Modulation of nonsense mediated decay by rapamycin

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Rapamycin is a macrolide targeting nutrient and stress regulation.
• Its role in inhibiting cap-dependent mRNA translation is established, but effects on other RNA processing remain unclear.

Purpose of the Study:

• To investigate rapamycin's impact on post-transcriptional gene regulation.
• To characterize rapamycin-induced changes in alternative mRNA splicing and NMD-sensitive isoforms.

Main Methods:

• Transcriptome analysis of rapamycin-treated cells.
• Quantification of premature termination codon (PTC)-containing mRNA isoforms.
• Assessment of mRNA half-life and polyribosome association.
• Analysis of nuclear Cap Binding Complex (CBC) enrichment.

Main Results:

• Rapamycin induces genome-wide changes in alternative mRNA splicing.
• It significantly reduces levels of PTC-containing mRNA isoforms in a dose-, UPF1-, and 4EBP-dependent manner.
• Rapamycin treatment shortens the half-life of PTC-containing SRSF6 transcripts and depletes them from polyribosomes.
• Enhanced NMD activity correlates with increased nuclear CBC.

Conclusions:

• Rapamycin modulates global RNA homeostasis through enhanced nonsense-mediated decay (NMD).
• This mechanism involves altered mRNA splicing, decay, and translation-NMD interplay.
• Rapamycin's effects on RNA processing extend beyond its known role in translation inhibition.