Dissecting quantitative, analogue, antisense-mediated transcriptional control

剖析定量、类似、反义介导的转录控制

• 批准号: BB/P020380/1
• 负责人: Martin Howard
• 金额: $ 95.83万
• 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: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP020380%2F1
• 关键词: Dissecting; quantitative; analogue; antisense; mediated

One of the most fundamental questions in molecular biology is how quantitative gene expression is achieved. Traditionally, such regulation is ascribed to sequence specific transcription factors that bind to regulatory DNA elements. According to the concentration of the transcription factors, gene expression can then be quantitatively up or down regulated. While in many systems, such regulation undoubtedly occurs, it has become abundantly clear in recent years that this paradigm is fundamentally incomplete. This is especially so in eukaryotes where transcription has to occur in the context of chromatin. There is now substantial data showing that quantitative regulation of transcription comes from modulation of the local chromatin environment of a gene. One possibility is that alteration of the chromatin environment could permit so-called kinetic regulation by, for example, altering the ability of RNA polymerase to progress through a gene. A further important feature of eukaryotic genes is non-coding transcription, often in an anti-sense direction. Whole genome studies have clearly shown that such transcription is pervasive, yet its role in regulating gene expression is obscure and hotly debated. Moreover, answering such mechanistic questions is difficult at the level of whole genomes. It is therefore imperative to focus on specific target loci, thoroughly dissect their mechanisms of regulation, and then leverage this knowledge to properly interpret whole genome datasets. We propose to implement this plan of action at a plant gene called FLC. FLC functions as a repressor of the transition to flowering, and as such is a gene whose expression is under tight, quantitative control. Our preliminary data indicates that FLC expression in warm temperature conditions is controlled in an analogue fashion, like a molecular dimmer switch. This is in contrast to its behaviour after exposure to prolonged cold where expression at individual loci is switched off permanently in an all or nothing digital fashion. Our goal here is to understand how analogue control is quantitatively achieved through a mechanism that appears to function through non-coding antisense transcription. Answering this question at a deep level will require a fusion of advanced multidisciplinary techniques from molecular biology and imaging to mathematical modelling, but will allow us to get to the mechanistic heart of quantitative transcriptional control.

分子生物学中最基本的问题之一是如何实现定量基因表达。传统上，这种调节归因于与调节DNA元件结合的序列特异性转录因子。根据转录因子的浓度，基因表达可以定量上调或下调。虽然在许多系统中，这种监管无疑会发生，但近年来已经非常清楚，这种模式从根本上说是不完整的。这在真核生物中尤其如此，其中转录必须在染色质的背景下发生。现在有大量的数据表明，转录的定量调控来自于基因局部染色质环境的调节。一种可能性是染色质环境的改变可以允许所谓的动力学调节，例如，改变RNA聚合酶通过基因的能力。真核基因的另一个重要特征是非编码转录，通常是反义方向。全基因组研究已经清楚地表明，这种转录是普遍存在的，但它在调节基因表达中的作用是模糊的，并引起了激烈的争论。此外，在整个基因组的水平上回答这样的机械问题是困难的。因此，必须专注于特定的目标基因座，彻底剖析其调控机制，然后利用这些知识来正确解释全基因组数据集。我们建议在一种名为FLC的植物基因上实施这一行动计划。FLC作为向开花转变的阻遏物起作用，并且因此是其表达处于严格定量控制下的基因。我们的初步数据表明，在温暖的温度条件下，FLC的表达控制在一个模拟的方式，像一个分子调光开关。这与其在长时间暴露于寒冷后的行为形成对比，在寒冷中，个体位点的表达以全或无的数字方式永久关闭。我们的目标是了解如何通过非编码反义转录的机制来定量地实现类似物控制。在深层次上解决这个问题将需要融合先进的多学科技术，从分子生物学和成像到数学建模，但这将使我们能够达到定量转录控制的机制核心。

项目成果

Integrating analog and digital modes of gene expression at Arabidopsis FLC.

• DOI: 10.7554/elife.79743
• 发表时间: 2023-07-19
• 期刊: eLife
• 影响因子: 7.7
• 作者: Antoniou-Kourounioti RL;Meschichi A;Reeck S;Berry S;Menon G;Zhao Y;Fozard J;Holmes T;Zhao L;Wang H;Hartley M;Dean C;Rosa S;Howard M
• 通讯作者: Howard M