High-throughput interrogation of programmed ribosomal frameshifting in human cells

Martin Mikl; Yitzhak Pilpel; Eran Segal

Replacing the first or second codon of the OAZ slippery site (UCC UGA) revealed a very limited 271 tolerance to sequence alterations, consistent with earlier results (Matsufuji et al., 1995) . Replacing 272 the second codon (UGA), the only variants leading to a +1 PRF signal over background where the 273 other two stop codons (UAA and UAG; Fig 2F, In this context, however, several different nucleotide combinations following the respective pattern 286 were tolerated. The only exception to this rule was human T-lymphotropic virus (Fig 2G, endogenous 287 slippery site UUUAAAC), which gave a robust -1 PRF signal corresponding to wild-type levels across 288 many variants following the (west nile virus) pattern XYYZZZZ. In summary, our data suggest that in 289 most cases a slippery site not following the canonical pattern requires a specific sequence context in The region downstream of the slippery site is thought to be crucial for PRF, typically because it creates 295 a roadblock for the translating ribosome by folding into a stable secondary structure like a hairpin or 296 a pseudoknot (Brierley and Pennell, 2001; Brierley et al., 1989; Parkin et al., 1992; Tu et al., 1992) . 297