Gene expression in amphibian development

两栖动物发育中的基因表达

• 批准号: 10377403
• 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 2023-05-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10377403
• 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 我们的目标是在分子水平上了解早期脊椎动物的发育。 非洲爪蟾，其丰富的卵很大，很容易通过显微注射和显微外科手术进行操作。 这些鸡蛋足够大，可以产生用于生化分析的材料，对于这个项目来说重要的是，有足够的鸡蛋 来自分阶段和操作的胚胎或外植体的材料用于深度测序，或染色质用于 免疫沉淀。 在之前的资助期间，我们已经确定了有效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关注后部的形成。 胚胎区域，由原肠胚中的 Wnt 和 FGF 信号传导指定。同时，我们也进行了改进。 热带 X. 和 X. laevis 的基因组组装和注释，实现了系统级方法。 集会不为社区的假设驱动研究提供必要的资源，而且 得出了令人惊讶的发现，在 X. laevis 通过亚种杂交变成四倍体后，基因 不同祖先基因组之间的损失和基因表达进化不同。 在下一个资助期内，我们将确定 Wnt 和 FGF 通路如何作用于特定基因调控 我们将组合或单独地表征基因和增强子元件。 一个或两个信号，并测试它们对分级信号或信号组合和时序的反应，以 解决了后模式形成是如何介导的，而信号传导时间的影响已经得到解决。 据记载，它对诱导前后轴不同命运的贡献尚未被证实。 已解决。 在并行工作中，我们将从基因组组装的资源方面转向测试如何进行假设 我们将构建新的物种杂交体并询问它们是否激活“杂交体”。 转座子激活的发育不良”程序，以及新的转座事件是否选择性地发生在一个转座子中 祖基因组，导致该基因组上的选择性基因丢失，我们还将探索替代方案。 假设新的染色质标记选择性地有利于一个基因组的基因表达和基因保留 超过其他祖先基因组。 这些实验的结果将提供对正常脊椎动物发育和发育的基本了解。 进化，以及出生缺陷和异常信号疾病的潜在机制，例如 癌症，可能会出现。