Tools for Functional Analysis and Cell Biology

功能分析和细胞生物学工具

• 批准号: 8375308
• 负责人: Jay C. Dunlap
• 金额: $ 61.2万
• 依托单位: DARTMOUTH COLLEGE
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-04-01 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8375308
• 关键词: Air; Ally; Animals; Antibiotics; Area; Aspergillus; Aspergillus nidulans; Basic Science; Binding Sites; Biological; Biological Models; Cells; Cellular biology; Characteristics; Chemicals; Chromatin Structure; Communities; Computer Simulation; DNA Methylation; Data; Deposition; Desiccation; Development; Engineering; Enzymes; Epitopes; Eukaryota; Eukaryotic Cell; Expressed Sequence Tags; Focus Groups; Fungi Model; Gene Expression Profile; Gene Proteins; Genes; Genome; Genomics; Goals; Growth; Growth and Development function; Histones; Informatics; Knock-out; Light; Maps; Measurement; Mediating; Modeling; Molds; Molecular; Molecular Biology; Neurospora; Neurospora crassa; Nucleosomes; Pharmacologic Substance; Plants; Proteins; Proteomics; RNA; Regulator Genes; Regulatory Pathway; Reproduction spores; Research; Research Personnel; Science; Site; Systems Biology; Techniques; Technology; Testing; Variant; Work; Yeasts; asexual; base; functional genomics; fungal genetics; fungus; gene replacement; histone modification; improved; killings; knockout gene; mutant; new technology; novel; pathogen; predictive modeling; programs; response; success; tool; tool development; transcription factor

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.

该计划中三项相互依存的努力的中心目标建立在成功的基础上 粗糙脉孢菌（主要丝状菌）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。主要目标是通过分子、细胞来靶向 生物学、基因组学和计算方法，将了解粗糙猪笼草如何从 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触发因素 发育：光照和干燥。此外，我们将利用之前的成功来扩展系统性 敲除另一个著名的模型系统，构巢曲霉。脉孢菌是一个重要的模型 真核生物的基础研究，如曲霉属，与这些物种相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。 由完整测序的 43 Mb 脉孢菌基因组编码的 9846 个基因中的基因预测为 由源自此 P01 的超过 250,000 个 EST 支持。在过去 4 年里，我们彻底改变了工具 丝状真菌基因敲除技术，超出了我们最初的目标 40% 以上。项目 #1 将完成脉孢菌基因敲除并将基因的系统破坏扩展到 曲霉属。我们将开发菌株、工具和背景信息来支持项目 #2 和 #3，以及 了解控制丝状真菌发育的调控途径的总体目标。 项目 #2 和 #3 将旨在描述和重建 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 作图 结合位点、DNA 甲基化位点和核小体与相应转录组的占据 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模型 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 和项目中产生的新数据进行充实测试 通过使用项目 #1 中开发的菌株进行扰动分析来完善 使用项目 #3 中使用的工具进行表征。 这项工作将在模型系统中锚定、促进和利用基因组探索，这些系统提供 通往真菌王国的门户。