Functional Analysis and Systems Biology of Filamentous Fungi

描述（由申请人提供）：本项目中三个相互依赖的工作的中心目标建立在对粗神经孢子菌的成功功能基因组学，注释和表达分析的基础上，粗神经孢子菌是超过25万种非酵母真菌的首要丝状真菌模型。通过分子、细胞生物学、基因组学和计算方法，我们的主要目标将是了解N.草是如何从菌丝生长过渡到完全无性孢子发育的。我们将关注无性发育的两个关键触发因素：光和干燥。此外，我们将利用我们之前的成功，将系统敲除扩展到另一个突出的模型系统，即空心曲霉。神经孢子菌是真核生物基础研究的重要模型，曲霉也是如此，与这些物种相关的真菌包括大多数动植物病原体以及生产抗生素、化学品、酶和药物的工业菌株。由该P01衍生的超过25万个ESTs支持了43 Mb神经孢子虫基因组编码的9846个基因的预测。在过去的4年里，我们彻底改变了丝状真菌基因敲除的工具和技术，超过了我们最初的目标40%以上。计划#1将完成神经孢子菌基因敲除，并将基因系统破坏扩展到曲霉。我们将开发菌株，工具和背景信息，以支持项目#2和#3，以及了解丝状真菌发育的调控途径的总体目标。项目#2和#3旨在描述和重建N. crassa对光和空气的发育反应的级联调控程序，从染色质结构水平到基因调控网络。项目#3将使用组蛋白修饰、转录因子结合位点、DNA甲基化位点和核小体占用位点的ChlP-seq图谱以及相应的转录组测量来生成基因组和表观基因组动力学的深入描述。项目#2，在信息密集型系统生物学方法中，将整合这些数据并使用计算建模来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中产生的新数据来充实和测试，并通过使用项目#1中开发的菌株进行扰动分析来改进，并使用项目#3中使用的工具进行表征。这项工作将锚定、促进和利用模型系统内的基因组探索，为真菌王国提供门户。

DESCRIPTION (provided by applicant): 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.