Control of polyA site choice by m6A RNA modification

基因存在于DNA中。当基因被激活时，它们的DNA代码被复制到一个名为RNA的相关分子中。有许多方法可以进一步处理RNA，这最终意味着有许多不同的密码可以由相同的基因组成。因此，控制RNA的加工对细胞来说至关重要。这些加工变化的一个例子与RNA的末端有关。通常情况下，同一基因的不同RNA拷贝可能会停在不止一个地方。因此，基因编码的长度会更长或更短，因此其中包含的指令也会有所不同。当RNA的末端被确定时，一串50多个“A”碱基(我们称之为Polya尾巴)被添加到每个RNA拷贝的末端，以在其生命周期中保护它。除了A，还有G、C和U。然而，有时这些碱基会被化学修饰改变。最常见的修饰是在A中添加化学甲基。我们知道这一点已经有一段时间了，但直到最近我们才意识到这些RNA修饰有多么重要。BBSRC之前给了我们资金来映射RNAs中修改的AS。我们通过开创一种名为纳米孔直接RNA测序的新技术来识别修饰的AS，从而成功地实现了这一目标。在同一项研究中，我们发现失去这种化学修饰的主要后果是RNA拷贝的长度发生了变化。换句话说，修改后的A可以指示细胞在哪里停止在数千个基因上复制的RNA。我们在这项研究中的目的是弄清楚修改后的A如何告诉细胞在哪里停止一个基因的RNA复制，当它这样做时，结果是什么？我们有一个很好的主意来解决这个问题。停止RNA复制和添加Polya尾巴的过程由一台由20多种不同蛋白质组成的生物机器控制。这些蛋白质在非常不同的物种中密切相关。然而，植物已经在其中一种蛋白质中进化出了一个特殊的特征，因为这种蛋白质的一部分可以特异性地识别修饰的AS。我们的初步数据分析表明，这一蛋白的这一部分与修饰的AS结合，当它这样做时，它防止RNA拷贝停止在附近。因此，植物似乎已经特殊地利用这种RNA修饰来控制基因的RNA拷贝停止的位置。唯一在相应蛋白质中具有这一特殊特征的其他物种似乎是一组被称为Apicomplexa的动物寄生虫。该组织的一些成员对疟疾和弓形虫病等人类疾病负有责任。为了解决这个问题，我们组建了一个在植物RNA生物学和大型RNA测序数据集分析方面拥有世界领先专业知识的团队。作为这个团队工作的结果，我们将了解到哪些基因对通过修饰的AS控制RNA长度敏感。我们将确定哪些基因直接受到这种修饰的控制，并确定参与这种调控的蛋白质和蛋白质复合体。我们将测试这些交互作用如何影响RNA复制的停止位置。我们将制造相关的蛋白质和RNA分子，并直接测试它们如何影响彼此的结合。然后，我们会问，当不能发生修饰AS的调控时，缩短基因中的RNA分子会产生什么后果。我们将确定缩短的RNA的降解速度是更快还是更慢，能够转化为蛋白质。我们希望解释为什么植物进化出一种特殊的方式来控制数千个基因的拷贝停止在哪里。通过理解这一点，我们应该能够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，以便在不久的将来对这些病原体进行相关研究。

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.