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.

奥地利僧侣格雷戈尔·门德尔（Gregor Mendel）在他的修道院花园中与豌豆植物一起工作，发现他们从父母那里继承了，我们现在知道是控制它们成长的基因。像豌豆一样，我们染色体DNA中的基因也有生命的代码。但是那是什么代码？ DNA由四种不同类型的化学物质的长链组成：A，C，G和T。遗传密码被复制到一个称为RNA的相关分子中，该分子是该代码的使者。 RNA由几乎相同的化学物质A，C和G组成，但U取代了T.核糖体的T.细胞机，采用消息并使用它来构建与此代码相对应的蛋白质。有趣的是，RNA化学物质可以改变，到目前为止，信使RNA链中最常见的修饰是M6A。因此，信使RNA有效地由五种不同的化学物质组成：A，C，G，U和M6A。你从未听说过吗？令人惊讶的是，它的关注很少，因为如果人类，苍蝇或植物没有它，他们就会死亡。最近，发现一种与几种人类疾病有关的人类基因，该基因被发现可以编码能够将M6A转换回A的蛋白质。这表明RNA中的M6A水平可以控制，如果这受到干扰，可能会导致疾病。似乎M6A不会改变遗传代码本身，但确实会影响信息，因此会影响代码在日常生活中的使用方式。这个项目与植物中的M6A有关，但是根据到目前为止我们所做的事情，它也应该告诉我们有关动物和人的信息。戈登·辛普森（Gordon Simpson）的团队在研究一种自然可以帮助植物开花的蛋白质时发现了它的控制信息。他们使用专门开发的技术发现，该蛋白与制造M6A的酶结合在一起。这是有道理的，因为RNA甲基化专家Rupert Fray先前表明M6A大多在消息结束附近发现。因此，使用相同的技术来查看哪些蛋白质与制造M6A的酶密切相关，Gordon Simpson与Rupert Fray合作，共同发现了几种在许多不同的动植物中高度相关的蛋白质，这些蛋白质在许多不同的动植物中都有高度相关的蛋白质，这些酶在人类中不仅在人类中不仅在植物中都可以通过植物来了解M6A。植物对我们的粮食和能源安全至关重要，因此我们必须知道它们的工作原理很重要。因为我们可以使实验室中的突变植物仍然活着但已经改变了M6A的水平，所以我们可以更简单地研究它们，并使用该知识来了解为什么植物和动物在其遗传密码的信息中使用M6A。首先，我们想知道哪些消息具有M6A，并且在此信息中找到了哪些信息。我们想知道，与叶子相比或植物的压力时，这种情况是否在不同情况下发生了变化。其次，我们想知道如何通过有助于我们发现的酶的因素制造M6A。他们是否对所有基因或仅在某些消息的特定部分中都这样做？他们如何谈论他们在制作和读取代码的细胞的所有其他部分中所做的事情？第三，我们想确切了解M6A更改时出了什么问题。单个消息会怎样？最后，我们想开始了解如何读取M6A代码。具有YTH域的蛋白质显然结合了M6a，它们是在植物中发现的，但我们不知道它们的作用。我们在该领域组建了一支经验丰富的团队，我们希望能够学习有关我们遗传密码信息的非常基本的知识。这项工作将为大型测序数据集的植物，遗传学，RNA，蛋白质和计算分析的早期职业科学家提供最先进的培训 - 组装现代植物科学的技能，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

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

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