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研究生:許眾棠
研究生(外文):Chung-Tang Hsu
論文名稱:分析發生在癌症轉錄體序列之核醣核酸編輯現象
論文名稱(外文):Investigation of RNA editing on cancer transcriptome
指導教授:鍾翊方林振慶
指導教授(外文):I-Fang ChungCheng-Ching Lin
學位類別:碩士
校院名稱:國立陽明大學
系所名稱:生物醫學資訊研究所
學門:生命科學學門
學類:生物化學學類
論文種類:學術論文
論文出版年:2019
畢業學年度:107
語文別:中文
論文頁數:109
中文關鍵詞:核醣核酸編輯次世代定序微型核醣核酸乳癌
外文關鍵詞:RNA editingNGSmiRNABRCA
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在生物體中存在著一種後轉錄修飾作用的分子生物學現象,也就是RNA編輯(RNA editing)。此作用可讓DNA核苷酸序列在不發生突變的情況之下,造成下游產物mRNA或甚至由mRNA所轉譯出的蛋白質之功能不再與原先一致,進而提供一個更多元的序列變異性。其產生的效果隨著基因區段的不同而有不一樣的結果:若在蛋白質編碼序列(coding DNA sequence, CDS)改變密碼子(codon),則可能會置換原胺基酸的組成;在3’UTR則會影響microRNA利用seed region來辨識mRNA的位置;又或者是作用在內含子(intron)的剪切序列,就有可能會讓修飾後的RNA帶有部份intron,使整個序列特性出現改變;而在其它非蛋白質編碼序列上,像是long non-coding RNA就可能會改變其二級結構與跟miRNA交互作用的方式等;至於Alu重複序列則因為易形成雙股RNA之結構,因此在其分佈的區域較容易為ADAR辨識而被編輯。
隨著次世代定序技術的發展,讓人們得以透過電腦的計算功能,繞過傳統實驗室的限制,利用各式的序列處理工具,幫助研究者從中找出可供討論的資訊。此次的研究是要藉由TCGA(The Cancer Genome Atlas)當中的浸潤性乳癌患者(breast invasive carcinoma, BRCA)的DNA與RNA序列比對,並用DNA與RNA的定序片段(read)在變異位點的涵蓋程度作為後續分析的篩選條件。此外,我們也從基因註解資訊及其它已知資料庫的比對,觀察到經由不同條件所篩選出的結果並不一樣,像如果是RNA或DNA涵蓋性比較低的位點就會傾向發生在非轉譯區,反之,在CDS的涵蓋性則會較高。除此之外,為了確認A-to-I的編輯是否有發生於miRNA targeting binding site,我們使用了miRNA之相關預測資料分析,最後也有找到可能會影響其作用於目標區域的位點。而針對重複性序列的部份,亦有拿來比對編輯位點在Alu repetitive element的出現情況。最後,在找出RNA的A-to-I編輯與癌症之關聯性方面,亦有對應到部份已知的癌症相關基因與miRNA,可供後續驗證生物意義上的探討方向。
One of the post-transcriptional modification is RNA edting. It can cause sequence form alternative nucleotide composition without mutation in DNA. RNA editing may affect the original function of gene. For example, A-to-I RNA editing is the most common event of RNA editing especially in mammalian. When base substitution occurs on mature transcripts, it might change codons of protein coding regions (CDS) or miRNA bind sites on 3’ untranslated regions (3’UTR). The aim of the study is to discover potential A-to-I RNA editing sites which may play a role in cancer progression. We downloaded RNA sequencing and DNA sequencing (whole exome sequencing and whole genome sequencing) data of breast invasive carcinoma (BRCA) from The Cancer Genome Atlas (TCGA). To identify potential A-to-I editing sites, variant calling was first performed with Genome Analysis Toolkit (GATK) to obtain variant sites in RNA which were further compared with the same sites in DNA sequencing results for confirmation of wild type DNA sequence. We then categorized RNA-seq variant sites into two main groups with different RNA and DNA read coverages. After that, we annotated each site with the variant effect predictor (VEP) and summarized it based on different regions to look into editing site distribution and probable affected functions. We identified some novel events on cancer-related miRNA and gene interaction , which are worthful for further experimental validation in the future.
目錄
致 謝 ii
中文摘要 iv
ABSTRACT v
第一章 緒論 1
1.1核醣核酸編輯介紹 1
1.1.1 分子生物學之中心法則 1
1.1.2 RNA編輯的分類與研究起源 1
1.1.3 第二類RNA編輯 (含氮鹼基的轉換或取代) 2
1.1.4 ADARs家族簡介 2
1.1.5 A-to-I的機制、作用效果與分佈範圍 3
1.1.6 A-to-I與生理調控 4
1.1.7 A-to-I與疾病 5
1.1.8 A-to-I研究方向 5
1.1.9 使用TCGA研究RNA editing之文獻 7
1.2研究動機 8
第二章 材料與方法 13
2.1 資料來源 13
2.1.1癌症基因體圖譜 (TCGA) 資料庫 13
2.1.2樣本選取類別 13
2.2 分析流程的建立 14
2.2.1 RNA-seq variant calling資料處理流程說明 17
2.2.2 WGS資料處理流程說明 20
2.3 分析工具簡介 21
2.3.1 Picard 與GATK 21
2.3.2 BWA 21
2.3.3 參考基因體序列 21
2.3.4 VEP 22
2.3.5 miRcode 22
2.3.6 miRTarBase 22
2.3.7 RepeatMasker 23
2.3.8 GENCODE 23
2.3.9 dbNSFP 23
2.3.10 COSMIC 24
2.3.11 OncoKB 24
2.3.12 miRCancer 24
2.1.13 Cytoscape 24
第三章 研究結果 25
3.1 位點篩選總覽 25
3.1.1 RNA和WGS對照 25
3.1.2 RNA與WXS的read數之限制 26
3.1.3 調整後的初步結果 27
3.2 對不同序列類別的特性分析 33
3.2.1 Alu重複序列 33
3.2.2 CDS區域 36
3.2.3 3’UTR區域 39
3.2.4 lncRNA序列 55
3.2.5 ADARs與editing level 56
3.2.6 基因富集分析 59
3.3 與過去相關研究比較 61
第四章 問題討論 62
第五章 結論與未來展望 65
第六章 參考文獻 66
附錄一、經dbNSFP預測、位在CDS且有RNA A-to-I editing或癌症相關報導的基因簡介 87

圖目錄
圖一、ADARS的家族成員與相關功能的結構分佈 8
圖二、ADENOSINE經DEAMINATION轉換成INOSINE 8
圖三、G-C BASE PAIR和I-C BASE PAIR 9
圖四、ADAR作用在DSRNA上的A-TO-I EDITING過程 9
圖五、A-TO-I作用在不同RNA功能區段之效果 10
圖六、ALU ELEMENT形成DSRNA結構示意圖 10
圖七、A-TO-I位點在人類基因組各區段類之佔比 11
圖八、分析流程與結果分類 16
圖九、RNA-SEQ VARIANT CALLING流程示意圖 19
圖十、WGS資料處理流程示意圖 20
圖十一、基因區段示意圖 25
圖十二、RNA EDITING在各類編輯位點之佔比 27
圖十三、不同樣本支持數之編輯位點數量分佈 28
圖十四、以不同的RNA READ數量來篩選RNA EDITING SITE之前後的基因區段分佈 29
圖十五、在IGV下所觀察RNA-SEQ、WXS與WGS之READ分佈示意圖 29
圖十六、用不同READ數篩選各基因區段下的A-TO-G位點數量分佈 30
圖十七、以不同READ數篩選在INTRON與INTERGENIC REGION的A-TO-G位點之數量分佈與CUT-OFF POINT位置 31
圖十八、以不同WXS READ數篩選A-TO-G位點後與WGS比較之相同比例分佈以及CUT-OFF POINT位置 31
圖十九、各類位點經篩選後的分佈 32
圖二十、A-TO-G與非A-TO-G位點總和在ALU中的數量分佈 34
圖二十一、以RNA READ < 10 與RNA READ >= 10區分A-TO-G在ALU、非ALU重複序列與非重複序列中的佔比,以及ALU中在各基因區段上的分佈比例 35
圖二十二、各編輯位點類別在ALU與L1中的數量分佈 35
圖二十三、RNA EDITING在CDS的流程分析 37
圖二十四、正常、腫瘤組織或共同位點的SAMPLE支持度分佈 40
圖二十五、基因EDITING FREQUENCY之排序與MIRNA TARGET對應在各基因之EDITING SITE上的次數分佈 42
圖二十六、GSEA的原理示意圖與ES的計算公式 44
圖二十七、以GSEA對只出現在正常或腫瘤組織的被編輯基因作圖 45
圖二十八、以GSEA對共同位點且在正常組織樣本較多或腫瘤組織樣本較多的被編輯基因作圖 46
圖二十九、編輯基因與未編輯基因在有MIRNA TARGET下的表現量分佈 47
圖三十、MIRNA與基因網路分佈圖 50
圖三十一、自MIRTARBASE所得的序列與MIRNA和MRNA配對情形 54
圖三十二、正常與腫瘤組織在LNCRNAS之不同序列類別的RNA A-TO-G EDITING SITE數量 分佈 55
圖三十三、(A) ADARS表現量分佈 (B) ADAR1表現量比值與EDITING SITE比值散佈圖 57
圖三十四、(A) EDITING LEVEL示意圖 (B) 正常與腫瘤組織EDITING LEVEL分佈圖 (C) 共同位點之EDITING LEVEL差異分佈圖 57
圖三十五、EDITING LEVEL以不同條件篩選後的分佈示意圖 58
圖三十六、富集分析示意圖 60
圖三十七、使用LOGISTIC REGRESSION之資料面與函式使用範例示意 62
圖三十八、以LOGISTIC REGRESSION建立模型後之作圖結果 64

表目錄
表一、RNA EDITING研究相關文獻整理 6
表二、ADARS之相關生理功能 12
表三、與ADARS相關的疾病 12
表四、使用之樣本類別與數量 14
表五、RNA EDITING在DOMAIN上或基因屬演化上的ORTHOLOG 37
表六、RNA EDITING不在DOMAIN上亦非屬演化上的ORTHOLOG 38
表七、與RNA EDITING或癌症相關的基因 38
表八、RNA EDITING在3’UTR上與MIRNA TARGETING之列聯表與檢定結果 39
表九、在MIRTARBASE中有直接對應至報導或預測範圍內的位點總覽 51
表十、GENCODE對LNCRNAS類別之定義 56
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