Methods to detect selection on noncoding DNA.
Methods to detect selection on noncoding DNA.
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DOI：
10.1007/978-1-61779-585-5_6
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发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Andolfatto, Peter
中科院分区：
文献类型：
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作者：
Zhen, Ying;Andolfatto, Peter
在高等真核生物中，大量的非编码DNA含有调节基因表达的元件。描述这些调控元件并了解它们如何进化是生物学家面临的主要挑战。调查基因组规模的DNA序列数据的能力的进步提供了前所未有的机会，使用进化模型和计算工具，以确定功能上重要的元素和选择的模式在多个物种。本章回顾了目前已经开发和应用于非编码DNA的一些方法，它们向我们展示了什么，以及它们如何受到限制。最近几项研究的结果表明，在真核生物中，非编码DNA的比例可能比以前认为的要大得多，这意味着这些生物中大多数非编码DNA的功能注释在很大程度上是不完整的。在果蝇中，最近的研究进一步表明，在物种之间观察到的大部分非编码DNA差异可能是周期性适应性替换的产物。在人类中进行的类似研究揭示了一种更复杂的模式，即反复出现的正选择的特征主要集中在保守的非编码DNA元件中。了解这些模式和它们推广到其他生物的程度，等待即将到来的基因组规模的多态性和分歧数据分析更多的物种。
Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data are providing unprecedented opportunities to use evolutionary models and computational tools to identify functionally important elements and the mode of selection acting on them in multiple species. This chapter reviews some of the current methods that have been developed and applied on noncoding DNA, what they have shown us, and how they are limited. Results of several recent studies reveal that a significantly larger fraction of noncoding DNA in eukaryotic organisms is likely to be functional than previously believed, implying that the functional annotation of most noncoding DNA in these organisms is largely incomplete. In Drosophila, recent studies have further suggested that a large fraction of noncoding DNA divergence observed between species may be the product of recurrent adaptive substitution. Similar studies in humans have revealed a more complex pattern, with signatures of recurrent positive selection being largely concentrated in conserved noncoding DNA elements. Understanding these patterns and the extent to which they generalize to other organisms awaits the analysis of forthcoming genome-scale polymorphism and divergence data from more species.