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，并由精致的遗传网络控制。为了调节开花时间，植物解释了各种信号，这些信号是从芽中的多个遗传途径收敛的，在芽的先端，生殖过渡的影响2,3。这些途径包括激素信号传导，对日长度的感知，发育阶段和资源可用性，环境温度，光质量以及寒冷或春季的通过2,3。这种过渡的遗传基础在单尾植物中的双子拟南芥和几种草种中都得到了很好的特征。基底双科属模型属具有明显的好处，作为研究开花时间的遗传基础的系统，最著名的是其进化和生态学的方面5-6。在开花植物中，拟南芥和草之间的系统发育中间是中间的，为深度系统发育比较提供了关键的第三个数据点。同时，Aquilegia属最近发生了多样化，导致数十个表型不同的物种在不同的环境中广泛分布，物种之间的序列多样性非常低。因此，Aquilegia代表模型自适应辐射。低序列多样性与大表型变异相结合，不仅有望极大地促进自适应特征的遗传鉴定，而且还为基因网络的功能研究提供了丰富的设置。该项目旨在通过利用当前模型系统中的开花时间知识来更好地了解转录因子网络的连通性。首先，它旨在对Aquilegia的生殖过渡进行全基因组的询问，以更好地了解控制这种自适应性状的网络。涉及控制生殖过渡的染色质状态变化的全基因组鉴定将与染色质免疫沉淀耦合到深层测序（CHIP-SEQ），并将通过转录组测序评估其输出。接下来，与开花时间控制有关的基因的遗传和生物化学功能，开花基因座T（FT），FD和LEADY（LFY）的盐水同源物的特征在于功能测定，包括通过病毒诱导的基因沉默和拟南芥中的生物化学保护和Seratu hybrications和In Insuals的生物化学保护的功能敲低。最后，该项目将利用关键积分蛋白LFY的最新基因组 - 转录因子结合图，这意味着数千个基因座是直接转录靶标。该项目将通过在Aquilegia Genus中执行全基因组LFY LFY芯片seq分析，除了对微观和宏观进化的比较中，除了更远的相关物种外，还可以通过对LFY功能至关重要的保守的体内结合位点。总而言之，目的是在Aquilegia属的自适应辐射模型中对进化重要特征进行功能研究，并通过利用当前对该网络的知识并利用物种在广泛的分类单元中利用物种来解决中心转录因子的遗传连通性的基本问题。呢