Developing tools to investigate combinatorial control of mRNA metabolism

我们的身体由200多种不同的细胞组成，它们具有不同的大小，形式和功能。例如，皮肤细胞是扁平的，可以保护我们的身体，而神经元可以很长，可以将信号从身体的远处传递到我们的大脑。然而，所有细胞都包含相同的遗传信息，这些信息被组织成基因。使细胞彼此独特和不同的是哪些基因被打开或关闭。当这个开关不能正常工作时，它会导致发育缺陷或癌症等疾病。遗传信息以DNA的形式存储。然后，DNA被复制到一种称为RNA的分子中，RNA是蛋白质合成的模板，这一过程称为翻译。蛋白质使我们的细胞看起来像什么，他们做什么。RNA在细胞中不是裸露的，而是被几种蛋白质覆盖，即所谓的RNA结合蛋白。这些RNA结合蛋白可以去除或重新排列RNA的部分，将它们储存或运送到特定位置，并最终破坏RNA。它们还控制RNA翻译成蛋白质的效率。因此，RNA结合蛋白就像一座控制塔，指挥RNA的命运，储存、翻译或破坏。因此，如果RNA结合蛋白不能正常工作，它可能会导致疾病。除了RNA结合蛋白，近年来的研究表明，还有某些类型的RNA-所谓的非编码RNA-可以结合并调节其他RNA。因此，RNA受RNA结合蛋白和非编码RNA的组合控制。因此，了解哪些蛋白质和非编码RNA与RNA相互作用以及在疾病情况下如何改变是非常有趣的。然而，获取这些信息是具有挑战性的，因为研究人员缺乏简单而强大的工具来调查它。我们的目标是开发这些工具，并全面识别与RNA结合的蛋白质和非编码RNA。我们的目标首先是获得细胞中与RNA相互作用的所有蛋白质的总体视图。然后，我们将在特定的RNA上设计一个把手，将其拉出来，并寻找其上的蛋白质和其他RNA。然后，我们将仔细观察这些“反式作用因子”的组成如何在模拟癌细胞环境的条件下发生变化。建立新的研究工具的一种方法是在一个比人类细胞更容易操作的模型中进行测试。因此，我们将首先在面包酵母中建立工具，这是一种称为酿酒酵母的单细胞生物。然后，我们向前迈出一步，建立人类细胞，以确定RNA结合蛋白和非编码RNA，这些蛋白和非编码RNA调节RNA在癌症中的关键功能。最后，我们期望更好地了解RNA结合蛋白和非编码RNA的组合如何影响RNA的命运。我们希望这一发现将为我们提供重要的线索，了解蛋白质的生产如何出错，从而在癌细胞中发挥关键作用。最终，这可能会为药物开发和人类疾病治疗带来新的目标。

Our body consists of more than 200 different cell-types that have different sizes, forms, and functions. For example, skin cells are flat and protect our body, whereas neurons can be very long and transmit signals from distant parts of the body to our brain. Nevertheless, all cells contain the same genetic information, which is organized into genes. What makes the cells unique and different from one to another is which genes are turned on or off. When this switch does not work properly, it can lead to developmental defects or diseases such as cancer.The genetic information is stored in the form of DNA. The DNA is then copied to a molecule called RNA, which is the template for the synthesis of proteins in a process called translation. The proteins make our cells how they look like and what they do. RNAs are not naked in a cell but rather covered by several proteins, so-called RNA-binding proteins. These RNA-binding proteins can remove or rearrange parts of the RNA, store or deliver them to particular locations, and ultimately destroy the RNA. They also control how efficiently RNAs are translated into proteins. RNA-binding proteins therefore act as a control tower directing the fate of RNA, being stored, translated or destroyed. As a consequence, if a RNA-binding protein does not work properly, it can lead to diseases.Besides the RNA-binding proteins, research in the last years revealed that there are certain classes of RNAs - so called non-coding RNAs - that can bind to and regulate other RNAs. RNAs are therefore combinatorially controlled by both RNA-binding proteins and non-coding RNAs. Therefore, it is of immense interest to know, which proteins and non-coding RNAs interact with RNA and how this may be changed in case of a disease. Nevertheless, accessing this information is challenging as researchers lack simple and robust tools to investigate it.Our objective is to develop these tools and comprehensively identify the proteins and non-coding RNAs that are bound to RNAs. We first aim to get a general view of all the proteins that interact with RNA in a cell. We will then engineer a handle on a particular RNA to pull it out and look for the proteins and other RNAs that sit on it. We will then have a close look how the composition of these 'trans-acting factors' changes upon conditions that simulate the environment in cancer cells.One way to establish a new tool for research is to test it in a model which is simpler to handle than human cells. We will therefore first establish the tool in the bakers yeast, which is a single-celled organisms called Saccharomyces cerevisiae. We then go one step ahead and establish it human cells in order to identify the RNA-binding proteins and non-coding RNAs that regulate RNAs with pivotal functions in cancer. At the end, we expect a better understanding how combinations of RNA-binding proteins and non-coding RNAs affect the fate of RNAs. We hope that this insight will give us important clues about how the production of proteins can go wrong to play a critical role in cancer cells. Ultimately, this may lead to new targets for drug development and the treatment of human disease.