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    The high-throughput sequencing of nuclease-protected mRNA fragments bound to ribosomes, a technique known as ribosome profiling, quantifies the relative frequencies with which different regions of transcripts are translated. This technique has revealed novel translation initiation sites with unprecedented scope and has furthered investigations into the connections between codon biases and translation rates. 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. These location assignments are in agreement with the proposed mechanisms for various ribosome pauses and further enhance the resolution of the profiling data.
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    Ribosome A and P sites revealed by length analysis of ribosome profiling data

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

    The involvement of defined regions of Escherichia coli 16S rRNA in the fidelity of decoding has been examined by analyzing the effects of rRNA mutations on misreading errors at the ribosomal A and P sites. These results indicate the involvement of all three regions of 16S rRNA in decoding functions at both the A and P sites. The functional similarity of all three mutant classes are consistent with close physical proximity of the region, the loop and helix 34 and suggest that all three regions of rRNA comprise a decoding domain in the ribosome. National Center for Biotechnology Information , U. Journal List Nucleic Acids Res v.
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    However, binding is impaired if the deoxy-codon is present at the E site. In sharp contrast, the A-site binding of Ac-aminoacyl-tRNA was severely reduced in the presence of the deoxy-codon at the A site as well as at the P site. The transfer of the genetic message into the amino acid sequence of a distinct protein is based on the ribosomal decoding process, which occurs at the ribosomal P site during initiation and at the A site during elongation.
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    Michael O'Connor, Cheryl L. Thomas, Robert A. Zimmermann, Albert E. The involvement of defined regions of Escherichia coli 16S rRNA in the fidelity of decoding has been examined by analyzing the effects of rRNA mutations on misreading errors at the ribosomal A and P sites. These results indicate the involvement of all three regions of 16S rRNA in decoding functions at both the A and P sites.
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