Transcriptional Networks Guiding Xenopus Development

描述(申请人提供)：非洲爪哇应该是系统生物学的前沿。生物化学、基因组学、胚胎学和分子生物学的独特组合可以很容易地用于非洲爪哇胚胎，使其成为阐明基因调控复杂性的理想工具。我们将利用这些优势来探索内胚层规范背后的调控网络。内胚层是胚胎发育过程中最早出现的细胞类型之一。这些细胞对脊椎动物最初的模式很重要，也是许多内部器官系统的前体。非洲爪哇生物学家广泛探索了定义内胚层的信号通路，包括特定的信号转导通路，如Nodal和相关的下游转录因子级联。然而，在任何生物体中，这些转录因子的基因调控网络(GRN)和对它们的转录反应在很大程度上仍然是未知的。此外，这些网络的结构和动态行为在不同的细胞谱系中以及在发育过程中从未在任何脊椎动物或体外等价物中被研究过。非洲爪哇胚胎的力量与测序技术的进步相结合--主要是染色质免疫沉淀，然后是大规模平行测序(ChIPSeq)--允许阐明每个转录因子使用的靶标以及这些转录因子定义的潜在基因调控网络。我们推测，识别非洲爪哇用于指定内胚层的网络将回答几个重要的和长期寻求的生物学问题，包括转录因子使用什么基序-及其组合-来调节其在胚胎发育不同阶段的活性，以及这些转录因子的结合，单独或组合，如何与表达和所产生的功能相关。我们进一步建议阐明当信令组件被移除时这些网络如何变化，并提供特定路径需要哪些元素的分析。这一资源将允许连接各种途径，并对非洲爪哇生物学的基本问题进行密集的探索。

DESCRIPTION (provided by applicant): Xenopus should be at the forefront of systems biology. The unique combination of biochemistry, genomics, embryology and molecular biology that can be easily used in the Xenopus embryo make it ideal for elucidating the complexities of gene regulation. We will use these strengths to explore the regulatory networks underlying endoderm specification. Endoderm is one of first cell types that emerges during embryogenesis. These cells are important for the initial patterning of the vertebrate and are the precursors to many internal organ systems. Xenopus biologists have extensively explored the signaling pathways that define endoderm; including specific signal transduction pathways like Nodal and associated downstream transcription factor cascades. Yet the gene regulatory networks (GRN) of these transcription factors and the transcriptional responses to them are still largely unexplored in any organism. Furthermore the structure and dynamic behavior of these networks within different cell lineages and through developmental time has never been examined in any vertebrate animal or in an in vitro equivalent. The power of the Xenopus embryo combined with advances in sequencing technology - primarily Chromatin Immunoprecipitation followed by Massively Parallel Sequencing (ChIPSeq) - allow the elucidation of targets used by each transcription factor and the underlying gene regulatory networks that these transcription factors define. We hypothesize that identifying the network used to specify endoderm in Xenopus will answer several important and long sought after biological questions, including what motifs - and combinations of motifs - are used by transcription factors to modulate their activity at different stages of embryogenesis and how binding of these transcription factors, alone or in combinations, correlate with expression and resulting function. We further propose to elucidate how these networks change when signaling components are removed, providing an analysis of which elements are needed for particular pathways. This resource will allow the connection of pathways and intense exploration into basic questions of Xenopus biology.