Widespread impact of nonsense-mediated mRNA decay on the yeast intronome

Area of Science:

• Molecular Biology
• Yeast Genetics
• RNA Metabolism

Background:

• Nonsense-mediated mRNA decay (NMD) is a surveillance pathway that eliminates aberrant mRNAs with premature termination codons.
• The role of NMD in degrading unspliced pre-mRNAs in yeast remains controversial.
• Efficient mRNA processing and degradation are crucial for maintaining cellular homeostasis.

Purpose of the Study:

• To investigate the role of NMD in the degradation of unspliced yeast pre-mRNAs.
• To identify factors influencing NMD targeting of unspliced transcripts.
• To elucidate the contribution of NMD to the quality control of spliced and unspliced transcripts.

Main Methods:

• Utilized tiling arrays to analyze the abundance of unspliced yeast pre-mRNAs.
• Examined pre-mRNA accumulation in yeast strains mutated for NMD components (e.g., Upf1p) and exonucleases (e.g., Xrn1p).
• Assessed the impact of intron identity and splicing signal strength on NMD targeting.

Main Results:

• Many unspliced yeast pre-mRNAs accumulate in strains deficient for NMD components (Upf1p) or the exonuclease Xrn1p.
• Intron characteristics and suboptimal splicing signals are key determinants for NMD recognition of unspliced precursors.
• NMD complements nuclear degradation pathways and limits the accumulation of unspliced pre-mRNAs under specific conditions, such as amino acid starvation or splice site mutations.

Conclusions:

• Nonsense-mediated mRNA decay plays a significant role in the degradation of unspliced yeast transcripts, extending beyond its canonical function.
• NMD contributes to the quality control of gene expression by eliminating unspliced precursors, especially those arising from regulated or inefficient splicing.
• Accumulation of unspliced pre-mRNAs in the cytoplasm, potentially in P-bodies, occurs in the absence of functional NMD.