Gene expression in amphibian development

两栖动物发育中的基因表达

• 批准号: 9900827
• 负责人: Richard M Harland
• 金额: $ 46.29万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-04-06 至 2023-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9900827
• 关键词: Address; Amphibia; Anterior; Biochemical; Chromatin; Communities; Congenital Abnormality; Development; Disease; Embryo; Embryonic Development; Event; Evolution; Fibroblast Growth Factor; Gastrula; Gene Duplication; Gene Expression; Genes; Genetic Enhancer Element; Genetic Transcription; Genome; Goals; Grant; Hybrids; Individual; Malignant Neoplasms; Mediating; Microinjections; Microsurgery; Molecular; Pathway interactions; Pattern; Pattern Formation; Rana; Regulation; Regulator Genes; Regulatory Element; Research; Resources; Signal Transduction; Specific qualifier value; System; Testing; Work; Xenopus; chromatin immunoprecipitation; deep sequencing; egg; experimental study; gene function; gene product; human disease; improved; progenitor; programs; relating to nervous system; vertebrate genome; whole genome

ABSTRACT Our goal is to understand early vertebrate development at the molecular level. We study the problem in the frog Xenopus, whose abundant eggs are large and readily manipulated by microinjection and microsurgery. The eggs are large enough to produce material for biochemical analysis, and importantly for this project, ample material from staged and manipulated embryos or explants for deep sequencing, or chromatin for immunoprecipitation. During previous grant periods, we have identified potent signaling and signal transduction activities that contribute to embryonic development and neural induction. Recently we focused on formation of the posterior region of the embryo, which is specified by Wnt and FGF signaling in the gastrula. In parallel we improved genome assemblies and annotation for X. tropicalis and X. laevis, enabling a systems level approach. These assemblies not provide the resources necessary for hypothesis driven research for the community, but also delivered the surprising finding that after X. laevis became tetraploid through subspecies hybridization, gene losses and gene expression evolved differently between the different progenitor genomes. In the next grant period, we will determine how the Wnt and FGF pathways act on specific gene regulatory elements, in combination or individually. We will characterize genes and enhancer elements that respond to one or both signals, and test how they react to graded signals, or combinations and timing of signals, to resolve how posterior pattern formation is mediated. While the effect of timing of signaling has been documented, its contribution to the induction of distinct fates in the Anterior Posterior axis has not been addressed. In parallel work, we will move from the resource aspect of genome assembly to testing hypotheses on how genomes respond to tatraploidy. We will construct new species hybrids and ask whether they activate a “hybrid dysgenesis” program of transposon activation, and whether new transposition events occur selectively into one progenitor genome, leading to selective gene loss on that genome. We will also explore the alternative hypothesis that new chromatin marks selectively favor one genome for gene expression and gene retention over the other progenitor genome. The results of these experiments will provide basic understanding of normal vertebrate development and evolution, and potentially the mechanisms by which birth defects, and diseases of aberrant signaling, such as cancers, may arise.

抽象的 我们的目标是了解分子水平的早期脊椎动物发育。我们研究了问题 青蛙异刺us，其丰富的鸡蛋很大，很容易通过显微注射和显微外科手术来操纵。 这些鸡蛋足够大，可以产生用于生化分析的材料，重要的是对于这个项目，足够的 分阶段和操纵的胚胎或外植体的材料，用于深度测序，或染色质 免疫沉淀。 在以前的赠款期间，我们已经确定了潜在的信号传导和信号转导活动 有助于胚胎发育和神经诱导。最近，我们专注于形成后部 胚胎的胚胎区域是胃中Wnt和FGF信号传导指定的。同时我们改进了 X. tropicalis和X. laevis的基因组组件和注释，实现了系统级方法。这些 集会不是为社区提供假设驱动研究所必需的资源，而是 提出了令人惊讶的发现，即X. laevis之后通过亚种杂交成为四倍体，基因 不同祖细胞基因组之间的损失和基因表达的演变不同。 在下一个赠款期间，我们将确定Wnt和FGF途径如何对特定基因调节作用 组合或单独的元素。我们将表征响应的基因和增强子元素 一个或两个信号，并测试它们对分级信号或信号的组合和时间的反应 解决如何介导后验模式形成。虽然信号时间的效果已经 记录到，其对诱导前轴诱导不同命运的贡献尚未 解决。 在并行工作中，我们将从基因组组装的资源方面转变为测试假设 基因组对tatraploidy有反应。我们将构建新物种混合动力，并询问它们是否激活“混合动力 转座子激活的失去障碍程序，以及新的换位事件是否有选择地发生在一个 祖细胞基因组，导致该基因组的选择性基因丧失。我们还将探索替代方案 假设新染色质选择性地标记了一个基因组来表达基因和基因保留 在另一个祖细胞基因组上。 这些实验的结果将提供对正常脊椎动物发育和 进化，以及可能出生缺陷和异常信号疾病的机制，例如 癌症可能会出现。