Tools for Functional Analysis and Cell Biology

本计划项目中三个相互依赖的努力的中心目标建立在成功的基础上 丝状脉孢菌的功能基因组学、注释和表达分析 超过250,000种非酵母真菌的真菌模型。通过分子、细胞定位的首要目标 生物学、基因组和计算方法，将是为了理解粗毛拟青霉是如何从 菌丝生长完成无性孢子发育。我们将重点关注无性恋的两个关键诱因 开发：轻便干燥。此外，我们将利用以往的成功经验，扩大系统性 击倒另一个重要的模型系统--尼杜拉曲霉。脉孢子虫是一种显著的 真核生物的基础研究，如曲霉菌，以及与这些物种有关的真菌包括大多数动物和 植物病原体以及产生抗生素、化学品、酶和药物的工业菌株。 在43Mb脉孢子虫全基因组编码的9846个基因中，基因预测为 由本P01衍生的超过250,000个EST支持。在过去的4年里，我们彻底改变了工具 和丝状真菌的基因敲除技术，比我们最初的目标高出40%以上。项目 #1将完成脉孢子菌基因敲除，并将基因的系统性破坏扩展到 曲霉菌。我们将开发压力、工具和背景信息来支持项目#2和#3，以及 主要目标是了解丝状真菌发育的调控途径。 项目#2和#3将旨在描述和重建构成N。 Crassa对光和空气的发育反应，从染色质结构水平到基因 监管网络。项目3将使用组蛋白修饰、转录因子的ChlP-seq图谱 DNA甲基化结合部位、核小体与相应转录体的占有率 测量以生成对基因组和表观基因组动态的深入描述。项目2，在一个 信息密集型系统生物学方法，将整合这些数据并使用计算建模来 开发相互连接的光和无性发育基因调控网络的预测模型。 这些模型将通过纳入项目#3和 通过使用项目1和项目1中开发的菌株促进的扰动分析进行了精炼 使用项目#3中使用的工具进行了表征。 这一努力将在模型系统内锚定、促进和利用基因组探索，这些模型系统提供 通往真菌王国的大门。

The central goal of the three interdependent efforts in this Program Project builds upon successful functional genomics, annotation, and expression analyses of Neurospora crassa, a premier filamentous fungus model for over 250,000 species of non-yeast fungi. A primary goal, targeted through molecular, cell biological, genomic and computational approaches, will be to understand how N. crassa transitions from mycelial growth to complete asexual spore development. We will focus on two key triggers of asexual development: light and desiccation. In addition, we will leverage our prior successes to expand systematic knockouts to an additional prominent model system, Aspergillus nidulans. Neurospora is a salient model for basic research in eukaryotes, as is Aspergillus, and fungi allied to these species include most animal and plant pathogens as well as industrial strains yielding antibiotics, chemicals, enzymes, and Pharmaceuticals. Gene predictions among the 9846 genes encoded by the fully sequenced 43 Mb Neurospora genome are supported by over 250,000 ESTs derived from this P01. During the past 4 years, we revolutionized the tools and techniques for gene knockouts in filamentous fungi and exceeded our initial goal by over 40%. Project #1 will complete the Neurospora gene knockouts and extend the systematic disruption of genes to Aspergillus. We will develop strains, tools, and background information in support of Projects #2 and #3, and of the overarching goal of understanding regulatory pathways governing filamentous fungal development. Projects #2 and #3 will aim to describe and reconstruct the cascading regulatory programs that underlie N. crassa's developmental response to light and air, from the level of chromatin structure through the gene regulatory network. Project #3 will use ChlP-seq mapping of histone modifications, transcription factor binding sites, sites of DNA methylation and nucleosome occupancy with corresponding transcriptome measurements to generate a deep description of genome and epigenome dynamics. Project #2, in an informatic-intensive systems biology approach, will integrate these data and use computational modeling to develop predictive models of the interconnected light and asexual development gene regulatory networks. These models will be fleshed out tested through incorporation of new data arising from Project #3 and refined via perturbation analyses facilitated through the use of strains developed in Project #1 and characterized using the tools employed in Project #3. This effort will anchor, promote, and exploit genomic exploration within model systems that provide gateways to the Kingdom of the Fungi.