Published online 15 December 2004
Nucleic Acids Research, Vol. 32 No. 22 © Oxford University Press 2004; all rights reserved
Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae
School of Engineering and Physical Sciences, Fraser Noble Building, Kings College, Aberdeen AB24 3UE, UK and 1 School of Medical Sciences, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen AB25 2ZD, UK
* To whom correspondence should be addressed. Tel: +44 1224 555806; Fax: +44 1224 555844; Email: i.stansfield{at}abdn.ac.uk
Present address: J. Richardson, Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
Received July 28, 2004; Revised November 4, 2004; Accepted November 28, 2004
In-frame stop codons normally signal termination during mRNA translation, but they can be read as ‘sense’ (readthrough) depending on their context, comprising the 6 nt preceding and following the stop codon. To identify novel contexts directing readthrough, under-represented 5' and 3' stop codon contexts from Saccharomyces cerevisiae were identified by genome-wide survey in silico. In contrast with the nucleotide bias 3' of the stop codon, codon bias in the two codon positions 5' of the termination codon showed no correlation with known effects on stop codon readthrough. However, individually, poor 5' and 3' context elements were equally as effective in promoting stop codon readthrough in vivo, readthrough which in both cases responded identically to changes in release factor concentration. A novel method analysing specific nucleotide combinations in the 3' context region revealed positions +1,2,3,5 and +1,2,3,6 after the stop codon were most predictive of termination efficiency. Downstream of yeast open reading frames (ORFs), further in-frame stop codons were significantly over-represented at the +1, +2 and +3 codon positions after the ORF, acting to limit readthrough. Thus selection against stop codon readthrough is a dominant force acting on 3', but not on 5', nucleotides, with detectable selection on nucleotides as far downstream as +6 nucleotides. The approaches described can be employed to define potential readthrough contexts for any genome.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  I. Hatin, C. Fabret, O. Namy, W. A. Decatur, and J.-P. Rousset Fine-Tuning of Translation Termination Efficiency in Saccharomyces cerevisiae Involves Two Factors in Close Proximity to the Exit Tunnel of the Ribosome Genetics, November 1, 2007; 177(3): 1527 - 1537. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Berger, N. A. Bulgakova, F. Grawe, K. Johnson, and E. Knust Unraveling the Genetic Complexity of Drosophila stardust During Photoreceptor Morphogenesis and Prevention of Light-Induced Degeneration Genetics, August 1, 2007; 176(4): 2189 - 2200. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Buchan, L. S. Aucott, and I. Stansfield tRNA properties help shape codon pair preferences in open reading frames Nucleic Acids Res., February 9, 2006; 34(3): 1015 - 1027. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Wilson, S. Meaux, R. Parker, and A. van Hoof Genetic interactions between [PSI+] and nonstop mRNA decay affect phenotypic variation PNAS, July 19, 2005; 102(29): 10244 - 10249. [Abstract] [Full Text] [PDF]
|
|