GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO

海洋特定细胞类型的全球基因调控网络 海胆胚胎 摘要 动物细胞的所有发育、形态发生和分化功能都是由大部分， 专门部署了下游蛋白质编码基因的电池和盒。的重大成功 近年来，生物科学一直在系统水平上阐明上游基因调控网络 控制图案形成并确定身体计划的发展的GRN。GRNs由基因组成 编码转录因子和信号分子，加上这些之间的转录联系， 基因，它们决定了每个细胞在发育过程中的每一个阶段的调控状态。因此 它们将控制输入包括到所有下游基因中，这些基因完成细胞的工作。但是一个巨大的 现在，我们开始了解的上游GRN之间存在着一个重要的理解鸿沟 从细胞功能的下游效应器：什么是决定细胞功能的实际控制电路？ 这些下游基因的部署？GRNs究竟是如何与细胞功能有因果关系的呢 分化和形态发生原则上，给定上游GRN和各种 新的可用技术，这个差距可以关闭，并在系统层面解决问题，这是 本提案的具体目标。我们将选择发育中的海胆的三种细胞类型 胚胎，每个人都感兴趣。关于这个胚胎的上游GRNs的知识比 对于任何其他系统。靶细胞类型是胚胎的免疫细胞，其中下游的免疫细胞是免疫细胞。 效应基因编码各种各样的先天免疫蛋白;原肠胚内胚层细胞， 下游基因介导原肠胚内陷;胚胎的全能性预留细胞 体腔囊，在幼虫阶段产生成年体计划，其中下游效应细胞 包括维持全能性那些。先天免疫、原肠胚内陷和全能细胞谱系 都是泛两侧对称的特征。简单地说，该方法将是使用特定的细胞分离每种细胞类型。 调控基因表达和FACS;深度转录组测序;生物信息学预测;以及 通过高通量顺式验证与特异性表达基因的因果调节连接， 监管分析。该项目将为任何发展中国家提供第一个全球上下游GRN 系统它将告知下游基因盒组织的基本原则。它还将 作为对哺乳动物系统采取类似办法的技术示范项目。

GLOBAL GENE REGULATORY NETWORKS FOR SPECIFIC CELL TYPES OF THE SEA URCHIN EMBRYO ABSTRACT All developmental, morphogenetic, and differentiation functions of animal cells are executed by large, specifically deployed batteries and cassettes of downstream protein coding genes. A major success of bioscience in recent years has been system level elucidation of the upstream gene regulatory networks (GRNs) that control pattern formation and determine development of the body plan. GRNs consist of genes encoding transcription factors and signaling molecules, plus the transcriptional linkages among these genes, and they determine the regulatory state of every cell at every point in developmental time. Therefore they include the control inputs into all the downstream genes that do the work of the cell. But an enormously important gap in understanding now separates the upstream GRNs that we are beginning to learn about from the downstream effectors of cell function: What is the actual control circuitry that determines the deployment of these downstream genes? How, exactly, are GRNs causally connected to cellular functions of differentiation and morphogenesis? In principle, given knowledge of the upstream GRN and various newly available technology, this gap can be closed, and the problem solved at a system level, and this is the particular object of the present proposal. We will choose three cell types of the developing sea urchin embryo, each of general interest. Knowledge of the upstream GRNs of this embryo is more advanced than for any other system. The target cell types are the immune cells of the embryo, where the downstream effector genes encode a great variety of innate immunity proteins; gastrulating endoderm cells, where the downstream genes mediate gastrular invagination; and the totipotent set-aside cells of the embryonic coelomic pouches that in larval stage produce the adult body plan, where the downstream effector cells include those that maintain totipotency. Innate immunity, gastrular invagination, and totipotent cell lineages are all pan-bilaterian features. The approach, briefly, will be isolation of each cell type using specific regulatory gene expression and FACS; deep transcriptome sequencing; bioinformatic prediction; and validation of causal regulatory connections to specifically expressed genes by high throughput cis- regulatory analysis. This project will provide the first global upstream-downstream GRN for any developing system. It will inform as to basic principles by which downstream gene cassettes are organized. It will also serve as a technological demonstration project for similar approaches to mammalian systems.