Evolutionarily conserved genes preferentially accumulate introns
Evolutionarily conserved genes preferentially accumulate introns
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DOI：
10.1101/gr.5978207
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发表时间：
2007-07-01
期刊：
影响因子：
7
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Carmel, Liran;Rogozin, Igor B.;Koonin, Eugene V.
中断真核生物蛋白质编码序列的内含子通常被认为是无功能的。然而，许多内含子的位置在进化过程中高度保守，其原因仍然知之甚少。以前的真核生物进化过程中的内含子获得和丢失事件的重建使用了各种简化的进化模型，产生了相互矛盾的结论，不适合揭示一些关键的潜在过程。我们结合联合收割机一个全面的概率模型和一个扩展的数据集，包括391个保守的基因，从19个真核生物，发现以前未被注意的方面的内含子进化，特别是分配内含子的增益和损失率的个别基因。同一基因内含子的增加和丢失率呈中度正相关。基因的内含子增加率与编码序列进化率呈极显著负相关，内含子丢失率与序列进化率也呈显著正相关。相反的迹象，虽然不太显着的相关性，观察内含子的增益和损失率和基因表达水平之间。有人提出，内含子进化包括一个中性的组件，这是表现在增益和损失率之间的正相关性和选择驱动的组件，反映在内含子增益和损失之间的联系和序列进化。在进化上保守的基因中增加的内含子增加和减少的内含子丢失表明内含子插入通常可能是适应性的，而一些内含子丢失可能是有害的。内含子的这种明显的功能重要性可能是由于，至少部分是由于它们对基因表达的多重影响。
Introns that interrupt eukaryotic protein-coding sequences are generally thought to be nonfunctional. However, for reasons still poorly understood, positions of many introns are highly conserved in evolution. Previous reconstructions of intron gain and loss events during eukaryotic evolution used a variety of simplified evolutionary models that yielded contradicting conclusions and are not suited to reveal some of the key underlying processes. We combine a comprehensive probabilistic model and an extended data set, including 391 conserved genes from 19 eukaryotes, to uncover previously unnoticed aspects of intron evolution-in particular, to assign intron gain and loss rates to individual genes. The rates of intron gain and loss in a gene show moderate positive correlation. A gene's intron gain rate shows a highly significant negative correlation with the coding-sequence evolution rate; intron loss rate also significantly, but positively, correlates with the sequence evolution rate. Correlations of the opposite signs, albeit less significant ones, are observed between intron gain and loss rates and gene expression level. It is proposed that intron evolution includes a neutral component, which is manifest in the positive correlation between the gain and loss rates and a selection-driven component as reflected in the links between intron gain and loss and sequence evolution. The increased intron gain and decreased intron loss in evolutionarily conserved genes indicate that intron insertion often might be adaptive, whereas some of the intron losses might be deleterious. This apparent functional importance of introns is likely to be due, at least in part, to their multiple effects on gene expression.