Analysing the chromatin landscape and transcriptome within sox17+ lineages during zebrafish embryonic development.

项目概述：这个由MRC资助的博士培训伙伴关系（DTP）将尖端的分子和分析科学与数据分析中的创新计算方法结合在一起，使学生能够解决以假设为主导的生物医学研究问题。这是一个为期4年的计划，其第一年涉及一系列教学模块和两个基于实验室的研究项目，导致跨学科生物医学研究硕士学位。前两个学期包括一系列教学模块，让学生在多学科科学中获得坚实的基础。学生还参加了一系列由学术和行业专家领导的大师班，这些专家在分子，细胞和组织动力学，微生物学和感染，应用生物医学技术以及人工智能和数据科学领域。在第三和夏季学期，学生在他们选择的实验室进行两个为期11周的研究项目。项目：干细胞和祖细胞产生多种成熟细胞类型，构成人体所有组织和器官。内胚层是一种特定类型的祖细胞，其有助于肝脏、胰腺、甲状腺以及呼吸道和胃肠道，所有这些都与发育缺陷相关，或者代表对组织替代疗法的未满足需求。为了了解发育缺陷是如何发生的，并设计治疗策略，有必要了解基因是如何在内胚层中正确控制的，从而导致这些主要器官系统的适当形成。细胞的特性和行为是由细胞内活跃的基因组合控制的。单个基因的激活受基因组内特定DNA序列对相关细胞机制的可及性控制。该项目旨在鉴定、表征和功能研究有助于内胚层基因活性的DNA序列。这将通过在模式生物斑马鱼中使用一系列定量实验和计算方法来实现。斑马鱼是了解人类发育的极好模型，因为它们的基因组和多器官系统与人类高度相似。也有建立的方法来操纵斑马鱼基因组荧光标记感兴趣的细胞，或创建突变。此外，斑马鱼在母体外发育，并且在早期发育中是透明的，允许容易地进行整个生物体分析。我将使用现有的荧光斑马鱼在发育过程中特异性地分离内胚层细胞，并鉴定控制基因活性的DNA序列。然后，我将产生新的荧光斑马鱼品系，使我能够了解在发育过程中，所识别的DNA序列何时何地控制基因活性。最后，我将研究这些DNA序列的子集如何通过使用CRISPR/Cas9基因组编辑在内胚层细胞中特异性删除或抑制它们来控制特定基因和器官形成，并表征发育后果。

Programme overview:This MRC-funded doctoral training partnership (DTP) brings together cutting-edge molecular and analytical sciences with innovative computational approaches in data analysis to enable students to address hypothesis-led biomedical research questions. This is a 4-year programme whose first year involves a series of taught modules and two laboratory-based research projects that lead to an MSc in Interdisciplinary Biomedical Research. The first two terms consist of a selection of taught modules that allow students to gain a solid grounding in multidisciplinary science. Students also attend a series of masterclasses led by academic and industry experts in areas of molecular, cellular and tissue dynamics, microbiology and infection, applied biomedical technologies and artificial intelligence and data science. During the third and summer terms students conduct two eleven-week research projects in labs of their choice. Project:Stem and progenitor cells give rise to the diverse range of mature cell types making up all tissues and organs in the human body. Endoderm is a particular type of progenitor cell that contributes to liver, pancreas, thyroid and the respiratory and gastrointestinal tracts, all of which are associated with developmental defects, or represent an unmet need for tissue replacement therapies. In order to understand how developmental defects occur, and to devise therapeutic strategies it will be necessary to understand how genes are correctly controlled in the endoderm, leading to appropriate formation of these major organ systems. The identity and behaviour of cells is controlled by the combination of genes which are active within them. Activation of individual genes is controlled by the accessibility of specific DNA sequences within the genome to the relevant cellular machinery. This project aims to identify, characterize and functionally study the DNA sequences that contribute to gene activity in the endoderm. This will be achieved using a range of quantitative experimental and computational approaches in the model organism zebrafish. Zebrafish is an excellent model for understanding human development since their genomes and multiple organ systems are highly similar to humans. There are also established methods to manipulate the zebrafish genome to fluorescently label cells of interest, or create mutations. Additionally, zebrafish develop external to the mother and are transparent in early development allowing easy whole organism analysis. I will use existing fluorescent zebrafish to specifically isolate endoderm cells during development and identify DNA sequences controlling gene activity. I will then generate new fluorescent zebrafish lines allowing me to understand when and where the identified DNA sequences control gene activity over developmental time. Finally, I will study how a subset of these DNA sequences control specific genes and organ formation by specifically deleting or inhibiting them in endoderm cells using CRISPR/Cas9 genome editing, and characterizing the developmental consequences.