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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.

View Article: PubMed Central - PubMed

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

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Statistical analysis of footprint codon composition. We count how many times each type of codon occurs in ribosome footprints, while keeping track of the position within the footprint as well as the length of the footprint. This information is stored in a matrix, where the color represents a type of codon and the number is the positioning away from the 3′ end of the footprint.
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Figure 1: Statistical analysis of footprint codon composition. We count how many times each type of codon occurs in ribosome footprints, while keeping track of the position within the footprint as well as the length of the footprint. This information is stored in a matrix, where the color represents a type of codon and the number is the positioning away from the 3′ end of the footprint.

Mentions: Briefly, using previously reported datasets, ribosome footprints were processed by determining where they align to the genome with Bowtie (16) and then categorized by length (in codons) using a Perl program. For each length category, the frequencies of codons at each position within the footprint were tabulated, where the position is defined relative to either the 5′ or 3′ end of the footprint. The resulting were structured as 64 2D matrices, where each matrix represents one of the 64 codons and each matrix position represents a codon of a particular footprint length and at a particular footprint position (Figure 1).


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

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

Statistical analysis of footprint codon composition. We count how many times each type of codon occurs in ribosome footprints, while keeping track of the position within the footprint as well as the length of the footprint. This information is stored in a matrix, where the color represents a type of codon and the number is the positioning away from the 3′ end of the footprint.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Statistical analysis of footprint codon composition. We count how many times each type of codon occurs in ribosome footprints, while keeping track of the position within the footprint as well as the length of the footprint. This information is stored in a matrix, where the color represents a type of codon and the number is the positioning away from the 3′ end of the footprint.
Mentions: Briefly, using previously reported datasets, ribosome footprints were processed by determining where they align to the genome with Bowtie (16) and then categorized by length (in codons) using a Perl program. For each length category, the frequencies of codons at each position within the footprint were tabulated, where the position is defined relative to either the 5′ or 3′ end of the footprint. The resulting were structured as 64 2D matrices, where each matrix represents one of the 64 codons and each matrix position represents a codon of a particular footprint length and at a particular footprint position (Figure 1).

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