開放染色質與基因表現的等位基因特異性於編碼與非編碼核糖核酸之研究

A Study of Allele-Specific Open Chromatin and Expression in Coding and Non-Coding RNAs

陳郁潔(Yu-Chieh Chen)

指導教授 ： 黃耀廷

國立中正大學/工學院/資訊工程學系/碩士(2013年)

摘要

近年來編碼RNA之轉錄已經被證明與相近之染色質結構之緊密程度有高度關聯性。然而因為人類的基因體為雙倍體，RNA轉錄與染色質結構應該分別根據父系與母系單體型來觀察。其實許多等位基因已經被證明具有等位基因特異性(Allele-Specific Expression)。同理，染色質結構也被證明在父系與母系單體型上亦有等位基因結構差異(Allele-Specific Chromatin)。由於定序過程會將父系與母系單體型序列混雜，造成後端分析時難以分離，進而很難精準測量到ASE或ASC現象。本篇論文提出了一種利用整合核糖核酸定序(RNA-Seq)和脫氧核糖核酸酶定序(DNase-Seq)技術，分析在編碼 (Coding RNA) 與非編碼核糖核酸 (Non-Coding RNA)其等位基因特異性與等位基因結構差異之調控關係。我們發展出一種無偏差之檢定方法來判讀等位基因是否有差異。由於大部分的編碼與非編碼核糖核酸和染色質區域含有兩個或兩個以上的雜合型單核苷酸多型性(SNP)，檢定結果需要被合併以提供任一編碼/非編碼基因和染色質區域之一評估結果。實驗結果顯示，許多編碼/非編碼基因的基因表現等位基因特異性，皆是由於具有等位基因結構差異所導致。我們亦發現全基因組序列之開放染色質結構數量，和編碼與非編碼核糖核酸之數量分布有高度相關。我們找到的等位基因特異性和等位基因結構差異，在三人家庭內遵守孟德爾法則。分析結果顯示具有等位基因特異性之編碼與非編碼RNA，通常由距離較遠之等位基因結構差異所導致。

關鍵字

編碼核糖核酸 ； 染色質的等位基因特異性 ； 基因表現的等位基因特異性 ； 脫氧核糖核酸酶定序 ； 核糖核酸定序 ； 非編碼核糖核酸

並列摘要

In recent years, the activation of coding and non-coding RNAs are known to associate with the compactness of localized chromatin structure. Because our human genome is a diploid, the RNA transcription and chromatin structure should be further distinguished according to the paternal or maternal haplotypes. This hides the fact that the any two alleles may not necessarily express at equal level, which is called allele-specific expression (ASE). Similarly, the chromatin structure of paternal and maternal haplotypes may differ in the donor genome, which is called allele-specific chromatin (ASC). In reality, the measurement of ASE or ASC is challenged by the fact that short reads from paternal and maternal haplotypes are mixed during massively parallel sequencing. This thesis proposes a framework for analyzing the regulation relationship between ASE and ASC in coding and non-coding RNAs by integrating DNase-Seq and RNA-Seq. An unbiased test is designed and implemented to measure the allele specificity between the paternal and maternal haplotypes. As the majority of coding/non-coding RNAs and chromatin regions have two or more heterozygous SNPs, the test statistics are combined for providing an overall assessment of each coding/non-coding gene and chromatin regions. The experimental results indicate that non-coding RNAs also exhibit ASE, and many coding/noncoding RNAs showing ASE are indeed due to ASCs. The distribution of open chromatin highly correlates with coding and non-coding RNAs across the entire genome. The ASE and ASC follows the law of Mendelian consistency within a trio. The correlation between ASE and distal ASC is more significant than nearby ASC.

並列關鍵字

RNA-Seq ； Allele-Specific Chromatin (ASC) ； Allele-Specific Expression(ASE) ； DNase-Seq ； Coding RNA ； Non-Coding RNA

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