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

项目概述：这个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创新的数据分析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年的课程，第一年包括一系列教学模块和两个基于实验室的研究项目，最终获得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方面打下坚实的基础。学生还将参加一系列由分子、细胞和组织动力学、微生物学和感染、应用生物医学技术、人工智能和数据科学等领域的学术和行业专家主持的大师班。在第三学期和夏季学期，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了各种成熟细胞类型，构成了人体的所有组织和器官。内胚层是一种特殊类型的祖细胞，对肝脏、胰腺、甲状腺、呼吸道和胃肠道都有贡献，所有这些都与发育缺陷有关，或者对组织替代疗法的需求尚未得到满足。为了了解发育缺陷是如何发生的，并制定治疗策略，有必要了解基因是如何在内胚层中被正确控制的，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。单个基因的激活是由基因组内特定DNA序列对相关细胞机制的可及性控制的。本项目旨在鉴定、表征和功能研究有助于内胚层基因活性的DNA序列。这将在斑马鱼模型生物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绝佳模型，因为它们的基因组和多器官系统与人类高度相似。也有既定的方法来操纵斑马鱼基因组荧光标记感兴趣的细胞，或制造突变。此外，斑马鱼在母体外发育，在早期发育时是透明的，便于对整个生物体进行分析。我将利用现有的荧光斑马鱼，在发育过程中特异性分离内胚层细胞，鉴定控制基因活性的DNA序列。然后，我将生成新的荧光斑马鱼系，使我能够了解何时何地鉴定的DNA序列在发育过程中控制基因活性。最后，我将研究这些DNA序列的一个子集如何通过使用CRISPR/Cas9基因组编辑在内胚层细胞中特异性地删除或抑制它们来控制特定基因和器官形成，并描述发育后果。

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.