人類微核醣核酸、目標基因與同源體之預測

Prediction of Human miRNAs, Targets and Homologs

張耀明(Yao-Ming Chang)

指導教授 ： 葉耀明 ； 施純傑

國立臺灣師範大學/理學院/資訊工程研究所/博士(2010年)

摘要

微核醣核酸(microRNAs)是一種長度大約22個鹼基的核醣核酸物質。它可以透過鹼基序列互補的特性抑制特定的目標基因以達到減少蛋白質生成的目的。大部分的人類基因都被發現可能是微核醣核酸的目標基因。許多研究也發現微核醣核酸在生物中扮演非常重要的角色。我們的研究主要著眼於兩個主題：未知的微核醣核酸之預測與微核醣核酸同源序列(homolog)之預測。透過這兩個研究主題我們可以對於微核醣核酸之起源與演化過程有更多的了解進而對相關的問題提出解決方案。
在第一部分的研究中，我們發展了一個新的微核醣核酸預測方法，有別於先前的研究，此方法不用跨物種保守的資訊。我們先找出在某些組織特有表現的基因(tissue-selective genes)，並於這些基因的3’UTR序列中找出頻繁出現的序列模式(frequent motif)。透過這些頻繁序列模式，我們找到許多已知微核醣核酸的目標基因。接著我們更利用這些頻繁序列預測出未知的微核醣核酸。在我們的預測結果中，有一部份也已經透過實驗的證實為真實的微核醣核酸。這樣高成功率的預測也大大地降低實驗所需的時間與成本。
第二部分的研究中，我們提出了一個新的方法在其他物種當中發掘更多可能是人類微核醣核酸的同源序列。透過成熟微核醣核酸(mature miRNA)序列在其他物種基因組中的搜尋之後，我們接著利用一些微核醣核酸結構與系列上的特性當作過濾條件得到許多之前未知的同源序列。在我們的結果中發現，許多人類的微核醣核酸同源序列在動物的祖先基因組中可能就已經出現。

關鍵字

微核醣核酸 ； 目標基因 ； 微核醣核酸預測 ； 目標基因預測 ； 同源微核醣核酸 ； 微核醣核酸同源序列預測 ； 組織特有基因 ； 頻繁序列模式

並列摘要

MicroRNAs (miRNAs) are small endogenous RNA molecules ~22 nt that target specific mRNAs to reduce the expression or translation. A large proportion of human protein-coding genes have been found that are probably regulated by miRNAs, suggesting that miRNAs play a critical role in a wide variety of biological functions. In this dissertation, we focus on two issues related to miRNA research: novel miRNA prediction and miRNA homolog prediction. We study these two issues from thorough the understanding of miRNA biogenesis and evolutionary characteristics and then propose two effective new approaches to solve biological problems.
In first work, we developed a method to predict novel human miRNAs and target genes without requiring cross-species conservation. We first identified lowly/moderately expressed tissue-selective genes using EST data and then identified overrepresented motifs of 7 nucleotides in the 3' UTRs of these genes. Using these motifs as potential target sites of miRNAs, we recovered more than two thirds of the known human miRNAs. We then used those motifs that did not match any known human miRNA seed region to infer novel miRNAs. We predicted 36 new human miRNA genes with 44 mature forms and 4 novel alternative mature forms of 2 known miRNA genes when a stringent criterion was used and many more novel miRNAs when a less stringent criterion was used. Some of our results have been experimentally verified with a highly successful rate (8 out of 11) which can definitely reduce much experimental cost and time.
In second work, we proposed a new search method to discover as more as possible human miRNA homologs in distant species, such as worm, fruit fly, lancelet, and zebrafish. We first searched miRNA homologous candidates in genomes according to a given known mature miRNA. Then, the similar mature candidates were extended to be precursor candidates and checked by filters of both sequence and structural criterions. The precursor candidates that passed all filters were considered as the possible miRNA homologs. In our results, many of human miRNA homologs were found in all four genomes. So, we infer that most human miRNAs may share the common ancestors with worm and fruit fly.

並列關鍵字

microRNA ； target gene ； miRNA prediction ； target prediction ； homologous miRNA ； miRNA homolog prediction ； tissue-selective genes ； frequent pattern

參考文獻

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