Journal
BIOINFORMATICS
Volume 29, Issue 12, Pages 1488-1491Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt184
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Funding
- Wellcome Trust [094423]
- Helen Hay Whitney Foundation
- Howard Hughes Medical Institute
- Science Foundation Ireland [08/IN.1/B1889]
- Science Foundation Ireland (SFI) [08/IN.1/B1889] Funding Source: Science Foundation Ireland (SFI)
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Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine-Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide evidence that in addition to pausing effect, internal SD sequences induce a caterpillar-like movement of mRNA through the ribosome cavity. Once an SD site binds to the ribosome, it remains attached to it while the ribosome decodes a few subsequent codons. This leads to asymmetric progressive elongation of ribosome footprints at the 3'-end. It is likely that internal SD sequences induce a pause not on a single, but on several adjacent codons. This finding is important for our understanding of mRNA movement through the ribosome and also should facilitate interpretation of ribosome profiling data.
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