Elucidating mechansims and roles of alternative polyadenylation

阐明替代聚腺苷酸化的机制和作用

基本信息

批准号：
BB/H002286/1
负责人：
Gordon Simpson
金额：
$ 98.74万
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：
2009
资助国家：
英国
起止时间：
2009 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FH002286%2F1
关键词：
Elucidating mechansims roles alternative polyadenylation

项目摘要

Our genes are made of DNA, but when they are switched on, copies are made in a related molecule called RNA and this RNA goes on to code for the protein products of our genes. As the gene is copied into RNA, the RNA is cut and a string of Adenine molecules (A for short) are added at the end. This so-called 'poly A tail' functions to protect the RNA from being degraded, and helps to transport the RNA around the cell and stimulates the formation of protein from the RNA. The site at which the poly A tail is added is not always the same, even for the same gene. For example, half of all human genes have RNAs with more than one site for adding a poly A tail. Controlling the site at which the poly A tail is added is very important because it ultimately affects how genes function. However, this is a process we know surprisingly little about. It's not just human RNAs that have different poly A tails, other animals and plants do too. We have been studying how plants control the time at which they flower, a process where genes are very precisely controlled. In the course of this work, we have discovered that three factors called FCA, FY and, most recently, FPA, function to control poly A site selection of some RNAs. Such basic aspects of gene expression are very similar in plants and animals and it turns out that there are human proteins highly related to FY and FPA. It is possible therefore, that these proteins control poly A site selection in humans too, but very little is known about them. As we have found that FCA and FPA don't need each other to control poly A site choice, we think they must be doing this in different ways. This gives us a chance to understand how poly A site choice can be controlled. In this proposal we plan to build on what we know about FCA and FPA in plants, but this knowledge should be of much more general interest. We want to know two things: (1) How do FCA and FPA control the site at which a poly A tail is added (2) What genes do FCA and FPA regulate by controlling alternative poly A site choice? We will work out how FCA and FPA control poly A sites by identifying the features of the RNA required. This should be quite straightforward. We will make test genes containing different parts of the target gene and see how they affect poly A site selection when placed back in plants. In order to find the other genes whose normal poly A tail depends on FCA and FPA, we will look at where RNAs are polyadenylated in normal plants and in mutant plants that lack FCA or FPA. It is now possible for us to look at nearly all the RNAs in a cell thanks to Next Generation Sequencing, a technology that is revolutionizing modern biology by giving us huge amounts of sequence data, very quickly and at a fraction of the cost to before. This technology has been developed to look at RNA by sequencing a short part of every RNA, sufficient to identify it, called a 'tag'. To find the tag, scientists use the poly A tail and sequence what is next to it. This is a happy coincidence for us, because it means that in addition to tagging a particular RNA, this method also tells us where a poly A tail has been added to RNA. To analyse the large amounts of data and make comparisons, we will need to develop specialized computational tools. Because we already know genes where FCA and FPA control poly A site selection, we should be able to find changes in these 'tags' if our tools are working well. Once we are sure they are, we can look for other shifts in 'tags' to identify other genes controlled by FCA and FPA. As lots of other scientists are also using this sequencing technology, but for completely different reasons, we can use our analysis tools to look at changes in polyadenylation in their data too. In this way we will be able to identify cell-types and situations where alternative polyadenylation is an important part of gene regulation.

我们的基因是由DNA制成的，但是当它们打开时，拷贝是用称为RNA的相关分子制成的，该RNA继续为我们基因的蛋白质产物代码。当将基因复制到RNA中时，切开RNA，并在末尾添加一串腺嘌呤分子（A短）。这种所谓的“ poly a尾巴”功能可保护RNA免受降解，并有助于将RNA转运在细胞周围并刺激从RNA中形成蛋白质。即使对于同一基因，添加多A尾的位置并不总是相同的。例如，所有人类基因中有一半的RNA具有多个位点用于添加多A尾的位置。控制添加多A尾的位点非常重要，因为它最终会影响基因的功能。但是，这是我们几乎不知道的过程。具有不同的聚尾部，其他动物和植物也这样做的不仅是人类RNA。我们一直在研究植物如何控制它们开花的时间，这一过程非常精确地控制了基因。在这项工作的过程中，我们发现三个称为FCA，FY和最近是FPA的因素可以控制某些RNA的位点选择。基因表达的基本方面在动植物中非常相似，事实证明，人类蛋白质与FY和FPA高度相关。因此，这些蛋白质也可能控制着人类中的位点选择，但对它们知之甚少。由于我们发现FCA和FPA不需要彼此来控制Poly A网站选择，因此我们认为他们必须以不同的方式进行此操作。这使我们有机会了解如何控制poly a网站选择。在此提案中，我们计划基于我们对植物中FCA和FPA的了解，但是这种知识应该更加普遍。我们想知道两件事：（1）FCA和FPA如何控制添加多A尾的位点（2）通过控制替代poly A网站选择，FCA和FPA调节了哪些基因？我们将通过识别所需RNA的特征来弄清FCA和FPA控制聚A位点。这应该很简单。我们将制作包含靶基因不同部分的测试基因，并查看它们在植物中的影响时如何影响多个位点的选择。为了找到正常聚A尾的其他基因取决于FCA和FPA，我们将研究RNA在正常植物中以及缺乏FCA或FPA的突变植物中的聚腺苷酸化的位置。现在，由于下一代测序，我们可以查看单元格中几乎所有的RNA，这项技术正在通过为我们提供大量序列数据的彻底彻底改变现代生物学，这是非常迅速的，以前的一小部分。该技术是通过对每个RNA的一小部分进行测序（足以识别它的“ TAG”的，来研究RNA的。为了找到标签，科学家使用poly a尾巴并顺序序列。这对我们来说是一个快乐的巧合，因为这意味着除了标记特定的RNA外，此方法还告诉我们，将多A尾添加到RNA中。为了分析大量数据并进行比较，我们将需要开发专门的计算工具。因为我们已经知道FCA和FPA控制Poly A网站选择的基因，所以如果我们的工具运行良好，我们应该能够在这些“标签”中找到更改。一旦确定它们是，我们就可以在“标签”中寻找其他变化，以识别由FCA和FPA控制的其他基因。由于许多其他科学家也在使用此测序技术，但是由于完全不同的原因，我们也可以使用分析工具来查看其数据中聚腺苷酸化的变化。通过这种方式，我们将能够鉴定出替代聚腺苷酸化是基因调节的重要组成部分的细胞类型和情况。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation.

DOI：
10.1038/srep02866
发表时间：
2013-10-09
期刊：
SCIENTIFIC REPORTS
影响因子：
4.6
作者：
Lyons, Rebecca;Iwase, Akira;Gansewig, Thomas;Sherstnev, Alexander;Duc, Celine;Barton, Geoffrey J.;Hanada, Kousuke;Higuchi-Takeuchi, Mieko;Matsui, Minami;Sugimoto, Keiko;Kazan, Kemal;Simpson, Gordon G.;Shirasu, Ken
通讯作者：
Shirasu, Ken

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使用 RoSA 检测和减轻虚假反义表达