Application of genomics to dissect Polycomb-group gene mediated control of plant development (PcG-CODE)

应用基因组学剖析多梳族基因介导的植物发育控制（PcG-CODE）

• 批准号: BB/H004319/1
• 负责人: Justin Goodrich
• 金额: $ 42.55万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2009
• 资助国家: 英国
• 起止时间: 2009 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FH004319%2F1
• 关键词: Application; genomics; dissect; Polycomb; group

A group of genes, called the Polycomb-group (Pc-G), have been found to control many aspects of plant development, including commercially important aspects such as seed size, flowering time, vernalization response (promotion of flowering time by overwintering) and production of embryos from somatic tissues. They do this by controlling the activity of other genes, called target genes, and making sure that these targets are only active in particular cell types and developmental stages. For example, the Pc-G ensure that a gene (AGAMOUS) that specifies sex organ development in flowers is only active in flowers. Until recently, very few of the Pc-G target genes were known. A breakthrough occurred when it was found that the target genes were distinguished by a chemical modification (methylation) to the histone proteins that coat their DNA. The rapid advance in genomics technologies in Arabidopsis allowed several groups to profile the distribution of this mark throughout the genome and so identify most Pc-G target genes. The target gene set is large(about 4000 genes) but includes many genes whose protein products are likely to be important developmental regulators. A high proportion of targets are predicted to encode transcription factors (these often control specific aspects of development, for example what type of organ or cell develops, what chemical products the cell makes) and are expressed at low levels at very specific times or places in development, consistent with their playing important roles. In some cases the function of the targets is known, and in these cases the targets are often useful genes (for example, one target gene, FT, produces a mobile signal triggering flowering in most plant species), but in many cases their role has not been determined. To exploit these recent technical and conceptual breakthroughs, the current consortium comprises various European groups with expertise in analysing plant development, plant polycomb group genes, and bioinformatic analysis (the analysis of the large datasets produced by genomics technologies is hugely demanding in computing resources). The first aim is to find out what the target genes do, as we believe the Pc-G target genes will include many genes with practically important roles. We will develop our bioinformatic tools to define those target genes that show tissue specific expression in seed, embryos, flowers, roots, shoot apices (where stem cells reside), and to select from this genes with unknown function but likely to have a developmental role and to act non redundantly (i.e. genes that aren't highly similar to other genes or if so are not expressed in the same time or place). We will then see what effect inactivating these genes has on seed size, seed viability, seed dormancy, flowering time, flower development etc (the different participants will target particular gene sets and traits). Our second aim is to refine the target gene lists by profiling the distribution of different Polycomb proteins and to see how this changes during a developmental transition, the regeneration of plants from adult tissue during cloning procedures. We will refine bioinformatic analysis to define whether there are specific DNA sequences that determine which genes are targetted by the Pc-G. Our third aim is to define the role of the Pc-G in stem cells, using the well studied root stem cell system. In particular we will define the targets of four transcription factors that play a key role in specifying root stem cell identity and which are themselves controlled by Pc-G.

Polycomb-group （Pc-G）基因控制着植物发育的许多方面，包括商业上重要的方面，如种子大小、开花时间、春化反应（通过越冬促进开花时间）和体细胞组织胚胎的产生。它们通过控制其他基因的活性来做到这一点，这些基因被称为靶基因，并确保这些靶基因只在特定的细胞类型和发育阶段活跃。例如，Pc-G确保指定花性器官发育的基因（AGAMOUS）只在花中活跃。直到最近，人们对Pc-G靶基因知之甚少。当发现目标基因通过包裹其DNA的组蛋白的化学修饰（甲基化）来区分时，一个突破发生了。随着拟南芥基因组学技术的快速发展，几个研究小组得以分析该标记在整个基因组中的分布，从而鉴定出大多数Pc-G靶基因。目标基因集很大（约4000个基因），但包括许多基因，其蛋白质产物可能是重要的发育调节因子。据预测，高比例的靶标编码转录因子（这些靶标通常控制发育的特定方面，例如什么类型的器官或细胞发育，细胞产生什么化学产物），并且在发育的非常特定的时间或地点低水平表达，这与它们发挥的重要作用一致。在某些情况下，靶标的功能是已知的，在这些情况下，靶标通常是有用的基因（例如，一个靶基因FT在大多数植物物种中产生触发开花的移动信号），但在许多情况下，它们的作用尚未确定。为了利用这些最新的技术和概念上的突破，目前的联盟由不同的欧洲小组组成，他们在分析植物发育、植物多梳群基因和生物信息学分析方面具有专业知识（基因组学技术产生的大型数据集的分析对计算资源的要求很高）。第一个目标是找出目标基因的作用，因为我们相信Pc-G目标基因将包括许多具有实际重要作用的基因。我们将开发我们的生物信息学工具来定义那些在种子、胚胎、花、根、茎尖（干细胞所在的地方）中显示组织特异性表达的靶基因，并从这些功能未知但可能具有发育作用和非冗余作用的基因中进行选择（即与其他基因不高度相似的基因，或者如果是这样，则不在同一时间或地点表达）。然后，我们将看到这些基因失活对种子大小、种子活力、种子休眠、开花时间、花朵发育等有什么影响（不同的参与者将针对特定的基因集和性状）。我们的第二个目标是通过分析不同Polycomb蛋白的分布来完善目标基因列表，并观察在发育过渡期间，在克隆过程中成体组织的植物再生过程中，这些基因是如何变化的。我们将改进生物信息学分析，以确定是否有特定的DNA序列决定哪些基因被Pc-G靶向。我们的第三个目标是利用已经得到充分研究的根干细胞系统来确定Pc-G在干细胞中的作用。特别是，我们将定义四个转录因子的靶标，这些转录因子在指定根干细胞身份中起关键作用，它们本身由Pc-G控制。

项目成果

Polycomb repressive complex 2 controls the embryo-to-seedling phase transition.

• DOI: 10.1371/journal.pgen.1002014
• 发表时间: 2011-03
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Bouyer D;Roudier F;Heese M;Andersen ED;Gey D;Nowack MK;Goodrich J;Renou JP;Grini PE;Colot V;Schnittger A
• 通讯作者: Schnittger A

Antagonistic roles of SEPALLATA3, FT and FLC genes as targets of the polycomb group gene CURLY LEAF.

• DOI: 10.1371/journal.pone.0030715
• 发表时间: 2012
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Lopez-Vernaza M;Yang S;Müller R;Thorpe F;de Leau E;Goodrich J
• 通讯作者: Goodrich J

Kicking against the PRCs - A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2.

• DOI: 10.1371/journal.pgen.1005660
• 发表时间: 2015-12
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Liang SC;Hartwig B;Perera P;Mora-García S;de Leau E;Thornton H;de Lima Alves F;Rappsilber J;Yang S;James GV;Schneeberger K;Finnegan EJ;Turck F;Goodrich J
• 通讯作者: Goodrich J