Control of polyA site choice by m6A RNA modification

通过 m6A RNA 修饰控制 PolyA 位点选择

基本信息

批准号：
BB/V010662/1
负责人：
Gordon Simpson
金额：
$ 110.13万
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：
2021
资助国家：
英国
起止时间：
2021 至无数据
项目状态：
未结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FV010662%2F1
关键词：
Control polyA site choice m6A

项目摘要

Genes are found within DNA. When genes are switched on, their DNA code is copied into a related molecule called RNA. There are many ways that RNA can be further processed and, ultimately, this means that there are many different codes that can be made from the same gene. As a result, controlling the processing of RNA is fundamentally important to a cell.One example of these processing changes relates to where an RNA ends. Often different RNA copies of the same gene can stop at more than one place. As a result, a longer or shorter stretch of the gene's code is made and so the instructions contained within them are different. When the end of an RNA is determined, a string of more than 50 "A" bases (which we call the polyA tail) is added to the end of each RNA copy to protect it through its lifetime.The RNA code comprises 4 bases. In addition to A, there is G, C and U. However, sometimes these bases are altered with chemical modifications. The most common modification is the addition of a chemical methyl group to A. We have known this for some time, but only recently have we realised how important these RNA modifications can be. The BBSRC previously gave us funding to map the modified As in the RNAs. We succeeded in this objective by pioneering a new technique, called nanopore direct RNA sequencing, to identify modified As. In the same study, we found that the main consequence of losing this chemical modification was that the length of RNA copies shifts. In other words, the modified A could instruct the cell where to stop the copies of RNA made at thousands of genes.Our aim in this study is to work out how a modified A can tell the cell where to stop an RNA copy of a gene and when it does so what is the consequence? We have a good idea how to tackle this problem. The process of stopping an RNA copy and adding a polyA tail is controlled by a biological machine of more than 20 different proteins. These proteins are closely related in very different species. However, plants have evolved a special feature in one of these proteins because part of the protein can specifically recognise modified As. Our preliminary data analysis suggests that this part of this protein binds to the modified As and when it does so, it prevents RNA copies stopping nearby.It therefore seems that plants have made special use of this RNA modification to control where RNA copies of genes stop. The only other species that have this same special feature in the corresponding protein appear to be a group of animal parasites called the Apicomplexa. Some members of this group are responsible for human diseases such as malaria and toxoplasmosis. To tackle this problem, we have assembled a team with world leading expertise in plant RNA biology and the analysis of large RNA sequencing datasets. As a result of the work of this team, we will learn which genes are sensitive to RNA length control by modified As. We will determine which genes are directly controlled by this modification and identify proteins and protein complexes involved in this control. We will test how these interactions affect where an RNA copy stops. We will make the relevant protein and RNA molecules and test directly how they affect binding to each other. We will then ask what the consequence is for shortening RNA molecules from genes when regulation by modified As cannot occur. We will determine if the shortened RNAs are degraded more quickly or less able to be translated into protein.We hope to explain why plants have evolved a special way to control where copies of thousands of their genes stop. By understanding this, we should be well placed to address the same question in the group of parasites that appear to control their genes in a similar way. Dundee is home to the largest University-based drug discovery unit in the world. Consequently, we hope to establish sufficient knowledge here to implement a related study into these pathogens in the near future.

基因在DNA中发现。当基因打开时，它们的DNA代码被复制到称为RNA的相关分子中。 RNA可以进一步处理多种方法，最终，这意味着可以通过同一基因制成许多不同的代码。结果，控制RNA的处理对细胞根本重要。这些处理变化的一个例子与RNA结束的位置有关。通常，同一基因的不同RNA副本可以在多个地方停止。结果，制作了基因代码的更长或更短的范围，因此其中包含的说明是不同的。当确定RNA的末端时，将超过50个“ A”碱基（我们称为Polya尾巴）的字符串添加到每个RNA副本的末端，以通过其寿命保护它。RNA代码包括4个碱基。除A外，还有G，C和U。但是，有时这些碱会随着化学修改而改变。最常见的修饰是将化学甲基添加到A中。我们已经知道了一段时间，但是直到最近我们才意识到这些RNA修饰的重要性。 BBSRC先前向我们提供了资金来绘制RNA中的修改后的绘制。我们通过开创一种称为Nanopore Direct RNA测序的新技术来成功实现这一目标，以确定修改为AS。在同一项研究中，我们发现失去这种化学修饰的主要结果是RNA拷贝的长度在移动。换句话说，修改后的A可以指示该细胞停止以数千个基因制作的RNA副本。我们的目的是确定修改后的A可以告诉细胞如何停止基因的RNA副本，何时会导致其结果？我们有一个好主意解决这个问题。停止RNA拷贝并添加Polya尾巴的过程由20多种不同蛋白质的生物机器控制。这些蛋白质在非常不同的物种中密切相关。然而，植物在这些蛋白质之一中发展了一个特殊特征，因为部分蛋白质可以特异性地识别为修饰。我们的初步数据分析表明，该蛋白质的这一部分与经过修饰的那部分结合，它可以防止RNA拷贝在附近停止。因此，植物似乎已特别使用这种RNA修饰来控制基因的RNA拷贝在哪里停止。在相应的蛋白质中具有相同特征的唯一其他物种似乎是一组称为Apicomplexa的动物寄生虫。该组的一些成员负责疟疾和弓形虫病等人类疾病。为了解决这个问题，我们召集了一个拥有世界领先的植物RNA生物学专业知识和大型RNA测序数据集的团队。由于该团队的工作，我们将通过修改为RNA的长度控制哪些基因对RNA的长度控制敏感。我们将确定哪些基因直接由这种修饰控制，并鉴定该对照中涉及的蛋白质和蛋白质复合物。我们将测试这些相互作用如何影响RNA副本停止的位置。我们将制作相关的蛋白质和RNA分子，并直接测试它们如何相互影响。然后，我们将询问当通过不可能发生的修改调节时，从基因缩短RNA分子的结果是什么。我们将确定缩短的RNA是否会更快地或更少地转化为蛋白质。我们希望解释为什么植物已经进化了一种特殊的方式来控制其数千个基因的副本停止的位置。通过理解这一点，我们应该很好地解决似乎以类似方式控制其基因的寄生虫组中的相同问题。邓迪（Dundee）是世界上最大的大学药物发现部门的所在地。因此，我们希望在这里建立足够的知识，以在不久的将来对这些病原体实施相关研究。