本文關(guān)鍵詞：順式天然反義轉(zhuǎn)錄本（cis-NATs）組學(xué)篩查及功能詮釋初探　出處：《南昌大學(xué)》2012年碩士論文　論文類型：學(xué)位論文

  更多相關(guān)文章： 順式天然反義轉(zhuǎn)錄本 正義反義轉(zhuǎn)錄本對 次代測序 Ensembl基因詮釋

【摘要】：目的：順式天然反義轉(zhuǎn)錄本（cis-NAT）是指自然狀態(tài)下源于基因相同區(qū)域的反義RNA,可與正義轉(zhuǎn)錄本形成正義反義轉(zhuǎn)錄本對（SA pair）。這種轉(zhuǎn)錄方式在真核生物的轉(zhuǎn)錄及轉(zhuǎn)錄后調(diào)控過程中發(fā)揮重要作用，，可影響多種生理或病理過程（如腫瘤）。近來測序數(shù)據(jù)的累積和高通量芯片技術(shù)的出現(xiàn)使利用組學(xué)方法系統(tǒng)研究cis-NATs成為可能。然而，目前這類研究僅限于少數(shù)模式生物的編碼基因，而基于非編碼序列的次代轉(zhuǎn)錄組測序數(shù)據(jù)分析方案尚缺乏。 方法：本研究首先設(shè)計(jì)了基于Ensembl基因詮釋信息的非編碼cis-NATs的篩查流程，在靈長目和嚙齒目18個(gè)物種中進(jìn)行搜索�？紤]到次代測序能夠提供更為豐富的組織轉(zhuǎn)錄信息，本研究同時(shí)研發(fā)了一套基于次代測序的新cis-NATs發(fā)現(xiàn)流程（Gene2DGE），并使用該流程在human143B細(xì)胞的ssRNA-seq（strand-specific RNA-seq）數(shù)據(jù)集中進(jìn)行搜索。最后基于候選的cis-NATs進(jìn)行驗(yàn)證和功能學(xué)實(shí)驗(yàn)。 結(jié)果：以人類為例，本研究在基因組中發(fā)現(xiàn)18,510個(gè)SA基因?qū)�，并鑒定出11,493個(gè)為非編碼cis-NATs，占所有cis-NATs的62.1%，提示非編碼基因是cis-NATs的重要來源。而在其他物種中，所發(fā)現(xiàn)的非編碼相關(guān)的數(shù)據(jù)均明顯低于人類。同時(shí)我們的篩查還發(fā)現(xiàn)一定數(shù)目的非編碼Cis-NATs具備物種間的保守性，提示非人物種中的非編cis-NATs尚待深入研究。鑒定出73個(gè)新的與cis-NATs相關(guān)的轉(zhuǎn)錄活性區(qū)域；其中43個(gè)位于線粒體染色體上，而基于大鼠的組織mRNA-seq以及相應(yīng)的細(xì)胞學(xué)實(shí)驗(yàn)提示：新的線粒體cis-NATs具有保守性，可能在線粒體中發(fā)揮重要功能。 結(jié)論：1.基于Ensembl基因詮釋系統(tǒng)和本實(shí)驗(yàn)室研發(fā)程序篩查出高覆蓋度的cis-NATs，并篩查同源性和保守型高SA基因。2.新的高通量核酸測序技術(shù)在已有詮釋信息的基礎(chǔ)上提供了新的cis-NATs，RNA-seq的結(jié)果極大提高對于非編碼cis-NATs的發(fā)現(xiàn)。3.驗(yàn)證實(shí)驗(yàn)和功能實(shí)驗(yàn)提示線粒體中的新cis-NATs確實(shí)存在并可能具有重要的生物功能。
[Abstract]:Objective: cis-natural antisense transcripts (cis-NATs) are antisense RNA derived from the same region of gene in natural state. Sense antisense transcripts can be formed with sense transcripts on SA pairs.This transcription mode plays an important role in the transcriptional and post-transcriptional regulation of eukaryotes. The recent accumulation of sequencing data and the advent of high-throughput microarray techniques have made it possible to systematically study cis-NATs using a genomics approach. At present, this kind of research is limited to the coding genes of a few model organisms, but the non-coding sequence based secondary generation transposed sequence analysis scheme is still lacking. Methods: in this study, we first designed the screening process of non-coding cis-NATs based on Ensembl gene interpretation information. Search in 18 species of primates and rodents. Considering that secondary generation sequencing can provide richer tissue transcription information. In this study, we also developed a new cis-NATs discovery process based on the next generation sequencing, Gene2DGE). And use this process in human143B cell ssRNA-seq(strand-specific RNA-seq). Finally, based on candidate cis-NATs for verification and functional experiments. Results: in this study, 18,510 pairs of SA genes were found in human genome, and 11,493 pairs were identified as non-coding cis-NATs. It accounts for 62.1% of all cis-NATs, suggesting that non-coding genes are an important source of cis-NATs, while in other species. The uncoded data found were significantly lower than those in humans. At the same time, we also found that a certain number of non-coding Cis-NATs have inter-species conservation. It is suggested that the non-coding cis-NATs in non-human species needs further study and 73 new transcriptional active regions related to cis-NATs have been identified. 43 of them were located on mitochondria chromosomes, and the tissue mRNA-seq based on rat and corresponding cytological experiments indicated that the new mitochondrial cis-NATs was conserved. It may play an important role in mitochondria. Conclusion 1. Cis-NATs with high coverage was screened based on Ensembl gene interpretation system and our laboratory development program. And screening homologous and conserved high SA gene. 2. The new high-throughput nucleic acid sequencing technology provides a new cis-NATs based on the existing interpretation information. The results of RNA-seq greatly improve the discovery of non-coding cis-NATs. 3. Validation and functional experiments suggest that new cis-NATs in mitochondria exists and may be important. Biological function.
【學(xué)位授予單位】：南昌大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2012
【分類號】：R346

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