Exon-Trap Sequencing Using Transposons in Arabidopsis

在拟南芥中使用转座子进行外显子陷阱测序

• 批准号: 9408042
• 负责人: Robert Martienssen
• 金额: $ 45万
• 依托单位: Cold Spring Harbor Laboratory
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 1994
• 资助国家: 美国
• 起止时间: 1994-08-01 至 1997-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9408042&HistoricalAwards=false
• 关键词: Exon; Trap; Sequencing; Using; Transposons

Abstract 9408042 An in vivo gene-trapping technique has been developed in Arabidopsis using the transposable elements Ac and Ds. Our modified Ds element (DsG) contains a Beta-glucuronidase reporter gene that is equipped with splice acceptor signals to allow multi- frame gene fusions (an "exon-trap"). When this Ds element inserts into a chromosomal gene, the pattern of chromosomal gene expression is mimiced by the Beta-glucuronidase reporter gene. Because expression depends on gene fusion, insertions that result in reporter gene expression will also result in gene disruption. Using a novel selection scheme, a collection of 5,000 plants will be generated that will each carry an insertion at a different location in the genome. Insertions into genes will be identified by staining the progeny of each plant for reporter gene expression: 15-20% of DsG insertions result in reporter gene expression, so that the proposed collection should include insertions into 500- 1,000 genes. We will use this collection to develop an exon-trap sequencing technique to enable the rapid sequencing of a portion of the chromosomal gene identified by each exon-trap tag. The chromosomal exon corresponding to each insertion will be amplified by RACE PCR, and its sequence determined. As many of the exons as possible will be mapped via anchored YAC contigs and recombinant inbred lines. A database of DsG insertion lines will be developed, each characterized by expression pattern, mutant phenotype and map location, as well as partial exon sequence. This database can be integrated with existing genomic and cDNA sequence databases. *** A major goal in the characterization of the Arabidopsis genome is to assign a function to genes identified by cDNA and genomic sequencing, gene-finding algorithms, and map location. Homology searches are expected to fulfill this goal for those genes that have similarity to sequences from other organisms. However, a majority of gene products will remain an onymous in these large collections of sequenced genes. In the proposed study, a function will be assigned to many of these genes by determining their patterns of expression, and by observing the mutant phenotype that results from gene disruption. This proposal will form the basis for establishing a large database of insertion lines, as other laboratories use the "starter" lines to generate collections of their own. This will allow a function to be assigned to many of the genes identified by DNA sequence alone, as well as providing a genetic resource of widespread use. %%%

摘要9408042利用转座因子Ac和Ds在拟南芥中开发了一种体内基因捕获技术。 我们的修饰的Ds元件（DsG）含有β-葡糖醛酸糖苷酶报告基因，其配备有剪接受体信号以允许多框基因融合（“外显子陷阱”）。 当此Ds元件插入到染色体基因中时，染色体基因表达的模式被β-葡萄糖醛酸酶报告基因模仿。 因为表达依赖于基因融合，导致报告基因表达的插入也将导致基因破坏。 使用一种新的选择方案，将产生5,000株植物的集合，每株植物将在基因组的不同位置携带插入。 通过对每株植物的后代进行染色以确定报告基因表达，从而鉴定基因中的插入： 15-20%的DsG插入导致报告基因表达，因此建议的收集应包括插入500- 1，000个基因。 我们将使用这些收集来开发外显子陷阱测序技术，以使每个外显子陷阱标签识别的染色体基因的一部分的快速测序。 将通过RACE PCR扩增对应于每个插入的染色体外显子，并测定其序列。 尽可能多的外显子将通过锚定的YAC重叠群和重组近交系作图。 将开发DsG插入系的数据库，每个数据库的特征在于表达模式、突变表型和图谱位置以及部分外显子序列。 该数据库可以与现有的基因组和cDNA序列数据库集成。 * 拟南芥基因组表征的一个主要目标是为通过cDNA和基因组测序、基因发现算法和图谱定位鉴定的基因分配功能。 同源性搜索有望为那些与其他生物序列相似的基因实现这一目标。 然而，大多数基因产物将在这些测序基因的大集合中保持恒定。 在拟议的研究中，通过确定这些基因的表达模式，并通过观察基因破坏导致的突变表型，将功能分配给许多这些基因。 这一建议将构成建立插入线大型数据库的基础，因为其他实验室使用“起始”线来产生自己的集合。 这将允许将功能分配给仅通过DNA序列识别的许多基因，并提供广泛使用的遗传资源。 %%%