Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/92371
標題: 人類與黑猩猩微核醣核酸轉錄起始位點的比較研究
Comparative studies of microRNA transcription start sites between human and chimpanzee
作者: Cheng-Kuo Lai
賴政國
關鍵字: microRNA
transcription start site
miRNA transcription
sequence alignment
微核醣核酸
轉錄起始位
微核醣核酸轉錄
序列比對
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摘要: Identifying the transcription start sites (TSSs) of microRNA (miRNA) genes is essential for understanding the regulation of miRNA transcription which is extremely important for determining the specific roles that miRNAs play in regulatory pathways. Because humans and chimpanzees share most of genes, comparative studies of the two species are the ways often used to comprehend humans more. In the past, most studies are focused on the divergence of proteins, genes and miRNAs. However, the divergence of the regulation of miRNA transcription between humans and chimpanzees seems still not to be addressed yet. In this study, 86 global-run-on-sequencing (GRO-Seq) validated TSSs of 125 human miRNAs were collected to search their homologous regions in the chimpanzee genome. An un-annotated homologous miRNA region was considered to be a putative chimpanzee miRNA if the sequence of the region can be folded into a hairpin structure. In addition, a homologous TSS location was then confirmed as a putative chimpanzee miRNA TSS if it was able to be identified by a semi-supervised statistical model trained on Pol II ChIP-sequencing data of chimpanzee and several sequence-associated features. From the result, most of the human TSS-miRNA pairs are still kept in chimpanzees. We identified 33 un-annotated chimpanzee miRNAs and 48 putative chimpanzee miRNA TSSs of 69 chimpanzee miRNAs. Interestingly, a number of human TSS-miRNA pairs were missing; we found that 18 miRNAs were lost in chimpanzee during evolution and another missing miRNA, mir-659, might be human specific. We studied the regulatory pathway of mir-659 and found that mir-659 could be involved in neurodevelopmental. These divergence of the regulation of miRNA transcription might be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages.
分析微核醣核酸 (microRNA; miRNA) 的轉錄起始位點 (transcription start sites; TSSs) 對於我們了解微核醣核酸基因的轉錄以及微核醣核酸以何種方式調控生理路徑有很大的幫助。由於人類與黑猩猩基因相似程度很高,所以這兩物種的比較一直是研究者用來更了解人類的方式。過去兩者的比較多是著墨在微核醣核酸、基因以及蛋白質上,然而目前還沒有研究探討過微核醣核酸本身的轉錄調控在演化上的變異,於是我們使用基因比對的方式去比較人類與黑猩猩在微核醣核酸轉錄上的差異,實驗從global-run-on sequencing (GRO-Seq) 收集了實驗驗證過的86筆調控著125筆微核醣核酸的微核醣核酸轉錄起始位點資料,將之與黑猩猩的基因體序列進行比對;若在黑猩猩基因體內找到的人類微核醣核酸同源序列區域且此區域還沒被註解過而且序列能夠被摺疊成髮夾二級結構,我們就會將之推定為黑猩猩的微核醣核酸基因。此外我們還收集了黑猩猩核醣核酸聚合酶Ⅱ的染色質免疫沉澱測序資料以及一些序列特性的資料以半監督式自動化學習的方式去驗證比對上黑猩猩基因體的人類微核醣核酸轉錄起始位點同源序列。我們發現人類與黑猩猩大部分的微核醣核酸與微核醣核酸轉錄起始點區域相同,並在黑猩猩基因體內找到33個還未被註解的微核醣核酸基因,此外我們也預測了48筆調控著69個微核醣核酸的黑猩猩微核醣核酸轉錄起始位點的序列。有趣的是兩物種在有一些微核醣核酸與微核醣核酸轉錄起始點區域發生改變;我們找到18個僅有在黑猩猩基因體遺失的微核醣核酸,另外還有注意到一個可能人類特有的微核醣核酸mir-659,此微核醣核酸參與了神經系統的發育路徑。這些微核醣核酸轉錄調控的差異有可能是在演化中人類與黑猩猩發生種化 (speciation) 的分子變化的紀錄。
URI: http://hdl.handle.net/11455/92371
其他識別: U0005-3008201523494800
文章公開時間: 2018-08-31
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