RNA G-quadruplexes promote codon repeat-associated ribosomal frameshifting in human genes

Programmed ribosomal frameshifting (PRF), a translational recoding process previously considered as a rare event in eukaryotes, has recently been demonstrated to occur extensively in humans. We have shown that codon repeats function as the signals for the production of trans-frame proteins in various human tissues. However, the molecular mechanism underlying this recoding process, termed codon repeat-associated ribosomal frameshifting (CRFS), remains largely unknown. In this study, we developed a reporter system by incorporating the CRFS sequence from histone deacetylase 1 (HDAC1), which directs efficient +1 ribosomal frameshifting at (UAC)3 repeats. Through a whole-genome CRISPR screening, we identified RBM4, an RNA-binding protein that interacts with RNA G-quadruplexes (rG4s), as an enhancer of ribosomal frameshifting in HDAC1 mRNA. Disruption of the rG4 immediately downstream of the (UAC)3 repeat region significantly reduces the frameshifting ratio, whereas application of rG4-stabilizing compounds or other rG4 structures enhances frameshifting. Importantly, this rG4 sequence could insert into other genes to significantly promote frameshifting efficiencies. As one of the critical elements for CRFS, our analysis suggests a significant enrichment of rG4s immediately downstream of codon repeats in the human genome, which could lead to ribosomal frameshifting in humans.