- 學位論文
利用計算方法分析水稻的外顯子剪接之調控序列
Computational analysis of candidate exonic splicing regulatory motifs in rice
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摘要
外顯子剪接增強子(exonic splicing enhancer, ESE)是一段特殊的寡核苷酸序列，當它出現在外顯子時，會加強pre-mRNA剪接作用。目前植物ESE序列的資料極為有限，本研究使用統計方法預測水稻的候選ESE序列，並提供分析資訊供生物學家參考。我們比較長度為6個核苷酸的短序列在外顯子和內含子出現的頻率，以及在弱剪接點的外顯子和強剪接點的外顯子出現的頻率差。我們找到的水稻候選ESE序列當中，有一部份與實驗已知的ESE序列相同，還有一些是水稻特有的序列。本研究分析水稻的pre-mRNA序列當中ESE motif之分布，發現在內含子保留序列之候選ESE密度高於內含子。部分候選ESE在外顯子出現的頻率高於UTR，並且在5`端的外顯子序列以及外顯子中間有較高的頻率。
並列摘要
Exonic splicing enhancers (ESEs), known as a kind of specific short oligonucleotides, appear in the exon and enhance pre-mRNA splicing. Although plant SR proteins and their functions have been studied, there is limited information about plant ESE elements. In this research, we used statistical methods to predict candidate rice ESE elements. We compared the frequency of occurrence of hexamers (6-mers) in two cases, i.e., exons versus introns, and exons with weak splice site versus exons with strong splice site. 115 candidate ESE motifs were identified and many of them match previously reported ESE sequences. Rice-specific putative ESE motifs were also identified in the study. Finally, we characterized the distribution of ESE in rice pre-mRNAs. It was found that candidate ESEs present at a higher density within intron retentions compared with introns. Density of some of candidate ESEs in exons was higher than UTR. Additionally the exons show higher ESE density in the vicinity of acceptor splice site and in the middle of exon.
參考文獻
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