Gene expression in amphibian development

摘要 我们的目标是在分子水平上了解脊椎动物的早期发育。我们研究这个问题在 非洲爪蛙，其丰富的卵子很大，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，可以产生生化分析所需的物质，对这个项目来说，更重要的是，足够 来自分期和处理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。 在之前的赠款期间，我们已经确定了有效的信号和信号转导活动， 有助于胚胎发育和神经诱导。最近我们集中在后部的形成上。 胚胎的区域，由原肠胚中的Wnt和Fgf信号指定。与此同时，我们改进了 热带血吸虫和莱维氏血吸虫的基因组组装和注释，使系统水平的方法成为可能。这些 汇编不仅为社区提供了假设驱动的研究所必需的资源，而且还 莱维氏X.laevis通过亚种杂交成为四倍体后，基因 缺失和基因表达在不同的祖先基因组之间进化不同。 在下一个授权期，我们将确定Wnt和Fgf通路如何作用于特定的基因调控。 元素组合在一起或单独使用。我们将描述基因和增强子元件对 一个或两个信号，并测试它们对分级信号或信号的组合和定时的反应，以 了解后方图案的形成是如何被调节的。虽然信令定时的影响已经被 有文献记载，它对诱导前后轴不同命运的贡献尚未得到证实。 地址。 在并行的工作中，我们将从基因组组装的资源方面转移到测试关于如何 基因组对四倍体有反应。我们将构建新的物种杂交种，并研究它们是否激活了一种“杂交种 转座子激活的“发育不全”程序，以及新的转座事件是否选择性地发生为一 先祖基因组，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偏向于一个基因组的基因表达和基因保留 而不是其他祖先的基因组。 这些实验的结果将提供对正常脊椎动物发育和 进化，以及出生缺陷和异常信号疾病的潜在机制，如 癌症，可能会出现。

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.