Tools for Functional Analysis and Cell Biology

本计划项目中三项相互依存的工作的中心目标是建立在成功的 粗糙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。一个主要目标，通过分子，细胞 生物学，基因组学和计算方法，将是了解如何N。粗过渡， 菌丝生长至完成无性孢子发育。我们将集中讨论无性生殖的两个关键触发因素 显影：光照和干燥。此外，我们将利用我们先前的成功， 敲除到另外的突出模型系统构巢曲霉。脉孢菌是一个突出的模式， 在真核生物的基础研究，如曲霉，和真菌的近亲，这些物种包括大多数动物和 植物病原体以及产生抗生素、化学品、酶和药物的工业菌株。 基因预测中的9846基因编码的43 Mb脉孢菌基因组全序列， 由来自该P01的超过250，000个EST支持。在过去的4年里，我们革新了工具， 以及丝状真菌基因敲除技术，并超过了我们最初的目标超过40%。项目 #1将完成脉孢菌基因敲除，并将基因的系统性破坏扩展到 曲霉菌我们将开发菌株、工具和背景信息，以支持项目#2和#3， 了解丝状真菌发育的调控途径的总体目标。 项目#2和#3的目标是描述和重建N. crassa的发育反应，光和空气，从染色质结构的水平，通过基因 监管网络。项目#3将使用组蛋白修饰、转录因子 结合位点、DNA甲基化位点和相应转录组的核小体占有率 测量以产生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， 开发相互关联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产生的新数据进行充实测试， 通过使用项目#1中开发的菌株促进的扰动分析进行改进， 使用项目#3中使用的工具进行表征。 这项工作将锚，促进和利用模型系统内的基因组探索，提供 通往王国真菌的大门

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 ChIP-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.