Reading the genome: how do transcription factors achieve target specificity?

读取基因组：转录因子如何实现目标特异性？

• 批准号: BB/M007081/1
• 负责人: Robert White
• 金额: $ 59.69万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM007081%2F1
• 关键词: Reading; genome; how; do; transcription

Animal development and the normal physiological responses of the body rely upon the precise control of the activity of genes within the genome, a process controlled by regulatory proteins known as transcription factors. How transcription factors identify the genes they control by binding to specific DNA sequences in the nucleus remains a considerable challenge for biologists. We know that information dictating where and when a gene is switched on is encoded in the DNA sequence; however, we do not yet understand this regulatory code. One group of regulatory proteins known to control multiple aspects of development, the Hox family, includes a set of closely related factors found in all animals, from flies to humans. Our current understanding is that specific Hox proteins are responsible for controlling the structures that are produced along the body axis, such as where arms, legs or ribs develop. Mutations in Hox genes have dramatic consequences on the way animals look, for example the loss of the Ultrabithorax gene in the fly can result in the production of a four wing rather than a normal two wing fly and Hox mutations in humans can result in limb abnormalities such as the development of extra digits. While it is clear from genetics that individual Hox proteins have very different effects on development, paradoxically all Hox proteins are very similar and appear to recognise virtually identical DNA sequences that are believed to dictate the sets of genes they control. This general problem of specificity is common to most families of transcription factors. Some of the specificity may come from specific interactions with co-factor DNA binding proteins and we will explore this. To understand more about how the important class of Hox proteins are able to control specific sets of genes we use the fruit fly as a model system. The Hox proteins of the fly are closely related to those in humans but the fly genome is 20 times smaller, making analysis much easier. We can test Hox gene interactions with DNA, and the functional consequences of binding, by expressing Hox proteins under controlled conditions in a defined fly cell culture system. Understanding how Hox genes recognise specific genomic sequences and control genes is important for our basic understanding of how all animals develop and it is also important if we wish to gain insights into how evolution has produced the huge range of body plans we see around us. Our experiments will use a cell culture system to determine where all core Hox proteins bind in the genome and the effects they have on gene expression with and without their key DNA binding cofactors. We will then relate this binding to general features of the DNA in the nucleus, essentially how available a stretch of DNA sequence is for binding, to further understand the rules that determine where Hox proteins bind. This will help us to determine how these very similar proteins give rise to different regulatory outcomes. We will use these data to better understand the rules by which Hox proteins are able to recognise the DNA sequences that control genes, and discover differences for each of the Hox proteins. Since the Hox genes of mammals are organised and operate in the same way as those in flies, our work will help us understand how Hox genes control development of higher animals, including man. In addition, it has recently become clear that Hox genes are involved in several diseases, including cancers, thus a better understanding of how Hox genes work may, in the future, be useful when studying aspects of human disease. Since most families of gene regulators show similar properties to Hox proteins, our studies will also help address the more general issue of how genes are specifically controlled by sets of similar regulators. By studying the basis for this specificity, we will be able to make progress in understanding the regulatory code of the genome.

动物发育和人体的正常生理反应取决于基因组中基因活性的精确控制，这一过程由被称为转录因子的调节蛋白控制。转录因子如何通过与核中特定的DNA序列结合来鉴定其控制的基因仍然是生物学家的巨大挑战。我们知道，在DNA序列中编码了决定基因的何时何地的信息；但是，我们尚不了解此法规代码。一组已知可以控制发育多个方面的调节蛋白HOX家族，包括从苍蝇到人类的所有动物中发现的一组紧密相关的因素。我们目前的理解是，特定的HOX蛋白负责控制沿体轴（例如手臂，腿或肋骨）产生的结构。 HOX基因中的突变对动物的外观产生了巨大的后果，例如，蝇中超细硫代基因的丧失会导致产生四个翅膀而不是正常的两翼蝇和人类中的HOX突变会导致肢体异常，例如额外数字的发展。虽然从遗传学可以清楚地看出，单个HOX蛋白对发育的影响非常不同，但矛盾的是，所有HOX蛋白都非常相似，并且似乎识别几乎相同的DNA序列，这些DNA序列被认为决定了它们控制的基因集。大多数转录因素家族的普遍特异性问题是常见的。某些特异性可能来自与共同因素DNA结合蛋白的特定相互作用，我们将探讨这一点。为了更多地了解重要类HOX蛋白如何控制特定基因集，我们将果蝇用作模型系统。苍蝇的HOX蛋白与人类中的HOX蛋白密切相关，但苍蝇基因组小的20倍，使分析变得容易得多。我们可以通过在定义的蝇培养系统中在受控条件下表达HOX蛋白来测试HOX基因与DNA的相互作用以及结合的功能后果。了解HOX基因如何识别特定的基因组序列和控制基因对于我们对所有动物发展方式的基本理解很重要，并且如果我们希望深入了解进化如何产生我们周围看到的大量身体计划，这也很重要。我们的实验将使用细胞培养系统来确定所有核心HOX蛋白在基因组中的结合及其对具有和没有关键DNA结合辅助因子的基因表达的影响。然后，我们将将这种结合与原子核中DNA的一般特征联系起来，从本质上讲，DNA序列的结合是如何可用的，以进一步了解确定HOX蛋白在何处结合的规则。这将有助于我们确定这些非常相似的蛋白质如何产生不同的调节结果。我们将使用这些数据更好地理解HOX蛋白能够识别控制基因的DNA序列的规则，并发现每种HOX蛋白的差异。由于哺乳动物的HOX基因与苍蝇相同的方式进行了组织和运作，因此我们的工作将有助于我们了解Hox基因如何控制包括人在内的高等动物的发展。此外，最近很明显，HOX基因参与了包括癌症在内的多种疾病，因此对HOX基因的工作方式有了更好的了解，将来可能在研究人类疾病方面时会很有用。由于大多数基因调节剂家族都表现出与HOX蛋白相似的特性，因此我们的研究还将有助于解决基因如何通过一组相似调节剂特异性控制的更一般的问题。通过研究这种特异性的基础，我们将能够在理解基因组的监管代码方面取得进展。

项目成果

Regions of very low H3K27me3 partition the Drosophila genome into topological domains.

• DOI: 10.1371/journal.pone.0172725
• 发表时间: 2017
• 期刊: PloS one
• 影响因子: 3.7
• 作者: El-Sharnouby S;Fischer B;Magbanua JP;Umans B;Flower R;Choo SW;Russell S;White R
• 通讯作者: White R

Additional file 1: of Chromatin accessibility plays a key role in selective targeting of Hox proteins

附加文件 1：染色质可及性在选择性靶向 Hox 蛋白中发挥关键作用

• DOI: 10.6084/m9.figshare.8223326
• 发表时间: 2019
• 作者: Porcelli D

Chromatin Architecture in the Fly: Living without CTCF/Cohesin Loop Extrusion?: Alternating Chromatin States Provide a Basis for Domain Architecture in Drosophila.

• DOI: 10.1002/bies.201900048
• 发表时间: 2019-07
• 期刊: BioEssays : news and reviews in molecular, cellular and developmental biology
• 作者: N. Matthews;R. White

Chromatin Architecture in the Fly: Living without CTCF/Cohesin Loop Extrusion?: Alternating Chromatin States Provide a Basis for Domain Architecture in Drosophila

飞行中的染色质结构：没有 CTCF/粘连蛋白环挤出的生活？：交替的染色质状态为果蝇的域结构提供了基础

• DOI: 10.17863/cam.40390
• 发表时间: 2019
• 作者: Matthews N

Regions of very low H3K27me3 partition the Drosophila genome into topological domains

H3K27me3 非常低的区域将果蝇基因组划分为拓扑结构域

• DOI: 10.1101/072900
• 发表时间: 2016
• 作者: El-Sharnouby S