Genome wide views of chromatin occupancy in the control of Aquilegia development

染色质占据控制耧斗菜发育的全基因组视角

• 批准号: 8202898
• 负责人: Levi Yant
• 金额: $ 4.84万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8202898
• 关键词: Address; Altitude; Angiosperms; Animals; Aquilegia; Arabidopsis; Barley; Binding; Binding Sites; Biochemical; Biological Assay; Biological Models; Biology; Candidate Disease Gene; Chromatin; Chromosome Mapping; Comparative Study; Complex; Coupled; Data; Development; Developmental Biology; Developmental Process; Environment; Epigenetic Process; Event; Evolution; Flowers; Food; Gene Expression; Gene Expression Profile; Gene Silencing; Genes; Genetic; Genetic Transcription; Genomics; Homologous Gene; Hormones; In Situ Hybridization; Individual; Investigation; Knowledge; Lasers; Light; Maps; MicroRNAs; Modeling; Modification; Mosses; North America; Orthologous Gene; Output; Pathway interactions; Perception; Phase; Phylogenetic Analysis; Plants; Poaceae; Production; Proteins; RNA; Radiation; Reproduction; Resources; Rice; Sea; Signal Pathway; Signal Transduction; System; Taiwan; Taxon; Temperature; Testing; Time; Variant; Viral; Wheat; Work; base; chromatin immunoprecipitation; chromatin modification; day length; foot; gene function; genetic evolution; genome sequencing; genome wide association study; genome-wide; in vivo; interest; mRNA Expression; mutant; novel; plant growth/development; programs; reproductive; response; rosin; trait; transcription factor

DESCRIPTION (provided by applicant): The timing of reproduction is a critical event in plant development and is controlled by a refined genetic network. To regulate flowering time, plants interpret a variety of signals that converge from multiple genetic pathways at the shoot apex where the reproductive transition is effected2,3. These pathways include hormone signaling, perception of day length, developmental phase and resource availability, ambient temperature, light quality, and the passage of cold, or vernalization2,3. The genetic basis for this transition has been well characterized in the dicot Arabidopsis and several grass species in the monocots2-4. The basal dicot model genus Aquilegia has clear benefits as a system for studying the genetic basis of flowering time, most notably aspects of its evolution and ecology5-6. Within flowering plants, Aquilegia is phylogenetically intermediate between Arabidopsis and the grasses, providing a critical third data point for deep phylogenetic comparisons. At the same time, the genus Aquilegia has diversified very recently, leading to several dozen phenotypically distinct species that are broadly distributed in different environments, with very low sequence diversity between species7. Thus Aquilegia represents a model adaptive radiation. The low sequence diversity coupled with large phenotypic variation not only promises to greatly facilitate the genetic identification of adaptive traits, but also to provide a rich setting for the functional study of gene networks. This project aims to better understand the connectivity of transcription factor networks by leveraging our knowledge of flowering time in current model systems. First, it aims to perform a genome-wide interrogation of the reproductive transition in Aquilegia to better understand the network controlling this adaptive trait. Genome-wide identification of chromatin state changes implicated in governing the reproductive transition will be mapped with chromatin immunoprecipitation coupled to deep sequencing (ChIP-seq) and their output will be assessed with transcriptome sequencing. Next, the genetic and biochemical functions of genes implicated in flowering time control, the Aquilegia homologs of FLOWERING LOCUS T (FT), FD, and LEAFY (LFY) will be characterized by functional assays including knockdown by viral induced gene silencing and tests of biochemical conservation in Arabidopsis, and in situ hybridization. Finally, this project will leverage very recent genome- wide transcription factor binding maps of the key integrator protein LFY, implicating thousands of loci as direct transcriptional targets. This project will winnow out the conserved in vivo binding sites that are critical for LFY function by performing genome-wide LFY ChIP-seq assays in the Aquilegia genus in addition to more distantly related species for both micro- and macro-evolutionary comparisons. In summary, the aim is to perform functional studies of evolutionary important traits in the adaptive radiation model of the Aquilegia genus, and to address basic questions of genetic connectivity of central transcription factors by leveraging current knowledge of this network and taking advantage of species across a wide range of taxa. ! PUBLIC HEALTH RELEVANCE: The connectivity of genetic regulatory networks is not well understood and there is recent indication that the direct connectivity of these networks is unexpectedly complex. Plants present highly tractable models to access gene networks in ways that are much more cumbersome and expensive in similarly complex animals. We are therefore mapping gene networks in several species to 1) understand which interactions are most important for core developmental processes and 2) better understand the basic mechanisms in evolution.

描述(由申请人提供)：繁殖的时机是植物发育中的关键事件，由精细的遗传网络控制。为了调节开花时间，植物解释从多条遗传途径汇聚的各种信号，这些遗传途径在枝梢发生生殖转换2，3。这些信号包括激素信号，对日长的感知，发育阶段和资源的可获得性，环境温度，光照质量，以及寒冷或春化的传递2，3。这种转换的遗传基础在双子叶拟南芥和几个单子叶植物2-4中得到了很好的描述。基本双子叶模式属Aquilegia作为研究开花时间的遗传基础的系统具有明显的益处，最显著的是它的进化和生态学方面的5-6。在开花植物中，Aquilegia在系统发育上介于拟南芥和禾本科之间，为深入的系统发育比较提供了关键的第三个数据点。与此同时，Aquilegia属最近变得多样化，导致数十个表型不同的物种广泛分布在不同的环境中，物种之间的序列多样性非常低7。因此，Aquilegia代表了一种自适应辐射模型。较低的序列多样性和较大的表型变异不仅极大地促进了适应性性状的遗传鉴定，而且为基因网络的功能研究提供了丰富的环境。这个项目旨在通过利用我们在当前模型系统中关于开花时间的知识来更好地理解转录因子网络的连通性。首先，它的目的是在全基因组范围内对阿奎莱贾的生殖转变进行询问，以更好地了解控制这种适应性特征的网络。通过染色质免疫沉淀与深度测序相结合(CHIP-SEQ)，将在全基因组范围内识别与控制生殖转变有关的染色质状态变化，并将通过转录组测序来评估它们的输出。接下来，我们将通过病毒诱导的基因沉默、拟南芥的生化保守性实验和原位杂交等功能分析，对与开花时间控制有关的基因、开花基因T(FT)、Fd和LEAFY同源基因的遗传和生化功能进行研究。最后，该项目将利用关键整合蛋白LFY的最新全基因组转录因子结合图，涉及数千个基因座作为直接转录目标。该项目将通过在蓝藻属中进行基因组范围的LFY芯片序列分析，以及更远缘物种的微观和宏观进化比较，筛选出对LFY功能至关重要的保守的体内结合位点。综上所述，本研究的目的是在蓝藻属的适应性辐射模型中对进化的重要特征进行功能研究，并通过利用该网络的现有知识和利用广泛分类群中的物种优势来解决中央转录因子的遗传连通性的基本问题。好了！ 与公共卫生的相关性：基因调控网络的连通性尚未得到很好的理解，最近有迹象表明，这些网络的直接连通性出人意料地复杂。植物提供了高度易处理的模型来访问基因网络，而在类似复杂的动物中，这种方法要麻烦得多，成本也高得多。因此，我们正在绘制几个物种的基因网络图，以1)了解哪些相互作用对核心发育过程最重要，2)更好地了解进化的基本机制。