Parmley Joanna L, Hurst Laurence D
Department of Biology and Biochemistry, University of Bath, Bath, UK.
Mol Biol Evol. 2007 Aug;24(8):1600-3. doi: 10.1093/molbev/msm104. Epub 2007 May 24.
In mammals there is a bias in amino acid usage near splice sites that is explained, in large part, by the high density of exonic splicing enhancers (ESEs) in these regions. Is there a similar bias for the relative use of synonymous codons, and can any such bias be predicted by their abundance in ESEs? Prior reports suggested that such trends may exist. From analysis of human exons, we find that 47 of the 59 codons with at least one synonym show differential usage in the proximity of exon ends, of which 42 remain significant after correction for multiple testing. Within sets of synonymous codons those more preferred near splice sites are generally those that are relatively more abundant within the ESEs. However, the examples given previously appear exceptionally good fits and there exist many exceptions, the usage of lysine's codons being a case in point. Similar results are observed in mouse exons. We conclude that splice regulation impacts on the choice of synonymous codons in mammals, but the magnitude of this effect is less than might at first have been supposed.
在哺乳动物中，剪接位点附近的氨基酸使用存在偏向性，这在很大程度上可由这些区域外显子剪接增强子（ESE）的高密度来解释。同义密码子的相对使用是否也存在类似的偏向性，以及能否通过它们在ESE中的丰度来预测这种偏向性？先前的报告表明可能存在这样的趋势。通过对人类外显子的分析，我们发现59个至少有一个同义密码子的密码子中有47个在外显子末端附近存在差异使用，其中42个在多重检验校正后仍具有显著性。在同义密码子组中，那些在剪接位点附近更受青睐的密码子通常是在ESE中相对更丰富的密码子。然而，先前给出的例子似乎拟合得特别好，也存在许多例外，赖氨酸密码子的使用就是一个典型例子。在小鼠外显子中也观察到了类似的结果。我们得出结论，剪接调控会影响哺乳动物中同义密码子的选择，但这种影响的程度小于最初的预期。
