Dynamics of global chromatin landscape through the cell cycle and differentiation

通过细胞周期和分化的整体染色质景观的动态

• 批准号: BB/L009358/1
• 负责人: James Murray
• 金额: $ 82.63万
• 依托单位: CARDIFF UNIVERSITY
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL009358%2F1
• 关键词: Dynamics; global; chromatin; landscape; through

The genomes of all higher organisms are packaged in a form known as chromatin, a combination of the DNA and proteins that are bound to it. This packaging of DNA into chromatin is essential because each individual chromosome consist of a single molecule of DNA up to several centimeters long but which must to be packaged up in a cell nucleus only a few micrometers across. Indeed the total DNA length in a normal human cell is about 2m. At the same time, the DNA must be accessible when required to allow a controlled expression of genes, or the copying of DNA during the cell division cycle. The basic unit of chromatin packaging is known as the nucleosome, which consists of a core of special highly conserved proteins known as histones around which the DNA is wrapped approximately twice. Nucleosomes appear to be located in specific positions, particularly around important features such as genes. It has become clear that many characteristics of organisms, and some diseases, are affected by so-called epigenetic modifications, resulting from changes in the chromatin or modification of the DNA rather than changes in the underlying DNA sequence itself. Hence understanding chromatin is of fundamental importance in many biological processes.In addition to nucleosomes, there are many other complexes of proteins that bind to DNA for a number of purposes, particularly the controlled expression of genes. The pattern of nucleosomes and other proteins binding to DNA can be visualised by using enzymes that cut DNA only where no proteins are bound. Regions that are protected are not cut, and digesting chromatin with such enzymes generates many millions of DNA fragments. These are predominantly the size of single or multiple nucleosomes. We have developed a new technology that can simultaneously determine all such protected regions across the entire genome, and hence map every nucleosome and other DNA-bound protein complex to generate a "chromatin landscape". This makes use of a high throughput sequencing to generate DNA sequence from both ends of around 180 million such fragments simultaneously. This data is then used to map the endpoints of the fragments onto the genome sequence, thus locating the positions of the bound proteins through regions with few cut ends. We have demonstrated this technology using the model plant Arabidopsis. In this proposal will use this new approach to understand how chromatin structure changes both through the cell cycle as cells divide and as cells differentiate to adopt new characteristics. This analysis will be carried out in both cell culture and in cells from intact tissues, allowing a detailed understanding of how chromatin changes occur during these processes. Specifically we will study how chromatin structure in Arabidopsis changes in response to light and how it is different in root and shoot cells. We will also investigate how this pattern is changed in a specific mutant in which chromatin structure is altered and in which differentiation is affected. As a result, we will develop a detailed understanding of the organization of chromatin in a higher organism, and how this is dynamically altered as the fate of cells changes during the processes of development. These techniques and approaches will be applicable to all eukaryotic organisms and will be of great significance in progressing our understanding of the genome.

所有高等生物的基因组都是以一种称为染色质的形式包装的，染色质是DNA和与之结合的蛋白质的组合。DNA包装成染色质是必不可少的，因为每个染色体都由一个长达几厘米的DNA分子组成，但它必须包装在只有几微米宽的细胞核中。事实上，正常人类细胞的DNA总长度约为2米。与此同时，DNA必须在需要时可接近，以允许基因的受控表达，或在细胞分裂周期中复制DNA。染色质包装的基本单位称为核小体，其由称为组蛋白的特殊高度保守蛋白质的核心组成，DNA围绕组蛋白包裹大约两次。核小体似乎位于特定的位置，特别是在重要特征如基因周围。很明显，生物体的许多特征和一些疾病都受到所谓的表观遗传修饰的影响，这种修饰是由染色质的变化或DNA的修饰引起的，而不是基础DNA序列本身的变化。因此，了解染色质在许多生物过程中具有根本的重要性。除了核小体之外，还有许多其他蛋白质复合物与DNA结合，用于许多目的，特别是控制基因的表达。核小体和其他蛋白质与DNA结合的模式可以通过使用仅切割没有蛋白质结合的DNA的酶来可视化。被保护的区域不会被切割，用这种酶消化染色质会产生数百万个DNA片段。这些主要是单个或多个核小体的大小。我们开发了一种新技术，可以同时确定整个基因组中所有此类受保护区域，从而绘制每个核小体和其他DNA结合蛋白质复合物的图谱，以生成“染色质景观”。这利用高通量测序从大约1.8亿个这样的片段的两端同时产生DNA序列。然后，这些数据用于将片段的端点映射到基因组序列上，从而通过具有很少切割末端的区域定位结合蛋白的位置。我们已经使用模式植物拟南芥证明了这一技术。在这项提案中，将使用这种新的方法来了解染色质结构如何在细胞分裂和细胞分化时通过细胞周期发生变化，以采用新的特征。该分析将在细胞培养物和来自完整组织的细胞中进行，从而详细了解在这些过程中染色质如何发生变化。具体来说，我们将研究如何在拟南芥染色质结构的变化，以响应光，以及它是如何在根和芽细胞的不同。我们还将研究这种模式是如何在一个特定的突变体中改变，其中染色质结构被改变，分化受到影响。因此，我们将详细了解高等生物体中染色质的组织，以及在发育过程中细胞命运的变化如何动态改变。这些技术和方法将适用于所有的真核生物，并将在我们的基因组的理解进步具有重要意义。

项目成果

Seed size plasticity in response to embryonic lethality conferred by ectopic CYCD activation is dependent on plant architecture.

• DOI: 10.1080/15592324.2016.1192741
• 发表时间: 2016-07-02
• 期刊: Plant signaling & behavior
• 影响因子: 2.9
• 作者: Sornay E;Dewitte W;Murray JA
• 通讯作者: Murray JA

Activation of CYCD7;1 in the central cell and early endosperm overcomes cell-cycle arrest in the Arabidopsis female gametophyte, and promotes early endosperm and embryo development.

• DOI: 10.1111/tpj.12957
• 发表时间: 2015-10
• 期刊: The Plant journal : for cell and molecular biology
• 作者: Sornay E;Forzani C;Forero-Vargas M;Dewitte W;Murray JA
• 通讯作者: Murray JA

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis.

• DOI: 10.1371/journal.pgen.1006988
• 发表时间: 2017-09
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Pass DA;Sornay E;Marchbank A;Crawford MR;Paszkiewicz K;Kent NA;Murray JAH
• 通讯作者: Murray JAH

WOX5 suppresses CYCLIN D activity to establish quiescence at the center of the root stem cell niche.

• DOI: 10.1016/j.cub.2014.07.019
• 发表时间: 2014-08-18
• 期刊: CURRENT BIOLOGY
• 影响因子: 9.2
• 作者: Forzani, Celine;Aichinger, Ernst;Sornay, Emily;Willemsen, Viola;Laux, Thomas;Dewitte, Walter;Murray, James A. H.
• 通讯作者: Murray, James A. H.

Untangling chromatin interactions.

解开染色质相互作用。

• DOI: 10.1093/jxb/eraa334
• 发表时间: 2020
• 期刊: Journal of experimental botany
• 影响因子: 6.9
• 作者: Parry G