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， 蛙爪蟾，其丰富的卵是大的，容易通过显微注射和显微外科手术操作。 这些蛋足够大，可以产生生化分析的材料，对这个项目来说，重要的是， 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。 在以前的资助期间，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，我们专注于后牙的形成， 在胚胎的一个区域，这是由原肠胚中的Wnt和FGF信号指定的。与此同时， X.的基因组组装和注释。tropicalis和X.这是一个系统级的方法。这些 大会不为社区提供假设驱动研究所需的资源，而且 发表了令人惊讶的发现，在X.通过亚种间杂交， 在不同的祖先基因组之间，基因丢失和基因表达的进化是不同的。 在下一个资助期，我们将确定Wnt和FGF途径如何作用于特定的基因调控。 元素，组合或单独。我们将描述基因和增强子元件， 一个或两个信号，并测试它们如何对分级信号或信号的组合和定时作出反应， 解决后模式形成是如何介导的。虽然信号的时机的影响已经被 有文献记载，其对诱导前后轴不同命运的贡献尚未被证实。 处理。 在平行的工作中，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体，并询问它们是否激活了一个“杂交体 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在一个 祖先基因组，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 优于其他祖先基因组。 这些实验的结果将提供对正常脊椎动物发育的基本了解， 进化，以及出生缺陷和异常信号传导疾病的潜在机制， 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.