Transcriptional Networks Guiding Xenopus Development

描述（由申请人提供）：爪蟾应该处于系统生物学的前沿。生物化学、基因组学、胚胎学和分子生物学的独特结合可以很容易地用于爪蟾胚胎，使其成为阐明基因调控复杂性的理想选择。我们将利用这些优势来探索内胚层规范的监管网络。内胚层是胚胎发生过程中最早出现的细胞类型之一。这些细胞对脊椎动物的初始模式很重要，是许多内部器官系统的前体。爪蟾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途径，如Nodal和相关的下游转录因子级联。然而，这些转录因子的基因调控网络（GRN）和对它们的转录反应在任何生物体中仍然很大程度上未被探索。此外，这些网络在不同细胞系和发育时间内的结构和动态行为从未在任何脊椎动物或体外等效物中进行过研究。非洲爪蟾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。我们假设，确定用于指定非洲爪蟾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，包括转录因子在胚胎发生的不同阶段使用哪些基序和基序组合来调节它们的活性，以及这些转录因子的结合（单独或组合）如何与表达和最终功能相关。我们进一步建议阐明当信号组件被移除时，这些网络是如何变化的，提供了特定途径所需的哪些元素的分析。这个资源将允许连接途径和深入探索爪蟾生物学的基本问题。

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.