Biology subjects

Petersen, R. J.

Publications and source records attributed to Petersen, R. J..

3 recordsLinked to original sources

bioRxiv2025

Sequence and ionic requirements of pUG fold quadruplexes

Poly(UG) or "pUG" repeat RNA can fold into a left-handed parallel quadruplex, the pUG fold. The pUG fold directs the amplification of RNAi in C. elegans, and pUG sequences are abundant in eukaryotic transcriptomes. Here, we report the sequence and ionic requirements for pUG folding. The pUG fold requires 12 guanosines but has an otherwise flexible sequence requirement. The uridines can be substituted with other nucleotides, with some sequence variants folding better than pUG RNA. The GA repeat sequence (GA)12 also forms a pUG-like fold, albeit with lower thermodynamic stability than (GU)12. The pUG fold can tolerate multiple deoxyribose substitutions but does not fold when the backbone is entirely deoxyribose. It has a high affinity and specificity for potassium ions (K1/2 = 6 mM) and does not fold in sodium or ammonium ions. Addition of 2 mM Mg2+ does not further stabilize the pUG fold, and the polyamines spermine and spermidine slightly decrease its stability. Finally, the pUG fold is sensitive to surrounding sequence context and complementary flanking sequences can stabilize pUG folds, while other sequences can interfere with folding. These data expand our understanding of RNA folding and provide a basis for understanding and predicting pUG folds.

biochemistry↗

bioRxiv2025

The structure, folding kinetics and dynamics of long poly(UG) RNA

Long poly(UG) or "pUG" dinucleotide repeats are abundant in eukaryotic transcriptomes. Thousands of human genes have pUGs longer than 24 repeats, including the cancer-associated lncRNA NEAT1. In C. elegans, enzymatic addition of long pUGs to RNA 3' ends (pUG tails) marks RNAs as vectors of gene silencing. Gene silencing requires at least one pUG fold, a left-handed quadruplex structure that incorporates 12 repeats, but longer pUG tails are more active. Here, we investigate the structure, folding kinetics and dynamics of long pUG RNAs. RNAs with 24 or more repeats slowly form compact, double pUG folds. The forward rate of pUG fold formation in vitro is length-dependent with a half-life (t1/2) of 13 minutes, while the unfolding rate is very slow (t1/2 [~]5 days). Long pUG RNAs display biphasic dynamics with an additional, faster unfolding phase (t1/2 [~]30 min). The amplitude of the faster phase indicates partial unfolding. From these data we propose a dynamic model for segmental register exchange and double pUG fold formation in long pUG RNAs. These data broaden our understanding of the structure and dynamics of long pUG RNAs and have implications for understanding the roles of pUG folds in biology and disease.

biochemistry↗

bioRxiv2021

An Atypical RNA Quadruplex Marks RNAs as Vectors for Gene Silencing

The addition of poly(UG) ("pUG") repeats to 3' termini of mRNAs drives gene silencing and trans-generational epigenetic inheritance in the metazoan C. elegans.1 pUG tails promote silencing by recruiting an RNA-dependent RNA Polymerase (RdRP) that synthesizes small interfering (si)RNAs.1 Here we show that active pUG tails require a minimum of 11.5 repeats and adopt a quadruplex (G4)2 structure we term the pUG fold. The pUG fold differs from known G4s in that it has a left-handed backbone similar to Z-RNA3,4, no consecutive guanosines in its sequence, and three G quartets and one U quartet stacked non-sequentially. Its biological importance is emphasized by our observations that porphyrin molecules bind to the pUG fold and inhibit both gene silencing and binding of RdRP. Moreover, specific N7-deaza RNA substitutions that do not adopt the pUG fold neither bind RdRP nor induce RNA silencing. These data define the pUG fold as a previously unrecognized RNA secondary structure motif that drives gene silencing. The pUG fold can also form internally within larger RNA molecules. Approximately 20,000 pUG-fold sequences are found in non-coding regions of human RNAs, suggesting the fold likely has biological roles beyond gene silencing.

molecular biology↗