GC3-biased gene domains in mammalian genomes.
GC3-biased gene domains in mammalian genomes.
复制标题
哺乳动物基因组中偏向 GC3 的基因域
DOI：
10.1093/bioinformatics/btv329
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发表时间：
2015-10-01
期刊：
影响因子：
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通讯作者：
Zhao Z
中科院分区：
文献类型：
--
作者：
Shen W;Wang D;Ye B;Shi M;Ma L;Zhang Y;Zhao Z
动机：同义密码子使用偏好性已被证明与不同生物体中的许多基因组特征相关。然而，密码子偏好性对基因功能和基因组结构的生物学意义仍不清楚。结果：第三密码子位置（GC 3）的鸟嘌呤和胞嘧啶含量可以作为密码子偏好性的一个很好的指标。在这里，我们使用相对GC 3偏倚值来比较人和小鼠中基因的GC 3偏倚强度。我们首次报道了GC 3丰富和GC 3贫乏的基因产物可能具有不同的亚细胞空间分布。此外，我们扩展了基因组基因结构域的观点，并确定了保守的GC 3偏向基因结构域沿着染色体。我们的研究结果表明，相似的GC 3偏向基因可能在特定的空间区域共翻译共享本地翻译机，GC 3可能参与基因组结构的组织。可用性和实施：源代码可根据作者的要求提供。联系方式：zhaozh@nic.bmi.ac.cn或zany1983@gmail.com补充信息：补充数据可在生物信息学在线获得。
Motivation: Synonymous codon usage bias has been shown to be correlated with many genomic features among different organisms. However, the biological significance of codon bias with respect to gene function and genome organization remains unclear. Results: Guanine and cytosine content at the third codon position (GC3) could be used as a good indicator of codon bias. Here, we used relative GC3 bias values to compare the strength of GC3 bias of genes in human and mouse. We reported, for the first time, that GC3-rich and GC3-poor gene products might have distinct sub-cellular spatial distributions. Moreover, we extended the view of genomic gene domains and identified conserved GC3 biased gene domains along chromosomes. Our results indicated that similar GC3 biased genes might be co-translated in specific spatial regions to share local translational machineries, and that GC3 could be involved in the organization of genome architecture. Availability and implementation: Source code is available upon request from the authors. Contact: zhaozh@nic.bmi.ac.cn or zany1983@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.