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Ribosome A and P sites revealed by length analysis of ribosome profiling data.

Martens AT, Taylor J, Hilser VJ - Nucleic Acids Res. (2015)

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.

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Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.

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GC content analysis of Escherichia coli ribosome footprints. Footprints were categorized by length and each nucleotide position was measured for its average GC content across all footprints. Shorter footprints were extended to the 5′ end, revealing what the mRNA sequence was prior to nuclease digestion (red dashed line). We see that the 5′ and 3′ ends of footprints, regardless of length, have some strong GC biases. Furthermore, the longer footprints have increasingly high GC content downstream from the 5′ end.
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Figure 7: GC content analysis of Escherichia coli ribosome footprints. Footprints were categorized by length and each nucleotide position was measured for its average GC content across all footprints. Shorter footprints were extended to the 5′ end, revealing what the mRNA sequence was prior to nuclease digestion (red dashed line). We see that the 5′ and 3′ ends of footprints, regardless of length, have some strong GC biases. Furthermore, the longer footprints have increasingly high GC content downstream from the 5′ end.

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.


Ribosome A and P sites revealed by length analysis of ribosome profiling data.

Martens AT, Taylor J, Hilser VJ - Nucleic Acids Res. (2015)

GC content analysis of Escherichia coli ribosome footprints. Footprints were categorized by length and each nucleotide position was measured for its average GC content across all footprints. Shorter footprints were extended to the 5′ end, revealing what the mRNA sequence was prior to nuclease digestion (red dashed line). We see that the 5′ and 3′ ends of footprints, regardless of length, have some strong GC biases. Furthermore, the longer footprints have increasingly high GC content downstream from the 5′ end.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402525&req=5

Figure 7: GC content analysis of Escherichia coli ribosome footprints. Footprints were categorized by length and each nucleotide position was measured for its average GC content across all footprints. Shorter footprints were extended to the 5′ end, revealing what the mRNA sequence was prior to nuclease digestion (red dashed line). We see that the 5′ and 3′ ends of footprints, regardless of length, have some strong GC biases. Furthermore, the longer footprints have increasingly high GC content downstream from the 5′ end.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA.

Show MeSH
Related in: MedlinePlus