RNA G-Quadruplex RIBOTAC-Mediated Targeted Degradation of lncRNA TERRA.

Abstract

Long noncoding RNAs (lncRNAs) regulate gene expression and play crucial roles in development and disease, including cancer. One important but still poorly understood lncRNA is TERRA (telomeric repeat-containing RNA), transcribed from telomeres and essential for telomere maintenance, genome stability, and cellular aging. TERRA adopts two structural features,R-loops and G-quadruplexes (G4s), that drive its biological activity. Its dysregulation is linked to telomere dysfunction and is prominent in Alternative Lengthening of Telomeres (ALT) cancers, where TERRA is highly upregulated and promotes telomere recombination. Here, first-in-class small molecules targeting TERRA using RIBOTAC (Ribonuclease-Targeting Chimera) technology is developed. These compounds selectively bind TERRA's G4 structures and recruit RNase L, inducing its degradation while sparing DNA G4s and other G4 RNAs. This selectivity results from ternary complex formation with RNase L and the repetitive G4 motifs enriched in TERRA. TERRA-RIBOTACs in HeLa and U2OS cells, the latter representing an ALT cancer model, are evaluated. TERRA degradation, particularly at 7p, 13q, 15q, and 20q loci, impairs telomere function and reduces colony formation. Manipulating lncRNAs like TERRA with chemical tools opens new avenues for drug development and deepens the understanding of RNA-based regulation in cancer biology.