Evolution of Gene Regulation through small RNA-mediated neofunctionalisation.

每一种植物或动物的基因组成都包含成千上万个基因，这就提出了基因从何而来的问题。一个主要的来源是“新功能化”过程，即一个基因被复制，其中一个副本获得了一种新的功能。这一过程对生物多样性的进化至关重要，并为育种或基因工程提供了重要的变异。传统上描述了两种类型的新功能化：编码蛋白质区域（C-NF）的变化，以及调节基因何时何地开启的区域（R-NF）的变化。最近的发现提出了第三种类型的可能性，我们称之为小rna介导的新功能化（S-NF）。S-NF涉及到一个基因的镜像复制，导致调节分子的产生，小rna，抑制另一个基因的活性。通过这种方式，基因可以发挥新的调节作用。我们最近获得的证据表明，S-NF有助于不同种类金鱼的花色差异的进化。从长期来看，一些S-NF反向复制可能会变得更短，产生更少的小rna，从而产生microRNA基因。该提案的目的是验证S-NF提供了一种具有广泛意义的自然机制，补充了R-NF和C-NF，以在进化过程中创造新基因并改善基因活性。我们将整合几种方法来测试这个想法。首先，我们将利用DNA测序的进步，使我们能够定义一系列不同植物物种的基因组序列变异。基于这些发现，我们将能够绘制出S-NF复制的起源、进化和多样化，并阐明它们与microrna的关系。其次，我们将使用遗传分析，即个体杂交并分析后代，以分离特定S-NF基因的贡献。第三，我们将通过测量S-NF基因及其靶基因在不同组织和区域中的活性来研究S-NF基因如何发挥其作用。第四，我们将使用系统遗传学，通过构建基因和基因组的进化树，来定义可能的进化路径。第五，我们将使用种群基因组学，通过在自然种群中测量遗传变异的频率，来推断哪些基因可能处于选择之下。第六，我们将使用转基因方法，通过基因工程将S-NF引入物种，研究和评估如何使用它来影响和改进基因活动模式。我们将把这些方法应用于金鱼鱼及其近亲。该系统已经建立了与花色相关的S-NF，为检测基因活性模式的变化提供了一种方便、灵敏的方法。此外，在颜色或其他特征上差异很大的snapdragon物种之间进行杂交的能力，使得基因的遗传贡献很容易被跟踪。花色工程育种也是评价S-NF贡献的试验台。综上所述，我们的研究将为新基因活动的产生以及S-NF对进化和育种的贡献提供新的见解。

The genetic makeup of every plant or animal comprises many thousands of genes, raising the question of where genes come from. A major source is the process of "neofunctionalization", whereby a gene becomes duplicated and one of the copies acquires a new function. This process is critical for the evolution of biological diversity and provides variation important for breeding or genetic engineering. Two types of neofunctionalisation have been traditionally described: changes in regions coding for proteins (C-NF), and changes in regions regulating where and when a gene is switched on (R-NF). Recent discoveries have raised the possibility of a third type, which we call small RNA-mediated neofunctionalisation (S-NF). S-NF involves mirror-image duplications of a gene which leads to the production of regulatory molecules, small RNAs, which inhibit another gene's activity. In this way a gene may adopt a new regulatory role. We have recently obtained evidence for S-NF contributing to the evolution of flower colour differences between species of snapdragon, Antirrhinum. In the longer term, some S-NF inverted duplications may become shorter and produce fewer small RNAs, giving rise to microRNA genes. The aim of this proposal is to test the idea that S-NF provides a natural mechanism of broad significance, complementing R-NF and C-NF, for creating new genes and refining gene activity during evolution.We will integrate several approaches to test this idea. First, we will use advances in DNA sequencing, allowing us to define genome sequence variation across a range of different plant species. Based on these findings, we will be able to map the origin, evolution and diversification of S-NF duplications and clarify their relation to microRNAs. Second, we will use genetic analysis, whereby individuals are crossed and progeny analysed, to separate the contribution of particular S-NF genes. Third, we will investigate how S-NF genes exert their effects by measuring their activity, and that of their targets, in different tissues and regions. Fourth, we will use phylogenetics, whereby evolutionary trees for genes and genomes may be constructed, to allow likely paths evolution has taken to be defined. Fifth, we will use population genomics, whereby the frequencies of genetic variants can be measured in natural populations, to infer which genes are likely under selection. Sixth, we will use transgenic approaches, introducing S-NF into species by genetic engineering, to investigate and evaluate how it can be used to influence and refine gene activity patterns. We will apply these approaches to snapdragon species and their relatives. S-NF has already been established in this system in relation to flower colour, which provides a convenient and sensitive way to detect variation in patterns of gene activity. Moreover, the ability to inter-cross snapdragon species that differ widely in colour or other traits, allows the genetic contribution of genes to be readily followed. Engineering and breeding flower colours is also a test bed for evaluating the contributions of S-NF. Taken together our studies should provide new insights into how new gene activities arise and the contribution of S-NF to evolution and breeding.