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

已经发现一组称为Polycomb组（Pc-G）的基因控制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）和从体细胞组织产生胚。他们通过控制其他基因（称为靶基因）的活性来做到这一点，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确保指定花中性器官发育的基因（AGAMOUS）仅在花中活跃。直到最近，还很少有人知道Pc-G靶基因。当人们发现靶基因是通过对包裹在它们DNA上的组蛋白进行化学修饰（甲基化）来区分的时候，一个突破就出现了。拟南芥基因组学技术的快速发展使得几个研究小组能够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，高比例的靶点编码转录因子（这些转录因子通常控制发育的特定方面，例如发育何种类型的器官或细胞，细胞产生何种化学产物），并且在发育中非常特定的时间或地点以低水平表达，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，并且在这些情况下，靶标通常是有用的基因（例如，一种靶基因FT产生移动的信号，触发大多数植物物种的开花），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突破，目前的联盟包括在分析植物发育，植物polycomb组基因和生物信息学分析（基因组学技术产生的大型数据集的分析在计算资源方面要求很高）方面具有专业知识的各种欧洲团体。第一个目标是找出靶基因的作用，因为我们相信Pc-G靶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，并从这些基因中选择功能未知但可能具有发育作用的基因，并且非冗余地发挥作用（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，我们将看到灭活这些基因对种子大小、种子活力、种子休眠、开花时间、花发育等有什么影响（不同的参与者将针对特定的基因组和性状）。我们的第二个目标是通过分析不同Polycomb蛋白的分布来完善靶基因列表，并了解在发育过渡期间这种变化，即在克隆过程中从成体组织再生植物。我们将完善生物信息学分析，以确定是否有特定的DNA序列，确定哪些基因是由PC-G靶向。我们的第三个目标是使用研究充分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目标，发挥了关键作用，在指定的根干细胞的身份，这本身是由PC-G控制。

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.