Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae
Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae
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DOI：
10.1017/s1355838299981682
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发表时间：
1999-02-01
期刊：
影响因子：
4.5
通讯作者：
Ares, M
中科院分区：
文献类型：
--
作者：
Spingola, M;Grate, L;Ares, M
内含子通常是以特定的方式发现的：内含子是在基因因其他原因而被表征时发现的。随着完整的真核基因组序列的出现，需要更好的方法来预测原始序列中的RNA加工信号，以便发现基因并预测其表达。在这里，我们提出了一个目录的228酵母内含子，通过生物信息学和分子分析相结合。对酵母基因组数据库（SGD）中注释的内含子进行了评价，在体内剪接测试失败后去除可疑内含子，并添加SGD注释中不存在的已知内含子。一个新的分支点序列，AAUUAAC，被确定在一个注释的内含子，缺乏一个高度保守的分支点共识UACUAAC的七分之六的匹配。数据库的分析证实了许多结论前体mRNA底物的要求剪接来自实验研究，但表明，在酵母中的剪接可能不会严格决定剪接位点的保护，如以前所认为的。使用这个数据库和一个分子技术，直接显示的lirene内含子产品的剪接转录本（内含子显示），我们认为，目前的一套228内含子仍然是不完整的，和额外的内含子含有基因仍有待发现酵母。该数据库可在http://www.cse.ucsc.edu/research/compbio/yeastintrons.html上查阅。
Introns have typically been discovered in an ad hoc fashion: introns are found as a gene is characterized for other reasons. As complete eukaryotic genome sequences became available, better methods for predicting RNA processing signals in raw sequence will be necessary in order to discover genes and predict their expression. Here we present a catalog of 228 yeast introns, arrived at through a combination of bioinformatic and molecular analysis. Introns annotated in the Saccharomyces Genome Database (SGD) were evaluated, questionable introns were removed after failing a test for splicing in vivo, and known introns absent from the SGD annotation were added. A novel branchpoint sequence, AAUUAAC, was identified within an annotated intron that lacks a six-of-seven match to the highly conserved branchpoint consensus UACUAAC. Analysis of the database corroborates many conclusions about pre-mRNA substrate requirements for splicing derived from experimental studies, but indicates that splicing in yeast may not be as rigidly determined by splice-site conservation as had previously been thought. Using this database and a molecular technique that directly displays the lariat intron products of spliced transcripts (intron display), we suggest that the current set of 228 introns is still not complete, and that additional intron-containing genes remain to be discovered in yeast. The database can be accessed at http://www.cse.ucsc.edu/research/compbio/yeastintrons.html.