Diversity and functional differentiation of preinitiation complex of transcription in plants

核心启动子是含有RNA聚合酶II的预起始复合体组装的区域，位于转录起始点附近。然而，大多数植物启动子没有任何可识别的核心启动子元件，这反映了我们对植物启动子的了解有限。我们通过阐明植物基因组的核心启动子结构来支持这一资助项目。为此，我们采取了新的核心启动子元件的电子检测和大规模转录起始位点(TSS)的确定相结合的方法。我们开发了一种新的鉴定TSS的方法，结合使用Cap-Trapper和大规模平行签名测序方法。这项名为CT-MPSS的技术使我们能够识别与38,311个TSS基因座相对应的158,237个拟南芥TSS标签，这为首次对植物启动子进行定量分析提供了机会。在…中分析了这些核心启动子的表达特征检测到更多针对核心启动子元件的ECT。通过我们的计算机分析，发现拟南芥启动子包含两种具有独特特征的主要类型，一种是TATA类型，一种是GA类型。TATA类启动子倾向于与Y补丁和INR相关，并导致TSS尖峰簇的高水平表达。相比之下，GA类型产生宽型TSS集群。与哺乳动物启动子不同，植物启动子与CpG岛无关。然而，植物特异的GA类启动子与哺乳动物的CpG类启动子有一些共同的特征。接下来，我们以拟南芥光合作用基因为模型案例，研究了核心启动子元件在组织特异性和光响应转录调控方面的功能分化。我们从不同的基因中构建了一系列调控启动子和核心启动子片段的互换结构，并将它们的报告融合引入植物。对这些嵌合启动子表达特征的分析表明，每个上游调控元件都对特定类型的核心启动子亚型有偏好。这一发现表明，核心启动子亚型的功能分化可能反映了转录预起始复合体的功能分化。较少

Core promoter is a region where preinitiation complex containing RNA polymerase II assembles, and located around the transcription start sites. However, the majority of plant promoters do not have any recognizable core promoter elements, which reflects our limited understanding of plant promoters.We hut:la fed this grant project by elucidating the core promoter architecture of the plant genome. For this sake, we took the combined approach of in silico detection of novel core promoter elements and large-scale determination of transcription start sites (TSSs). We developed a novel methodology for TSS identification, using a combination of the Cap-Trapper and Massively Parallel Signature Sequencing methods. This technique, CT-MPSS, allowed us to identify 158,237 Arabidopsis TSS tags corresponding to 38,311 TSS loci, which has provided an opportunity for quantitative analysis of plant promoters for the first time. The expression characteristics of these core promoters were analyzed in resp … More ect to core promoter elements detected. by our in silico analyses, revealing that Arabidopsis promoters contain two major types with exclusive characteristics, a TATA type and a GA type. The TATA-type promoters tend to be associated with the Y Patch and Inr, and cause high-level expression with TSS clusters of sharp peak. By contrast, the GA type produces broad-type TSS clusters. Unlike mammalian promoters, plant promoters are not associated with CpG islands. However, plant-specific GA-type promoters share some characteristics with mammalian CpG-type promotersNext, we examined the functional differentiation of core promoter elements with respect to tissue-specific and light-responsive transcriptional regulation, using Arabidopsis photosynthesis genes as a model case. We made a series of swapping constructs of regulatory and core promoter segments from various genes, and their reporter fusions were introduced into plants. Analysis of the expression characteristics of these chimeric promoter constructs revealed that upstream regulatory elements each have preference to specific type of core promoter subtypes. This finding implies that the functional differentiation of core promoter subtypes may reflect the functional differentiation of transcriptional preinitiation complexes. Less