The non-coding Arabidopsis genome

我们过去的想法是这样的：我们的染色体是由DNA组成的，嵌入其中的是我们的基因。当我们的基因被打开时，它们被转化为一种称为RNA的相关分子，最终将我们基因的密码转化为蛋白质，这些蛋白质在我们的细胞中执行所有任务。我们染色体中的大部分DNA不编码这些基因，因此是垃圾。但我们现在对事情的看法有点不同：尽管人类基因组在10年前就被测序了，但我们仍在研究它的编码。令我们惊讶的是，它被复制到RNA中的数量远远超过编码蛋白质的数量。我们称之为非编码RNA，事实证明，许多RNA在控制蛋白质编码基因的开启、关闭或修饰方面发挥着关键作用。我们现在意识到，要了解基因和基因组是如何工作的，我们需要发现非编码RNA并弄清楚它们的作用。我的实验室对植物如何控制花的发育很感兴趣。我们发现非编码RNA控制着花的形成，这让我们对非编码RNA产生了兴趣。DNA测序最近被所谓的下一代测序技术彻底改变。这种方法也可以用来测序RNA的拷贝，使我们能够识别细胞中产生的所有RNA。RNA的复制是由一种叫做RT的东西制造的，所以我们几乎从不直接观察RNA。不幸的是，RT可能会出错，所以我们对RNA的解释可能是错误的。去年，一家名为Helicos Biosciences的公司开发了第三代测序技术，可以直接对RNA进行测序。我们与这家公司合作，对拟南芥（Arabidopsis）中RNA分子的末端进行了测序（这是第一种对其整个基因组进行测序的植物）。在这样做的同时，我们也发现了许多非编码RNA，以及之前使用RT观察RNA的实验中存在的许多问题。在这个提议中，我们希望利用这项技术来发现和注释拟南芥的非编码RNA。由于所有其他植物基因组的注释大部分来自拟南芥，这将对理解其他植物基因组非常宝贵，包括我们赖以获取食物和燃料的作物。我们将寻找隐藏的RNA和长的非编码RNA。一些非编码RNA几乎和它们被制造一样快被破坏，所以它们通常被有效地隐藏起来。但是它们可以在缺乏外泌体的植物中看到-外泌体是一组破坏RNA的蛋白质。我们已经证明，在之前观察这些RNA的尝试中存在很多错误，所以我们知道我们的方法是准确显示这些RNA细节的好方法。我们已经进行的RNA测序鉴定了许多以前没有发现的RNA。问题是我们的测序只确定了这些RNA的末端，我们不知道整个RNA分子的性质。最近一项对人类非编码RNA的研究发现，将RNA片段化、测序和比较染色体上的特殊标记有助于发现基因的起始位置和基因的“主体”。我们将在拟南芥中采用相同的方法，但直接测序RNA而不是RT复制。在这个提议中，我们还将尝试识别我们发现的大量RNA的功能。在人类中，长的非编码RNA充当了特殊蛋白质的支架，这些蛋白质可以关闭基因。我们将在拟南芥中找到与这些蛋白质结合的RNA。我的实验室在这方面有特殊的专业知识，因为我们是第一个展示如何在拟南芥中做到这一点的实验室。最后，我们最近的突破确定了一组非编码RNA，它们大多完成了相当好的工作：snoRNA帮助修饰其他RNA。不幸的是，我们发现人们看待拟南芥非编码RNA的方式存在很多问题，这些问题可以用snoRNA和RT错误来解释。为了防止将来发生这种情况，我们将整理这些RNA的注释。

What we used to think goes something like this: Our chromosomes are made of DNA and embedded within them are our genes. When our genes are switched on, they are converted into a related molecule called RNA, which eventually converts the code of our genes into proteins that carry out all the tasks in our cells. Much of the DNA in our chromosomes doesn't encode such genes and is therefore junk. But we think of things a little differently now: Although the human genome was sequenced 10 years ago we are still working out what it codes for. To our surprise much more of it is copied into RNA than that which codes for proteins. We call these non-coding RNAs and it turns out that many play critical roles in controlling how protein coding genes are switched on, off, or modified. We now realize that to understand how genes and genomes work, we need to discover non-coding RNAs and work out what they do. My lab is interested in how plants control flower development. We have discovered that non-coding RNAs control when flowers are made and this has got us interested in non-coding RNAs. DNA sequencing has been revolutionized recently by so-called next generation sequence technology. This approach can be used to sequence copies of RNA too, allowing us to identify all the RNAs made in a cell. Copies of RNA are made by something called RT, so we almost never look at RNA directly. Unfortunately RT can make mistakes so our interpretations about RNA can be wrong. Last year a company called Helicos Biosciences developed a 3rd Generation sequencing technology that can sequence RNA directly. We have collaborated with this company to sequence the ends of RNA molecules in Arabidopsis (the first plant to have its entire genome sequenced). While doing this we also found lots of non-coding RNAs and lots of problems with previous experiments that used RT to look at RNA. In this proposal we want to build on our breakthroughs with this technology to discover and annotate the non-coding RNAs of Arabidopsis. As the annotation of all other plant genomes largely derives from Arabidopsis, this will be invaluable in understanding other plant genomes, including the crops that we depend on for food and fuel. We will look for hidden RNAs and long non-coding RNAs. Some non-coding RNAs are destroyed almost as quickly as they are made, so they are normally effectively hidden. But they can be seen in plants that lack the exosome - a group of proteins that destroy RNAs. We have already shown there are lots of mistakes in a previous attempt to look at these RNAs, so we know that our approach is a great way to show these RNAs in accurate detail. The RNA sequencing we have already carried out identified lots of RNAs not previously found before. The trouble is our sequencing only identified the ends of these RNAs and we don't know the nature of the whole RNA molecule. A recent study of human non-coding RNAs found it helpful to fragment RNA, sequence, and compare special marks on chromosomes found where genes start and where the 'body' of a gene is. We will take the same approach here with Arabidopsis, but sequence RNA directly rather than RT made copies. In this proposal, we will also try to identify a function for a large number of the RNAs we find. In humans, long non-coding RNAs act as a scaffold for special proteins that switch genes off. We will find RNAs that bind to these proteins in Arabidopsis. My lab has special expertise here, as we were among the first to show how to do this in Arabidopsis. Finally, our recent breakthroughs identified a set of non-coding RNAs that mostly do a quite well worked out job: snoRNAs help modify other RNAs. Unfortunately, we found lots of problems in the way people have looked at Arabidopsis non-coding RNAs that can be explained by snoRNAs and RT mistakes. To prevent this happening in the future, we will sort out the annotation of these RNAs.