Abstract:
: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. 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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Martens AT,Taylor J,Hilser VJdoi
10.1093/nar/gkv200subject
Has Abstractpub_date
2015-04-20 00:00:00pages
3680-7issue
7eissn
0305-1048issn
1362-4962pii
gkv200journal_volume
43pub_type
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