Epigenetics of non-model organisms

在20世纪的大部分时间里，模型生物一直是研究的中流砥柱。在某种程度上，模式生物因其简单的发育和恒定的形态而被选中。然而，快速基因组测序的出现和分子工具向非传统模式生物的随时转移模糊了模式生物、新兴模式生物和非传统模式生物之间的界限。非传统模式生物更复杂的生活史为我们提供了一个独特的机会来扩大我们对生物学的理解。*我提出的研究计划将探索非传统模式生物生物学的表观遗传学基础。例如，果蝇和老鼠和人类一样，在发育过程中对适度的营养匮乏做出的反应，没有什么比发育成小的成年人更令人兴奋的了。相比之下，水蚤对不利的环境环境的反应是产生额外的雄性。同样，在捕食者的存在下，大型水蚤的形态发生了巨大的改变，这种动物可以产生巨大的头盔、尾刺、棍棒、颈齿和其他完全改变它们外表的形态细节。这些活跃的形态变化必然是表观遗传学的，因为它们发生在具有相同基因组的克隆中。这些戏剧性的和生物学上必要的表观遗传反应表明了非传统模式生物的优势。*表观基因组反映了基因表达的一系列表观遗传变化；即，基因表达的变化不是由于DNA序列的改变。表观基因组对外界环境因素做出反应，如营养、毒素暴露、荷尔蒙环境、社会互动，甚至可能是天气。较少文献记载的是细胞内部环境的影响，特别是内生细菌的影响。在内生菌中，具有专性细胞内繁殖的细菌中，a-蛋白细菌可以说是最著名的，因为这一组中的一个古老成员产生了我们的线粒体。然而，这一无处不在的细菌群还包括较少驯化的现存近亲沃尔巴克氏菌和立克次体，它们分别是无脊椎动物和脊椎动物的专性内生细菌。*我将通过探索内生细菌在非传统模式系统中对寄主基因组的控制作用来扩展我们在果蝇中内生细菌的表观遗传效应的工作，例如大型水蚤、扁虱和哺乳动物细胞培养。无处不在的内生细菌控制宿主的多种方式，从而影响宿主的表型和生物学，这是本研究计划将解决的问题。

Model organisms have been the mainstay of research for much of the 20th century. In part, model organisms have been selected for their straightforward development and constant morphology. However, the advent of rapid genome sequencing and the ready transfer of molecular tools to non-traditional model organisms have blurred the lines between model, emerging and non-traditional model organisms. The more complex life histories of non-traditional model organisms provide a unique opportunity to expand our understanding of biology. ******My proposed research program will explore the epigenetic foundation of the biology of non-traditional model organisms. For example, Drosophila like mice and humans, responds to modest nutrient deprivation in development by nothing more exciting than developing as smaller adults. In contrast, Daphnia responds to adverse environmental circumstances by producing an additional sex - males. Similarly, in the presence of predators, the morphology of Daphnia is grossly remodeled and the animals can produce massive helmets, tail spines, clubs, neck teeth and other morphological elaborations that completely change their appearance. These exuberant morphological changes are necessarily epigenetic, as they occur in clones with identical genomes. These dramatic and biologically essential epigenetic responses demonstrates the advantages of non-traditional model organisms. ******The epigenome reflects the suite of epigenetic changes in gene expression; that is, changes in gene expression not due to altered DNA sequence. The epigenome is responsive to external environmental factors such as nutrition, toxin exposure, hormonal milieu, social interactions, and possibly even the weather. Less well documented is the effect of the internal environment of cells, in particular the effect of endobacteria. Among the endobacteria, bacteria with obligate intracellular reproduction, a-proteobacteria is arguably the most famous, as an ancient member of this group gave rise to our mitochondria. However, this ubiquitous group of bacteria also includes less domesticated extant relatives, Wolbachia and Rickettsia, obligate endobacteria of inverterbrates and vertebrates, respectively. ******I will extend our work on the epigenetic effects of endobacteria in Drosophila by exploring their control of their host's genome in the non-traditional model systems, Daphnia, ticks and mammalian cell culture. The manifold ways in which ubiquitous endobacteria control their host, and so influence host phenotype and biology, are the questions that will be tackled in this research programme. **