Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes.
Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes.
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DOI：
10.1371/journal.pone.0010654
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发表时间：
2010-05-14
期刊：
影响因子：
3.7
通讯作者：
Samuelsson T
中科院分区：
文献类型：
--
作者：
Dávila López M;Martínez Guerra JJ;Samuelsson T
真核生物的基因顺序并不是完全随机的。研究基因序列的保守性对于理解基因组进化和揭示某些邻近基因在进化过程中更难分离的机制是重要的。这里汇编了种的全基因组基因序列信息，代表了真核生物门的广泛多样性。这些信息被呈现在浏览器中，在浏览器中可以显示和比较不同物种之间的基因顺序。通过考虑相邻基因对，研究了真核生物中与非随机基因顺序有关的因素。从基因本体论的角度，从相对转录方向、基因间距离和功能关系等方面研究了基因对的进化保守性。结果表明，在保守的基因对中，差异转录和共定向转录的基因比聚合转录的基因更常见。此外，高度保守的基因对，特别是真菌的基因对，具有较短的基因间距离。最后，与保守程度较低的基因对相比，进化保守且转录方式不同的后生动物和真菌的基因对在功能上更有可能相关。一个例子是核糖体蛋白基因对L13/S16，这是不寻常的，因为它既存在于真菌中，也存在于肺泡中。这两种蛋白质是真细菌和古菌中相同操纵子的一部分，这一事实也表明了这两种蛋白质之间的特定功能关系。综上所述，与真核生物中非随机基因顺序相关的因素包括相对基因定位、基因间距离和功能关系。似乎某些基因对是保守的，因为所涉及的基因具有转录和/或功能关系。结果还表明，基因顺序保守的研究有助于识别在转录控制方面相关的基因。
The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.
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影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
6.4
作者：
Agirre, X;Román-Gómez, J;Prósper, F
通讯作者：
Prósper, F
影响因子：
16
作者：
Cho, RJ;Campbell, MJ;Davis, RW
通讯作者：
Davis, RW
影响因子：
4.8
作者：
Grasberger, Helmut;Refetoff, Samuel
通讯作者：
Refetoff, Samuel
影响因子：
64.8
作者：
James, Timothy Y.;Kauff, Frank;Vilgalys, Rytas
通讯作者：
Vilgalys, Rytas