The function of the RNA methylome in animals

我们的DNA包含了我们的孩子继承的核心遗传信息。这种遗传信息决定了基因将如何以及何时在生物体中不同数量的细胞内表达。染色质和DNA修饰等表观遗传机制可引起可遗传的基因表达变化，而不影响DNA密码。表观遗传学的研究导致了具有可遗传特征的新的基因调控机制的发现。现在，RNA也出现了类似的范例。RNA携带DNA中编码的信息。然而，这一信息本身也可以通过化学修饰来改变。目前在RNA上发现了150多种不同的修饰，它们的生物发生和识别需要更多的蛋白质。最近的发现表明，RNA修饰可以动态调节，它们与人类和动物模型的胚胎发育、长寿、神经疾病和癌症有关。表观遗传机制的遗传本质要求生殖细胞内的基因表达发生变化，从而产生后代。生殖系发育、生殖细胞增殖和特性对生物体的生存至关重要。表观遗传机制通过靶向外源成分在基因组防御中发挥关键作用，并阻止生殖细胞中体细胞基因的表达。尽管如此，在一些动物中，有可能重新编程表观遗传途径，以建立可持续许多世代的可遗传基因表达变化。大多数RNA修饰在多细胞生物体中的生物学作用仍不清楚，它们在可遗传基因表达调控中的作用尚未被探索。以线虫秀丽线虫为动物模型的研究为发现和理解动物种系的表观遗传基因调控途径做出了开创性的贡献。直到最近，人们还不知道线虫的RNA修饰情况。为了建立秀丽线虫作为研究RNA修饰作用的模型系统，我开发了能够识别和定量修饰RNA的质谱学方法。使用这些方法，我证明了在线虫中发现的几种RNA修饰在压力下会发生变化，比如饮食限制或高温。在某些情况下，RNA修饰的这些变化是可以逆转的。我的研究旨在揭示包含甲基的一组特定RNA修饰的作用。通过了解RNA甲基化如何对生殖细胞中的基因表达变化做出贡献，我的目标是发现它们的表观遗传功能。我将结合生物化学和遗传学方法，(I)开发一种甲基化RNA的酶特异性测序方法(Ii)研究RNA甲基化在动物生殖细胞中的作用(Iii)研究RNA甲基化本身如何受饮食代谢的调节这项研究是重要的，因为，首先，拟议的测序方法将使大型研究群体受益，并使多细胞生物体中的RNA甲基化的图谱成为可能。其次，了解生殖细胞中RNA修饰的作用将揭示它们在细胞增殖和分化中的作用，这将有助于对癌症和生育等人类疾病的研究。最后，我的研究有可能开创一个新的研究方向，即我们的饮食如何通过RNA修饰来影响基因表达。

Our DNA contains the core genetic information that is inherited by our children. This genetic information programs how and when genes will be expressed within the diverse number of cells of an organism. Epigenetic mechanisms such as chromatin and DNA modifications give rise to heritable gene expression changes without affecting the DNA code. Research in epigenetics led to the discoveries of novel gene regulatory mechanisms with heritable features. A similar paradigm has now emerged with RNA. RNA carries the message encoded in the DNA. Yet this message itself can also be altered by chemical modifications. There are currently more than 150 diverse modifications found on RNA and a greater number of proteins are required for their biogenesis and recognition. Recent discoveries have shown that RNA modifications can be dynamically regulated and they have been implicated in embryonic development, longevity, neurological diseases and cancers in humans and in animal models.The heritable nature of epigenetic mechanisms requires gene expression changes within the germ cells, which give rise to the offspring. Germline development, germ cell proliferation and identity are essential for the survival of organisms. Epigenetic mechanisms play key roles in genome defence by targeting foreign elements and they also prevent somatic gene expression in the germ cells. Still, in some animals, it is possible to reprogram the epigenetic pathways to establish heritable gene expression changes that can last many generations.The biological role of most RNA modifications remains unclear in multicellular organisms and their role in heritable gene expression regulation is not explored. Research using the nematode Caenorhabditis elegans as an animal model made pioneering contributions to the discovery and understanding of epigenetic gene regulatory pathways in animal germlines. Up until recently, the RNA modification landscape of C. elegans was not know. In order to establish C. elegans as a model system to study the role of RNA modifications, I developed mass spectrometry methods that enable the identification and quantification of modified RNAs. Using these methods, I showed that several RNA modifications found in C. elegans show changes upon stress such as dietary restriction or high temperatures. In some instances, these changes in RNA modifications can be reversed.My research aims to uncover the role of a specific group of RNA modifications that contain a methyl group. By understanding how RNA methylations contribute to gene expression changes in germ cells, I aim to discover their epigenetic functions. Using a combination of biochemical and genetic methods, I will(i) develop an enzyme specific sequencing method for methylated RNAs(ii) study the role of RNA methylations in animal germ cells(iii) investigate how RNA methylome itself is regulated by dietary metabolismThis research is important because, first the proposed sequencing method will benefit a large research community and enable the profiling of RNA methylations in multicellular organisms. Second, understanding the role of RNA modifications in germ cells will reveal their role in cell proliferation and differentiation that will benefit research in human diseases such as cancer and fertility. And finally, my research has the potential to pioneer a new research direction on how our diet can affect gene expression through RNA modifications.