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: 8311869
• 负责人: Levi Yant
• 金额: $ 5.22万
• 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/8311869
• 关键词: Address; Altitude; Angiosperms; Animals; Aquilegia; Arabidopsis; Barley; Binding; Binding Sites; Biochemical; Biological Assay; Biological Models; Biology; Candidate Disease Gene; ChIP-seq; 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. !

描述（由申请人提供）：繁殖时间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，植物解释从影响生殖转变的茎尖处的多种遗传途径汇聚的各种信号2,3。这些途径包括激素信号传导、对日长的感知、发育阶段和资源可用性、环境温度、光质量以及寒冷或春化的传播2,3。这种转变的遗传基础已在双子叶植物拟南芥和单子叶植物中的几种禾本科植物中得到了很好的表征2-4。基础双子叶植物模型属耧斗菜属作为研究开花时间遗传基础的系统具有明显的优势，最显着的是其进化和生态学方面5-6。在开花植物中，耧斗菜在系统发育上介于拟南芥和禾本科植物之间，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，耧斗菜属最近发生了多样化，产生了几十种表型不同的物种，这些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。因此耧斗菜代表了一种自适应辐射模型。低序列多样性加上大表型变异不仅有望极大地促进适应性性状的遗传鉴定，而且还为基因网络的功能研究提供丰富的环境。该项目旨在利用我们对当前模型系统中开花时间的了解，更好地了解转录因子网络的连接性。首先，它的目的是对耧斗菜的生殖转变进行全基因组询问，以更好地了解控制这种适应性特征的网络。与控制生殖转变有关的染色质状态变化的全基因组鉴定将通过染色质免疫沉淀结合深度测序 (ChIP-seq) 进行绘制，并通过转录组测序评估其输出。接下来，将通过功能测定来表征与开花时间控制有关的基因、FLOWERING LOCUS T (FT)、FD 和 LEAFY (LFY) 的耧斗菜同源物的遗传和生化功能，包括病毒诱导的基因沉默敲低和生化测试拟南芥保护和原位杂交。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谱，将数千个基因座作为直接转录目标。该项目将通过在耧斗菜属以及更远亲的物种中进行全基因组 LFY ChIP-seq 分析，筛选出对 LFY 功能至关重要的保守体内结合位点，以进行微观和宏观进化比较。总之，目的是对耧斗菜属的适应性辐射模型中的进化重要特征进行功能研究，并通过利用该网络的现有知识并利用跨物种的物种来解决中央转录因子遗传连接的基本问题。分类群范围广泛。 ！