The Arabidopsis Epitranscriptome

拟南芥表观转录组

• 批准号: BB/M010066/1
• 负责人: Gordon Simpson
• 金额: $ 103.27万
• 依托单位: University of Dundee
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM010066%2F1
• 关键词: Arabidopsis; Epitranscriptome

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.

奥地利修道士格雷戈尔·孟德尔（Gregor Mendel）在他的修道院花园里研究豌豆时发现，豌豆从父母那里继承了我们现在所知道的基因，控制着它们的生长。就像豌豆一样，我们染色体DNA中的基因也有生命的密码。但那密码到底是什么？DNA由四种不同类型的化学物质组成：A，C，G和T。遗传密码被复制到一种称为RNA的相关分子中，RNA是该密码的信使。RNA由几乎相同的化学物质A、C和G组成，但U取代了T。被称为核糖体的细胞机器，接收信息并使用它来构建与此代码相对应的蛋白质。有趣的是，RNA的化学物质是可以改变的，到目前为止，信使RNA链中最常见的修饰是m6 A。因此，信使RNA有效地由五种不同的化学物质组成：A，C，G，U和m6 A。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，一种名为FTO的人类基因被发现编码一种能够将m6 A转化回A的蛋白质，该基因与几种人类疾病有关。这表明RNA中的m6 A水平是可以控制的，如果这种水平被破坏，可能会导致疾病。m6 A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m6 A的，但是基于我们目前所做的，它应该告诉我们关于动物和人的信息。像孟德尔一样，我们的项目是我们在植物中发现的结果。在研究一种天然帮助植物开花的蛋白质时，戈登·辛普森的团队发现它控制着信息的结束。使用一种专门开发的技术，他们发现这种蛋白质与制造m6 A的酶紧密结合。这是有道理的，因为RNA甲基化专家鲁珀特弗雷（Rupert Fray）此前曾证明，m6 A大多出现在信息的末尾。因此，为了研究哪些蛋白质与制造m6 A的酶密切相关，戈登·辛普森和鲁珀特·弗雷一起使用同样的技术，他们发现了几种在许多不同的植物和动物中高度相关的蛋白质，这些蛋白质不仅帮助这些酶在植物中制造m6 A，也帮助人类制造m6 A。这个项目的目的是通过植物更好地了解m6 A。植物对我们的粮食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中制造突变植物，这些植物仍然存活，但m6 A的水平发生了变化，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其遗传密码的信息中使用m6 A。我们想知道哪些消息有m6 A，以及在消息中的什么地方找到了m6 A。我们想知道这在不同的情况下是否会发生变化，例如在花和叶子中的变化。或者当植物受到压力时。第二，我们想知道m6 A是如何被那些帮助我们发现的酶的因子制造出来的，它们是对所有基因都这样做，还是只对某些基因，或者只对某些信息的特定部分这样做？它们如何谈论它们对细胞的其他部分做了什么，这些部分也在制造和阅读代码？第三，我们想确切地了解m6 A改变时会出现什么问题。个人信息会发生什么？最后，我们想开始了解m6 A代码是如何读取的。具有YTH结构域的蛋白质显然与m6 A结合，它们在植物中发现，但我们不知道它们做什么。我们在这一领域组建了一支经验丰富的团队，我们希望了解有关我们遗传密码信息的基本知识。这项工作将为早期职业科学家提供最先进的培训，他们作为一个团队在植物，遗传学，RNA，蛋白质和大型测序数据集的计算分析方面工作-组装现代植物科学所需的技能，以确保未来的粮食和能源安全。

项目成果

How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome?

• DOI: 10.1101/090753
• 发表时间: 2016-12
• 期刊: bioRxiv
• 作者: Kimon Froussios;N. Schurch;Katarzyna Mackinnon;M. Gierliński;Céline Duc;G. Simpson;G. Barton

Detection and mitigation of spurious antisense expression with RoSA

使用 RoSA 检测和减轻虚假反义表达

• DOI: 10.12688/f1000research.18952.1
• 发表时间: 2019
• 期刊: F1000Research
• 作者: Mourão K

Detection and Mitigation of Spurious Antisense Reads with RoSA

使用 RoSA 检测和减少虚假反义读取

• DOI: 10.1101/425900
• 发表时间: 2018
• 作者: Mourão K

Identifying differential isoform abundance with RATs: a universal tool and a warning

• DOI: 10.1101/132761
• 发表时间: 2017-05
• 期刊: bioRxiv
• 作者: Kimon Froussios;Kira Mourão;G. Simpson;G. Barton;N. Schurch

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

• DOI: 10.1101/2020.12.15.422694
• 发表时间: 2020-12
• 期刊: eLife
• 影响因子: 7.7
• 作者: Matthew T. Parker;Katarzyna Knop;Vasiliki Zacharaki;Anna V. Sherwood;Daniel Tomé;Xuhong Yu;Pascal Martin;J. Beynon;S. Michaels;G. Barton;G. Simpson