Ribosome clearance during RNA interference

Area of Science:

• Molecular Biology
• Genetics
• RNA Biology

Background:

• RNA interference (RNAi) machinery targets messenger RNAs (mRNAs) for degradation.
• Ribosomes, responsible for translation, coexist with RNAi machinery on mRNAs.
• The interaction between RNAi and translation machinery is not fully understood.

Purpose of the Study:

• To investigate the fate of actively translated mRNAs during RNAi in *C. elegans*.
• To determine how ribosomes affect RNAi efficiency.
• To elucidate the role of ribosome quality control factors in RNAi.

Main Methods:

• Quantification of RNA levels using RNA-sequencing (RNA-seq).
• Assessment of ongoing translation using ribosome profiling (Ribo-seq).
• Analysis of gene silencing in wild-type and mutant *C. elegans* lacking SKI or PELOTA.

Main Results:

• RNAi causes greater repression of translation than RNA loss alone.
• Translation repression is stronger than RNA repression across multiple genes and RNAi triggers.
• Ribosomes stall at the 3' end of mRNAs in SKI and PELOTA deficient animals, upstream of the RNAi trigger.
• Evidence suggests active ribosome clearance by SKI and PELO during or after mRNA cleavage.

Conclusions:

• Ribosome clearance by SKI and PELO is crucial for efficient RNA silencing during RNAi.
• Nonstop translation surveillance plays a widespread role in RNA silencing.
• RNAi can target mRNAs during active translation, with implications for gene regulation.