The Arabidopsis Epitranscriptome

奥地利修道士格雷戈尔·孟德尔（Gregor Mendel）在修道院花园里研究豌豆植物时，发现它们从父母那里遗传了我们现在所知的基因，这些基因控制着它们的生长方式。就像豌豆一样，我们染色体DNA中的基因拥有生命的密码。但是这个代码到底是什么呢？DNA是由四种不同类型的化学物质组成的长链：A、C、G和t。遗传密码被复制到一种叫做RNA的相关分子中，RNA是这种密码的信使。RNA由几乎相同的化学物质A、C和G组成，但U取代了t。细胞机器称为核糖体，接收信息并用它来构建与该密码相对应的蛋白质。有趣的是，RNA化学物质可以被改变，到目前为止，信使RNA链中最常见的修饰是m6A。因此，信使RNA实际上由五种不同的化学物质组成：A、C、G、U和m6A。你没听说过吗？令人惊讶的是，它很少受到关注，因为如果人类、苍蝇或植物没有它，它们就会死亡。最近，一种与几种人类疾病有关的名为FTO的人类基因被发现编码一种能够将m6A转换回a的蛋白质。这表明RNA中的m6A水平是可以控制的，如果这种水平被破坏，就可能导致疾病。m6A似乎不会改变遗传密码本身，但它确实会影响信息，从而影响密码在日常生活中的使用方式。这个项目是关于植物中的m6A的，但根据我们目前所做的，它也应该告诉我们关于动物和人类的情况。像孟德尔一样，我们的项目源于我们对植物的发现。在研究一种天然帮助植物开花的蛋白质时，戈登·辛普森（Gordon Simpson）的团队发现，这种蛋白质控制着信息结束的位置。使用一种特殊开发的技术，他们发现这种蛋白质与制造m6A的酶紧密相连。这在一定程度上是有道理的，因为RNA甲基化专家鲁伯特·弗赖（Rupert Fray）此前曾表明，m6A主要存在于信息的末尾。因此，戈登·辛普森和鲁伯特·弗赖用同样的技术来观察哪些蛋白质与制造m6A的酶密切相关，他们一起发现了几种蛋白质，这些蛋白质在许多不同的植物和动物中都高度相关，不仅在植物中，而且在人类中也帮助这些酶制造m6A。这个项目的目的是通过使用植物来更好地了解m6A。植物对我们的食物和能源安全至关重要，所以我们知道它们是如何工作的很重要。因为我们可以在实验室里培育出m6A水平发生改变但仍然存活的突变植物，我们可以更简单地研究它们，并利用这些知识试图理解为什么植物和动物在它们的遗传密码信息中使用m6A。首先，我们想知道哪些消息具有m6A，以及在消息中的哪个位置可以找到m6A。我们想知道这在不同的情况下是否会发生变化，比如花与叶的对比，或者当植物受到压力时。其次，我们想知道帮助我们发现的酶的因子是如何产生m6A的。它们是对所有基因都起作用，还是只对某些信息的某些特定部分起作用？它们是如何谈论它们对细胞中产生和读取代码的其他部分所做的事情的呢？第三，我们想要确切地了解当m6A发生变化时出现了什么问题。单独的消息会发生什么？最后，我们想开始了解如何读取m6A代码。带有YTH结构域的蛋白质显然与m6A结合，它们在植物中被发现，但我们不知道它们的作用。我们在这个领域组建了一个经验丰富的团队，我们希望了解关于我们遗传密码信息的非常基本的知识。这项工作将为在植物、遗传学、RNA、蛋白质和大型测序数据集的计算分析方面作为一个团队工作的早期职业科学家提供最先进的培训——汇集现代植物科学所需的技能，以确保未来的粮食和能源安全。

Working with pea plants in his monastery garden, the Austrian monk Gregor Mendel discovered that they inherit from their parents, what we now know to be genes, which control how they grow. Like peas, the genes in the DNA of our chromosomes have the code for life. But what is that code exactly? DNA is comprised of long chains of chemicals of four different types: A, C, G and T. The genetic code is copied into a related molecule called RNA that is the messenger of this code. RNA is comprised of almost the same chemicals, A, C, and G, but U replaces T. Cellular machines called ribosomes, take the message and use it to build proteins corresponding to this code. Interestingly, the RNA chemicals can be altered, and by far the most common modification within the messenger RNA chain is m6A. Consequently, messenger RNA is effectively comprised of five different chemicals: A, C, G, U and m6A. You never heard of it? It is surprising how little attention it has had because if humans, flies or plants don't have it, they die. Recently, a human gene called FTO, which is linked to several human diseases, was found to encode a protein able to convert m6A back to A. This revealed that m6A levels in RNA could be controlled, and if this was disrupted, disease could result. It seems that m6A doesn't change the genetic code itself, but it does affect the message and so affects how the code is used in everyday life. This project is all about m6A in plants, but based on what we have done so far, it should tell us about animals and people as well.Like Mendel, our project results from discoveries we have made with plants. While studying a protein that naturally helps plants flower, Gordon Simpson's team discovered it controlled where messages end. Using a specially developed technique, they discovered that this protein is found close together with enzymes that make m6A. This made some sense because Rupert Fray, an RNA methylation expert, had previously shown that m6A is mostly found near the end of messages. So, using the same techniques to see what proteins were closely associated with the enzymes that make m6A, Gordon Simpson worked with Rupert Fray, and together, they discovered several proteins that were highly related across lots of different plants and animals, that helped these enzymes make m6A not only in plants but in humans as well.The aim of this project is to understand m6A a lot better by using plants. Plants are vital to our food and energy security so it is important that we know how they work. Because we can make mutant plants in the lab that still live but have altered levels of m6A, we can study them more simply and use that knowledge to try to understand why plants and animals use m6A in the message of their genetic code.First, we want to know which messages have m6A and where in the message is this found. We want to know if this changes in different situations such as in flowers compared to leaves or when the plant is stressed. Second, we want to know how m6A is made by the factors that help the enzymes we have found. Do they do it to all genes, or only some and only in specific parts of some messages? How do they talk about what they are doing to all the other parts of the cell that are making and reading the code as well? Third, we want to understand exactly what goes wrong when m6A is changed. What happens to individual messages? Finally, we'd like to begin to understand how the m6A code is read. Proteins with YTH domains apparently bind m6A, they are found in plants but we don't know what they do. We form a hugely experienced team in this area and we hope to learn very basic knowledge about the message of our genetic code. This work will provide state-of-the-art training for early career scientists working as a team on plants, genetics, RNA, proteins and computational analysis of large sequencing datasets - assembling the skills modern plant science needs to ensure future food and energy security.