From Live Cells to Single-molecules: Unravelling the interplay between 3D genomic structure and gene expression

这个学生奖学金的重点是应用最先进的单分子成像技术来研究DNA凝聚的分子基础及其对基因表达的影响。你将成为一个新的，多学科的合作部门之间的一部分。肿瘤和代谢部与谢菲尔德核酸研究所（http：//genome.sheffield.ac.uk/）有密切联系的化学研究所。人类细胞必须将约2米的DNA包装到直径约10微米的细胞核中。DNA必须是包装好的，高度组织化的，并可用于基因表达、DNA复制和DNA修复机制。3D组织也会随着时间的推移而变化，以响应细胞刺激，如DNA损伤或感染。这种组织的核心是DNA包裹在组蛋白周围，形成核小体，核小体可以被包装（浓缩）或解包装，以允许蛋白质进入基因组。一系列修饰酶调节这些过程。我们最近鉴定了NDP 52/CALCOCO 2作为假定的转录调节因子（1），初步数据显示该蛋白质使核小体去致密化。NDP 52与NF-kB炎症通路有关，因此我们认为该蛋白质调节促炎症基因的表达。因此，这种蛋白质与健康和疾病的基本细胞过程有关，但其作用机制仍然未知。本项目的目标是通过细胞生物学和体外方法相结合的方法来剖析NDP 52的DNA缩合机制，确定任何相互作用的蛋白质的作用，并因此定义支撑这一基本过程的分子机制。您将使用“自上而下”和“自下而上”的多学科方法来研究

This studentship is focused on applying state-of-the-art single molecule imaging techniques to study the molecular basis of DNA condensation and its impact upon gene expression. You will be part of a new, multidisciplinary collaboration between the Dept. of Oncology and Metabolism and Dept. of Chemistry with close ties to the Sheffield Institute for Nucleic Acids (http://genome.sheffield.ac.uk/).Human cells must pack ~2 metres of DNA in to a cell nucleus approximately 10um in diameter. The DNA must be packaged yet, highly organised and accessible for gene expression, DNA replication and DNA repair machinery. The 3D organisation also changes over time in response to cell stimulation such as DNA damage or infections. Central to this organisation is the wrapping of DNA around histone proteins to form nucleosomes that can be packed (condensed) or unpacked to allow proteins to access the genome. An array of modifying enzymes regulate these processes.We have recently identified NDP52/CALCOCO2 as a putative transcription regulator (1) and preliminary data shows that this protein decondenses nucleosomes. NDP52 is connected to the NF-kB inflammation pathway and we therefore believe the protein regulates the expression of pro-inflammation genes. Therefore, this protein is related to fundamental cellular processes critical to health and disease, however it's mechanism of action remains unknown.The goal of this project is to dissect the mechanism of DNA condensation by NDP52 through a combined cell biology and in vitro approach, identifying the roles of any interacting proteins, and therefore define the molecular mechanism underpinning this fundamental process.You will use a "top-down" and "bottom-up" multidisciplinary approach to investigate