Identifying regulators of morphogenesis with a transcriptional lineage of C. elegans development

 描述（由申请人提供）：形态发生是细胞在胚胎中移动以形成身体形状和结构的过程，对多细胞生命至关重要。它的失调导致了广泛的疾病，包括出生缺陷，癌症转移和伤口愈合不当。遗传筛选对于识别参与这些过程的基因至关重要，但传统的遗传筛选对大类基因是盲目的，例如那些与其他途径具有部分冗余功能的基因，以及多效性基因。基因表达谱分析技术，如RNA-seq，通过对每个基因的转录水平进行快照，无论它是否是多效性的， 或者部分冗余。我假设存在未发现的多效性或部分冗余基因，以及遗传方法尚未发现的基因，这些基因对形态发生至关重要，并将通过RNA-seq揭示。自从C.在线虫的发育过程中，线虫一直是一种强大的胚胎学工具，使研究人员能够准确预测感兴趣的事件将在何时何地发生。诸如神经元特化、凋亡、极化细胞分裂或细胞迁移的现象可以用单个细胞的空间分辨率和分钟的时间分辨率来预测。但是这种细胞谱系并不能直接说明这些现象是如何发生的，以及哪些基因对此负责。单细胞RNA-seq使我们能够在整个发育过程中分析这些细胞中每个细胞的转录水平，以识别与发育现象相关的基因。我将对C.线虫胚胎，直到16细胞阶段，从而创建一个分子谱系，以补充已知的细胞谱系的发展。形态发生的调控因子很难确定，这在很大程度上是由于这些基因通常具有多效性或部分冗余的功能。我将分析各种原肠胚细胞类型的转录组随着时间的推移导致原肠胚形成。我假设，有基因的表达相关的跨细胞类型，因为每种细胞类型启动原肠胚形成，这些基因在调节形态发生的功能作用。该项目的主要贡献之一将是转录谱系，这将是一个资源，细胞和 发育生物学家为了确保这个资源的实用性，我将编写一个交互式数据可视化Web工具。该工具将允许用户通过可视化查询我的数据 描述感兴趣的时空表达模式，以及接收关于与所述模式匹配的所有基因的信息。该工具将弥合计算和非计算生物学家之间的沟通差距。虽然这些数据将与发育和细胞生物学中的许多问题有关，但我将用它们来产生关于形态发生调节的假设，然后我将在原肠胚线虫中进行测试。

 DESCRIPTION (provided by applicant): Morphogenesis, the process by which cells move through the embryo to form the shapes and structures of the body, is critical for multicellular lif. Its misregulation leads to a wide range of diseases including birth defects, cancer metastasis and improper wound healing. Genetic screens have been crucial for identifying genes involved in these processes, but traditional genetic screens are blind to large categories of genes, such as those that have a partially redundant function with other pathways, as well as pleiotropic genes. Gene expression profiling techniques such as RNA-seq shed light on these blind spots by taking a snapshot of the transcript level of every gene, regardless of whether it is pleiotropic or partially redundant. I hypothesize that there are undiscovered pleiotropic or partially redundant genes, as well as genes simply not yet found by genetic approaches, that are critical to morphogenesis and which will be revealed by RNA-seq. Ever since the description of the invariant cell lineage of C. elegans development, the nematode has been a powerful embryological tool, allowing researchers to predict exactly when and where an event of interest will take place. Phenomena such as neuron specification, apoptosis, polarized cell division, or cell migration can be anticipated with a spatial resolution of a single cell, and a temporal resolution of minutes. But this cell lineage does not directly address how these phenomena are taking place, and what genes are responsible. Single-cell RNA-seq allows us to profile transcripts levels from each of these cells throughout development, to identify genes that correlate with the well-documented phenomena of development. I will perform single-cell RNA-seq on each individual cell of the C. elegans embryo until the 16-cell stage, thereby creating a molecular lineage to complement the known cellular lineage of development. Regulators of morphogenesis have been difficult to identify, in large part due to the often pleiotropic or partialy redundant functions of these genes. I will analyze the transcriptomes of a variety of gastrulating cell types over time leading up to gastrulation. I hypothesize that there are genes whose expression correlates across cell types as each cell type initiates gastrulation, and that these genes have functional roles in regulating morphogenesis. One of the main contributions of this project will be the transcriptional lineage, which will be made available as a resource to cell and developmental biologists. In order to ensure the utility of this resource, I will program an interactive data visualization web tool. This tool will allow the user to query my data by visually describing a spatiotemporal expression pattern of interest, and receiving information about all the genes that match the described pattern. This tool will bridge a communication gap between computational and non-computational biologists. While these data will be relevant to many questions in developmental and cell biology, I will use them to generate hypotheses about the regulation of morphogenesis, which I will then test in the gastrulating nematode.