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首页> 外文期刊>BMC Molecular Biology >Identifying novel genes in C. elegans using SAGE tags
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Identifying novel genes in C. elegans using SAGE tags

机译：使用SAGE标签鉴定秀丽隐杆线虫中的新基因

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Despite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required. In this project, we have developed a method of reconstructing full-length cDNA sequences based on short expressed sequence tags which is called s equence t ag-based a mplification of c DNA e nds (STACE). Expressed tags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We have demonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags mined in an array of serial analysis of gene expression (SAGE) of C. elegans cDNA libraries. We have successfully applied STACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used to successfully recover full-length cDNA sequences for seven of these genes. The STACE method can be used to effectively reconstruct full-length cDNA sequences of genes that are under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods, but their existence has been suggested by short sequence tags such as SAGE tags.
机译：尽管致力于预测基因组序列中蛋白质编码基因的大量努力，但尚未发现许多真正的基因，并且许多现有的基因模型在所有测序的真核生物基因组中均不准确。由于我们对基因特征信息（例如剪接和启动子特征）的不完全了解而开发了基因预测程序，部分地解释了这种情况。另外，由于其低水平或罕见的表达，难以获得许多基因及其同工型的全长cDNA。为了获得所有蛋白质编码基因的全长序列，需要替代方法。在这个项目中，我们开发了一种基于短表达序列标签的全长cDNA序列的重建方法，这种方法称为基于序列DNA的c DNA扩增（STACE）。表达的标签在两轮PCR扩增中用作检索全长转录本的锚点。我们已经证明了STACE在使用表达的标签重建线虫cDNA文库的基因表达系列分析（SAGE）阵列中挖掘的表达标签中的应用。我们已成功地将STACE应用到12个基因的序列信息中，其中两个我们发现了同工型。 STACE用于成功恢复其中七个基因的全长cDNA序列。 STACE方法可用于有效地重建基因的全长cDNA序列，这些基因在cDNA测序项目中代表性不足，并且已被现有的基因预测方法所遗漏，但是短序列标签（例如SAGE标签）暗示了它们的存在。

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