Genome-Wide Mapping of Decay Factor-mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets...

Area of Science:

• Molecular Biology
• Yeast Genetics
• Gene Regulation

Background:

• The Ccr4-Not complex is a key regulator of cellular stress responses, controlling gene expression at multiple stages.
• Ccr4, a core subunit, is the primary cytoplasmic deadenylase in yeast, but its genome-wide mRNA targets remain uncharacterized.

Purpose of the Study:

• To identify genome-wide mRNA targets bound by Ccr4 and its associated proteins Dhh1 and Puf5.
• To elucidate the role of Ccr4 in mRNA decay and its relationship with other regulatory complexes.

Main Methods:

• RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) was employed to map RNAs bound to Ccr4, Dhh1, and Puf5.
• Analysis focused on the location of protein binding on transcripts and correlation with mRNA abundance and decay rates.

Main Results:

• Ccr4, Dhh1, and Puf5 preferentially bind to lowly abundant mRNAs, predominantly at the 3' end.
• These proteins are recruited to mRNAs targeted by decay-promoting and translation-inhibiting factors.
• Ccr4 recruitment correlates strongly with mRNA decay rates, suggesting a primary role in transcript degradation.
• Ccr4-bound mRNAs are resistant to regulation by the Pan2/3 deadenylation complex, indicating a division of labor.

Conclusions:

• The Ccr4-Not complex, along with Dhh1 and Puf5, plays a significant role in mRNA decay, particularly for transcripts involved in nutrient utilization and stress responses.
• Ccr4's primary function appears to be controlling transcript abundance through mRNA decay, with distinct roles compared to the Pan2/3 complex.
• These findings provide insights into the regulation of gene expression during nutrient starvation and stress conditions in yeast.