An atypical RNA quadruplex marks RNAs as vectors for gene silencing

Area of Science:

• Molecular Biology
• RNA Structure
• Epigenetics

Background:

• Poly(UG) repeats at mRNA 3' termini induce gene silencing and epigenetic inheritance in *C. elegans*.
• This silencing is mediated by RNA-dependent RNA polymerase (RdRP) synthesizing small interfering RNAs.

Purpose of the Study:

• To elucidate the structural basis of poly(UG) repeat-mediated gene silencing.
• To characterize the novel RNA structure formed by poly(UG) repeats and its functional implications.

Main Methods:

• Structural analysis of poly(UG) repeats using biophysical techniques.
• Biochemical assays to assess RdRP binding and activity.
• Mutational analysis to probe the importance of the pUG fold structure.

Main Results:

• Active poly(UG) tails require at least 11.5 repeats and form a unique quadruplex structure, the "pUG fold".
• The pUG fold exhibits a left-handed backbone, lacks consecutive guanines, and contains non-sequential G and U quartets.
• Porphyrin binding to the pUG fold inhibits gene silencing and RdRP recruitment; specific mutations disrupting the fold abolish these functions.
• The pUG fold is conserved and found in human noncoding RNAs, suggesting broader biological relevance.

Conclusions:

• The pUG fold is a novel RNA structural motif essential for poly(UG) repeat-driven gene silencing in *C. elegans*.
• This structure directly interacts with RdRP, mediating the silencing pathway.
• The prevalence of the pUG fold in human RNAs suggests potential roles beyond gene silencing, possibly in RNA regulation.