Regularities of context-dependent codon bias in eukaryotic genes
Regularities of context-dependent codon bias in eukaryotic genes
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DOI：
10.1093/nar/30.5.1192
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发表时间：
2002-03-01
影响因子：
14.9
通讯作者：
Gilbert, W
中科院分区：
文献类型：
--
作者：
Fedorov, A;Saxonov, S;Gilbert, W
密码子周围的核苷酸影响从可能的同义密码子组中选择该特定密码子。对密码子使用的最强影响来自紧接在密码子之后的核苷酸，并且被称为N-1上下文。我们研究了四种真核生物基因中N-1密码子的相对丰度，这些真核生物的整个基因组已经测序：智人，黑腹果蝇，秀丽隐杆线虫和拟南芥。对于所有研究的生物体，发现90%的密码子具有统计学显著的N-1上下文依赖密码子偏好。将具有N-1背景的每个密码子的相对丰度与全基因组中相同4聚体寡核苷酸的相对丰度进行比较。这一比较表明，在大约一半的。在所有情况下，依赖于上下文的密码子偏好不能用基因组的序列组成来解释。应用排序统计来比较来自不同同义组的密码子的上下文依赖的密码子偏好。我们发现，N-I的上下文依赖的密码子偏好相对于密码子核苷酸组成。在第二和第三位置具有相同核苷酸和相同N-1背景的密码子具有其相对丰度的统计学显著相关性。
Nucleotides surrounding a codon influence the choice of this particular codon from among the group of possible synonymous codons. The strongest influence on codon usage arises from the nucleotide immediately following the codon and is known as the N-1 context. We studied the relative abundance of codons with N-1 contexts in genes from four eukaryotes for which the entire genomes have been sequenced: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. For all the studied organisms it was found that 90% of the codons have a statistically significant N-1 context-dependent codon bias. The relative abundance of each codon with an N-1 context was compared with the relative abundance of the same 4mer oligonucleotide in the whole genome. This comparison showed that in about half of. all cases the context-dependent codon bias could not be explained by the sequence composition of the genome. Ranking statistics were applied to compare context-dependent codon biases for codons from different synonymous groups. We found regularities in N-1 context-dependent codon bias with respect to the codon nucleotide composition. Codons with the same nucleotides in the second and third positions and the same N-1 context have a statistically significant correlation of their relative abundances.