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: 8518387
• 负责人: Levi Yant
• 金额: $ 5.39万
• 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/8518387
• 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 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; 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; deep sequencing; 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; transcriptome sequencing

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）：繁殖的时间是植物发育中的关键事件，并由精细的遗传网络控制。为了调节开花时间，植物解释了多种信号，这些信号从多个遗传途径聚集在茎尖，生殖过渡受到影响2，3。这些途径包括激素信号，白天长度的感知，发育阶段和资源可用性，环境温度，光质量和寒冷的通道，或春化2，3。这种转变的遗传基础已经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。作为研究开花时间的遗传基础的系统，Aquilegia的基础双子叶模式属具有明显的益处，最显着的是其进化和生态学方面5 -6。在开花植物中，Aquilegia是拟南芥和禾本科植物之间的中间遗传学，为深入的系统发育比较提供了关键的第三个数据点。同时，Aquilegia属最近已经多样化，导致几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代表了一种适应性辐射模型。低的序列多样性加上大的表型变异不仅有望大大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了丰富的背景。该项目旨在通过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，它旨在对Aquilegia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。涉及控制生殖过渡的染色质状态变化的全基因组鉴定将用染色质免疫沉淀结合深度测序（ChIP-seq）进行映射，并将用转录组测序评估其输出。接下来，涉及开花时间控制的基因的遗传和生物化学功能，将通过功能测定来表征，包括通过病毒诱导的基因沉默和拟南芥中的生物化学保守性测试的敲除，以及原位杂交。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，暗示数千个位点作为直接转录靶点。该项目将通过在Aquilegia属中进行全基因组LFY ChIP-seq测定，以及在微观和宏观进化比较中更远的相关物种中筛选出对LFY功能至关重要的保守体内结合位点。总之，我们的目的是进行功能研究进化的重要特征的适应性辐射模型的Aquilegia属，并解决基本问题的遗传连接的中央转录因子，利用目前的知识，这个网络，并利用物种在广泛的类群。!

项目成果

Meiotic adaptation to genome duplication in Arabidopsis arenosa.

• DOI: 10.1016/j.cub.2013.08.059
• 发表时间: 2013-11-04
• 期刊: CURRENT BIOLOGY
• 影响因子: 9.2
• 作者: Yant, Levi;Hollister, Jesse D.;Wright, Kevin M.;Arnold, Brian J.;Higgins, James D.;Franklin, F. Chris H.;Bomblies, Kirsten
• 通讯作者: Bomblies, Kirsten