斑馬魚胚胎在缺氧環境之轉錄體分析

10.29428/9789860544169.201801.0194

林佑融；吳亭慧；洪國勝；白敦文

長鏈非編碼蛋白 ； 轉錄體 ； 基因本體論 ； 生物訊息路徑 ； 缺氧 ； long non-coding RNA ； transcripts ； gene ontology ； biological pathway ； hypoxia

NCS 2017 全國計算機會議

2017（2018 / 01 / 01）

1036 - 1040

繁體中文

長鏈非編碼蛋白(lncRNA)大量存在於各種生物體，陸續被證明具有複雜與精確的調控機制影響不同基因表達，但目前探討lncRNA調控基因表現及直接影響生物功能的生物實驗驗證仍不容易。為有效協助生物學家辨識lncRNA的調控機制，本研究使用轉錄體RNA-seq定序以及基因差異表現比較機制進行分析。實驗採用弱化hif2α表現的斑馬魚胚胎作為測試樣本，並利用不同的斑馬魚lncRNA註釋資料庫(zflncRNApedia和ZFLNC)進行序列比對與表現量分析。本研究鎖定具有表現量差異之基因群及lncRNA 集合為主要標的，並假設與具表現量差異lncRNA 重疊或鄰近的基因可能為其結合目標基因(lncGenes)進行完整訊息路徑分析。透過RNA-seq、zflncRNApedia以及ZFLNC之比對後分別可以辨識118個及171個基因對本實驗可能具有影響的lncGenes。將這些lncGenes加入超幾何分布分析後發現在基因本體論GO及KEGG生物訊息路徑有額外發現重要的功能資訊，這些增加的生物功能註釋可推測lncRNA 在其相關的基因上下游進行調控，進而影響這些重要生物功能。

Long non-coding RNAs (lncRNAs) are found abundantly in different organisms and possess many kinds of biological functions through gene regulation mechanisms. LncRNAs perform accurately and complicatedly regulation mechanism that control gene expression. However, it is not easy to identify the relationship of lncRNAs, genes expression and biological functions. To discover important lncRNAs candidates and specific associated functions, we used transcriptomes by RNA-seq and hypergeometric distribution statistical analysis. In this study, hif2α knockdown zebrafish embryo was applied as our testing samples and using different zebrafish lncRNAs databases (zflncRNApedia and ZFLNC) for sequence alignment and expression analysis. In hypergeometric distribution analysis, differential expression genes and genes (lncGenes) associated with differentially expressed lncRNAs were used for functional analysis. As a result, a total of 118 and 171 lncGenes were found by zflncRNApedia and ZFLNC respectively. When using these lncGenes in hypergeometric distribution analysis, the Gene Ontology(GO) and KEGG pathway annotations were additionally discovered compared to using differential expression genes only. This increased biological functions revealed that lncRNAs regulate associated genes and play important roles.