation.
• The relationship between gene looping and APA site selection remains largely unexplored.

Purpose of the Study:

• To investigate the link between gene looping and alternative polyadenylation site selection.
• To elucidate the role of growth phase and specific factors in this process.

Main Methods:

• Utilized the KlCYC1 gene in Kluyveromyces lactis for studying alternative polyadenylation.
• Employed chromatin immunoprecipitation to track Ssu72 phosphatase activity.
• Analyzed gene loop formation (L1 and L2) and mRNA synthesis across different growth phases.

Main Results:

• Demonstrated the formation of alternative gene loops (L1 and L2) in yeast, connecting the KlCYC1 promoter to proximal or distal poly(A) sites.
• Showed that synthesis of short and long KlCYC1 mRNA isoforms and L1/L2 loop formation are dependent on the yeast growth phase.
• Found that Ssu72 phosphatase activity at poly(A) sites changes with growth phase, correlating with loop formation and APA.

Conclusions:

• Established a direct cause-and-effect relationship between gene looping and alternative poly(A) site selection.
• Highlighted the role of Ssu72 phosphatase and its phosphorylation-dependent activity in mediating this response.
• Indicated that gene looping and APA are regulated by physiological signals tied to the cell cycle and growth phase.