Transcriptome maps of general eukaryotic RNA degradation factors

Area of Science:

• Molecular Biology
• Yeast Genetics
• RNA Biology

Background:

• RNA degradation is crucial for cellular RNA processing, regulation, and quality control.
• Understanding RNA-binding proteins involved in degradation is key to deciphering RNA metabolism.

Purpose of the Study:

• To map the transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in Saccharomyces cerevisiae.
• To elucidate the distribution and function of these factors across different RNA classes.

Main Methods:

• Transcriptome-wide RNA-binding profiling of 30 degradation factors.
• Bioinformatic analysis of binding profiles and RNA classes.
• Modeling based on mRNA half-lives and codon optimality.

Main Results:

• Degradation factors show distinct distributions across RNA classes, aligning with canonical mRNA decay pathways.
• Most degradation factors bind intact mRNAs; decapping factors are recruited specifically for mRNA degradation.
• Decapping factors preferentially bind mRNAs with non-optimal codons, indicating rapid degradation of inefficiently translated transcripts.
• Nuclear surveillance machinery targets aberrant nuclear RNAs and processes snoRNAs.

Conclusions:

• RNA degradation pathways are precisely regulated by specific protein factor recruitment.
• Decapping is a rate-limiting step in mRNA degradation, influenced by translational efficiency.
• Nuclear surveillance pathways play a significant role in managing aberrant RNAs and processing specific non-coding RNAs.