i-Motifs: Sequence, Structure and Function in Ageing

i-Motifs：衰老过程中的序列、结构和功能

• 批准号: BB/W001616/1
• 负责人: Zoë Ann Ella Waller
• 金额: $ 61.41万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FW001616%2F1
• 关键词: Motifs; Sequence; Structure; Function; Ageing

DNA is often assumed to be a double helix, the "twisted ladder" structure which was first proposed by Watson and Crick in 1953. However, it is less well known that DNA can adopt different shapes and these can be used as switches to control how it works. DNA is comprised of four bases, often described as the "building blocks" for life because they encode all the information required to build and maintain an organism. The sequence of these four bases (adenine, guanine, thymine and cytosine) is what defines us as humans and what makes us different to bacteria, yeast and plants. DNA sequences which contain lots of the base cytosine can form alternative secondary structures which instead of appearing like the normal "twisted ladder" of two strands, are a very tightly packed "knot" of four strands of DNA. We call these structures i-motifs. Sequences of this type have been used as pH-dependent switches in nanotechnology but are also widespread throughout the human genome, exist in cells and have been shown to play a role in gene expression and defining how long our cells live. Despite these recent advances, we lack the detail about how these structures work in the body. We know that for some regions of DNA, these types of sequences may play a role in our predisposition to getting certain diseases, such as Diabetes. We also know that these sequences are actively mutated and deleted as we age and in diseases such as Cancer. To be able to understand the effects of these structures have on disease, we need to understand how they can be changed and what difference this makes to how they work in biology. This could potentially give us ways to diagnose or treat certain genetic diseases. The central aim of this proposal is to investigate the relationship between sequence, structure and function of DNA i-motif structures in switching genes on and off and how this changes during ageing. We will examine this using a wide range of computational, biological and biophysical techniques. Our previous work has given us an understanding of which types of sequences could potentially fold into i-motif structures. Using biophysical and molecular biology methods, we will investigate the importance of the structure of i-motif in humans and their precise influence in controlling gene switching. This will give us information about how important the structure of i-motif is to function. We have preliminary data to show that i-motif forming sequences are mutated and deleted as we age, and this can affect the progression of disease. We aim to decipher whether there are "hot spots" in critical regions of the genome that are critically affected by mutations. Finally, we will perform a global study of where i-motif structures are present in human cells and observe whether their distribution changes as cells age. This will involve development of a new technique, based on looking at a "footprint" these structures have.The project will advance our understanding of how i-motifs work in biology and how they are controlled by mutations affected by the ageing process. The outcomes of the work will also improve our understanding about the folding of i-motifs under different conditions, allowing better prediction of regulating properties based on DNA sequence. This will impact the design and creation of DNA/RNA based nanotechnologies. The development of a new tool to study the prevalence of i-motif structures in human cells will be able to be applied to any other organism, which will expand the scope of our research to plant scientists and microbiologists.

DNA通常被认为是双螺旋，即“扭曲的梯子”结构，这是沃森和克里克在1953年首次提出的。然而，鲜为人知的是，DNA可以采用不同的形状，这些形状可以用作开关来控制它的工作方式。DNA由四种碱基组成，通常被描述为生命的“基石”，因为它们编码了构建和维持生物体所需的所有信息。这四种碱基（腺嘌呤、鸟嘌呤、胸腺嘧啶和胞嘧啶）的序列是我们人类的定义，也是我们与细菌、酵母和植物不同的原因。含有大量碱基胞嘧啶的DNA序列可以形成替代的二级结构，而不是像正常的两条链的“扭曲的梯子”，而是一个非常紧密的四条DNA链的“结”。我们称这些结构为i-motifs。这种类型的序列已被用作纳米技术中的pH依赖性开关，但也广泛存在于整个人类基因组中，存在于细胞中，并已被证明在基因表达中发挥作用，并定义我们的细胞寿命。尽管最近取得了这些进展，但我们缺乏关于这些结构如何在体内工作的细节。我们知道，对于DNA的某些区域，这些类型的序列可能在我们患某些疾病的倾向中发挥作用，例如糖尿病。我们还知道，随着年龄的增长和癌症等疾病的发生，这些序列会发生积极的突变和缺失。为了能够理解这些结构对疾病的影响，我们需要了解它们是如何被改变的，以及这对它们在生物学中的工作方式有什么影响。这可能为我们提供诊断或治疗某些遗传疾病的方法。该提案的主要目的是研究DNA i基序结构在打开和关闭基因中的序列、结构和功能之间的关系，以及这种关系在衰老过程中如何变化。我们将使用广泛的计算，生物和生物物理技术来研究这一点。我们以前的工作使我们了解了哪些类型的序列可能折叠成i基序结构。利用生物物理学和分子生物学方法，我们将研究i基序结构在人类中的重要性及其在控制基因转换中的精确影响。这将为我们提供关于i基序的结构对功能的重要性的信息。我们有初步的数据表明，随着年龄的增长，i基序形成序列会发生突变和缺失，这可能会影响疾病的进展。我们的目标是破译基因组的关键区域是否存在受突变严重影响的“热点”。最后，我们将对人类细胞中存在的i基序结构进行全面研究，并观察它们的分布是否随着细胞年龄的变化而变化。这将涉及一种新技术的开发，该技术基于对这些结构的“足迹”的研究。该项目将促进我们对i-motifs在生物学中如何工作以及它们如何受到衰老过程影响的突变的控制的理解。这项工作的结果也将提高我们对不同条件下i-motifs折叠的理解，从而可以更好地预测基于DNA序列的调节特性。这将影响基于DNA/RNA的纳米技术的设计和创造。研究人类细胞中i-motif结构流行的新工具的开发将能够应用于任何其他生物体，这将扩大我们的研究范围到植物科学家和微生物学家。

项目成果

Handbook of Chemical Biology of Nucleic Acids

核酸化学生物学手册

• DOI: 10.1007/978-981-16-1313-5_97-1
• 发表时间: 2022
• 作者: Waller Z

The Potent G-Quadruplex-Binding Compound QN-302 Downregulates S100P Gene Expression in Cells and in an In Vivo Model of Pancreatic Cancer.

• DOI: 10.3390/molecules28062452
• 发表时间: 2023-03-07
• 期刊: Molecules (Basel, Switzerland)
• 作者: Ahmed AA;Greenhalf W;Palmer DH;Williams N;Worthington J;Arshad T;Haider S;Alexandrou E;Guneri D;Waller ZAE;Neidle S
• 通讯作者: Neidle S

Replication-induced DNA secondary structures drive fork uncoupling and breakage.

• DOI: 10.15252/embj.2023114334
• 发表时间: 2023-11-15
• 期刊: EMBO JOURNAL
• 影响因子: 11.4
• 作者: Williams, Sophie L.;Casas-Delucchi, Corella S.;Raguseo, Federica;Guneri, Dilek;Li, Yunxuan;Minamino, Masashi;Fletcher, Emma E.;Yeeles, Joseph T. P.;Keyser, Ulrich F.;Waller, Zoe A. E.;Di Antonio, Marco;Coster, Gideon
• 通讯作者: Coster, Gideon

QN-302 demonstrates opposing effects between i-motif and G-quadruplex DNA structures in the promoter of the S100P gene.

• DOI: 10.1039/d3ob01464a
• 发表时间: 2023-12-20
• 期刊: ORGANIC & BIOMOLECULAR CHEMISTRY
• 影响因子: 3.2
• 作者: Alexandrou, Effrosyni;Guneri, Dilek;Neidle, Stephen;Waller, Zoe A. E.
• 通讯作者: Waller, Zoe A. E.