Novel genes exhibit distinct patterns of function acquisition and network integration.
Novel genes exhibit distinct patterns of function acquisition and network integration.
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DOI：
10.1186/gb-2010-11-12-r127
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发表时间：
2010
期刊：
影响因子：
12.3
通讯作者：
Singh M
中科院分区：
文献类型：
--
作者：
Capra JA;Pollard KS;Singh M
基因是由多种进化过程产生的，其中一些会产生整个基因的重复拷贝，而另一些则会重新排列预先存在的遗传元件或增选先前的非编码序列，以创建具有“新”序列的基因。这些新基因被认为有助于区分生物体的不同表型。复制基因的产生、进化和功能已经得到了很好的研究;然而，新基因的起源和早期进化还没有得到很好的表征。我们开发了一种计算方法，通过整合全基因组比较系统发育分析与来自小规模和高通量实验的功能和相互作用数据来调查这些问题。我们研究了酵母酿酒酵母中新基因的功能和进化。我们观察到在不同的时间和不同的机制创建的基因的功能属性和相互作用的显着差异。新基因最初比重复基因更少地整合到细胞网络中，但它们似乎比重复基因更快地获得功能和相互作用。最近创建的重复基因显示出适应环境变化的现有功能的证据，而年轻的新基因没有表现出任何特定功能的富集。最后，我们发现了一个显着的偏好，基因与其他基因的年龄和起源相似。我们的研究结果表明，基因的产生方式和时间与它们在细胞中的作用之间存在密切关系。总的来说，随着时间的推移，基因往往会越来越多地整合到细胞的功能网络中，但这一过程的动力学在重复基因和新基因之间存在显着差异。
Genes are created by a variety of evolutionary processes, some of which generate duplicate copies of an entire gene, while others rearrange pre-existing genetic elements or co-opt previously non-coding sequence to create genes with 'novel' sequences. These novel genes are thought to contribute to distinct phenotypes that distinguish organisms. The creation, evolution, and function of duplicated genes are well-studied; however, the genesis and early evolution of novel genes are not well-characterized. We developed a computational approach to investigate these issues by integrating genome-wide comparative phylogenetic analysis with functional and interaction data derived from small-scale and high-throughput experiments. We examine the function and evolution of new genes in the yeast Saccharomyces cerevisiae. We observed significant differences in the functional attributes and interactions of genes created at different times and by different mechanisms. Novel genes are initially less integrated into cellular networks than duplicate genes, but they appear to gain functions and interactions more quickly than duplicates. Recently created duplicated genes show evidence of adapting existing functions to environmental changes, while young novel genes do not exhibit enrichment for any particular functions. Finally, we found a significant preference for genes to interact with other genes of similar age and origin. Our results suggest a strong relationship between how and when genes are created and the roles they play in the cell. Overall, genes tend to become more integrated into the functional networks of the cell with time, but the dynamics of this process differ significantly between duplicate and novel genes.
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影响因子：
1
作者：
Brandes, U
通讯作者：
Brandes, U
影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
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Dessimoz, Christophe
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Tyers M
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3.3
作者：
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通讯作者：
Jones, Corbin D.
影响因子：
3.3
作者：
Amerik, AY;Nowak, J;Hochstrasser, M
通讯作者：
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