Tuning gene expression through antisense transcript dynamics

通过反义转录动力学调节基因表达

• 批准号: BB/K007203/1
• 负责人: Martin Howard
• 金额: $ 90.48万
• 依托单位: John Innes Centre
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FK007203%2F1
• 关键词: Tuning; gene; expression; through; antisense

How is gene expression controlled? This most fundamental of questions in molecular biology has been intensively studied over many decades. The overwhelming paradigm has been that expression is regulated by transcription factors that bind to regulatory DNA to switch on or off associated genes. The realisation about 10 years ago that such processes can be significantly influenced by noise has augmented but not overturned this framework. However, recent experiments from the genomic era of massive sequencing have begun to reveal gaps in this paradigm. In particular these experiments have revealed that most genomes are pervasively transcribed, so that not only protein-coding genes but also many other regions of the genome are transcribed to produce so called non-coding RNA. As a result, DNA is often transcribed not only in the direction needed to make a protein (the sense direction) but also in the opposite (antisense) direction. The question then arises as to what all this extra transcription is doing: is it an accident, the inevitable by-product of the noisy cellular environment, or does it perform some regulatory function? Increasingly, the conclusion that it does have an important regulatory role is becoming accepted. However, the actual mechanistic role played by non-coding, often antisense, RNA is very unclear. The majority of previous studies have probed these questions at the level of a whole genome from which it is very difficult to draw conclusions about the regulation of specific genes. In this project, we propose to take a tightly focused look at antisense RNA regulation in the context of a plant flowering gene called FLC.FLC is a repressor of flowering, and is a gene whose quantitative level of transcription is vital in ensuring that the plant flowers at an optimal time for reproductive success. Under normal conditions the precise level of transcription is believed to be controlled by two antisense non-coding RNAs. Here, we are seeking to understand how the differential production of these two antisense RNAs is able to tune the expression of the FLC gene. One possibility that we will attempt to prove (or disprove) is that each individual FLC gene makes only one of the two antisense transcripts for extended periods of time and switches randomly back and forth between one state and the other over time. The two different states are believed to have very different effects on the expression state of the FLC gene. By controlling the length of time the system spends in one or other of the (bistable) states, the sense FLC expression level can then be precisely tuned. We will test this hypothesis (and others) to reveal in unprecedented detail how non-coding RNA works as a quantitative regulator of expression. If we can get to the heart of this mechanism we will have moved closer to answering our starting question: how is gene expression controlled?

基因表达是如何控制的？这个分子生物学中最基本的问题已经被深入研究了几十年。压倒性的范式一直认为，表达受转录因子的调节，转录因子与调节DNA结合，以打开或关闭相关基因。大约10年前，人们认识到这些过程会受到噪音的显著影响，这增强了但没有推翻这一框架。然而，最近大规模测序的基因组时代的实验已经开始揭示这种范式的差距。特别是，这些实验揭示了大多数基因组是普遍转录的，因此，不仅蛋白质编码基因，而且基因组的许多其他区域也被转录以产生所谓的非编码RNA。因此，DNA不仅在合成蛋白质的方向上（正义方向）转录，而且在相反的方向上（反义方向）转录。那么问题来了，所有这些额外的转录在做什么：这是一个意外，是嘈杂的细胞环境不可避免的副产品，还是它发挥了某种调节功能？它确实发挥着重要的监管作用，这一结论正逐渐被人们所接受。然而，非编码（通常是反义）RNA的实际机制作用尚不清楚。以往的大多数研究都是在全基因组水平上探讨这些问题，很难从中得出关于特定基因调控的结论。在这个项目中，我们建议在植物开花基因FLC的背景下密切关注反义RNA调控。FLC是一种抑制开花的基因，其转录水平对确保植物在最佳时间开花繁殖成功至关重要。在正常情况下，转录的精确水平被认为是由两个反义非编码rna控制的。在这里，我们试图了解这两种反义rna的差异产生如何能够调节FLC基因的表达。我们将试图证明（或反驳）的一种可能性是，每个FLC基因在很长一段时间内只产生两种反义转录物中的一种，并随时间在一种状态和另一种状态之间随机地来回切换。这两种不同的状态被认为对FLC基因的表达状态有非常不同的影响。通过控制系统在一种或另一种（双稳态）状态中花费的时间长度，可以精确地调节感FLC表达水平。我们将测试这一假设（以及其他假设），以前所未有的细节揭示非编码RNA如何作为表达的定量调节剂。如果我们能找到这个机制的核心，我们就更接近于回答我们开始的问题：基因表达是如何被控制的？

项目成果

Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation.

• DOI: 10.1016/j.cels.2017.05.010
• 发表时间: 2017-06-28
• 期刊: Cell systems
• 影响因子: 9.3
• 作者: Ietswaart R;Rosa S;Wu Z;Dean C;Howard M
• 通讯作者: Howard M