Ribosome A and P sites revealed by length analysis of ribosome profiling data.
Bottom Line: Yet the location of the codon being decoded in ribosome footprints is still unknown, and has been complicated by the recent observation of footprints with non-canonical lengths.Here we show how taking into account the variations in ribosome footprint lengths can reveal the ribosome aminoacyl (A) and peptidyl (P) site locations.We also show that GC-rich motifs at the 5' ends of footprints are found in yeast, calling into question the anti-Shine-Dalgarno effect's role in ribosome pausing.
Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.Show MeSH
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Mentions: We confirm that E. coli ribosome footprints 5′ ends are G-rich and that this enrichment grows with footprint length (Figure 7). Furthermore, the extended 5′ regions of the shorter footprints are not enriched, supporting the aSD model. However, we notice that the extreme 5′ end position is GC-poor, an observation not predicted by the aSD model. In addition, an analysis of yeast ribosome profiling data also reveals GC-enriched sequence at the 5′ ends of longer footprints (Figure 8), which was not expected.
Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.