本文關(guān)鍵詞：擬南芥中內(nèi)含子來源環(huán)形RNA的識別與分析　出處：《昆明理工大學(xué)》2017年碩士論文　論文類型：學(xué)位論文

  更多相關(guān)文章： 擬南芥 內(nèi)含子 分支點(diǎn) 識別 環(huán)形RNA

【摘要】：環(huán)形RNA(circRNA)是一種結(jié)構(gòu)與常見線性RNA不同的環(huán)狀的非編碼RNA轉(zhuǎn)錄物。在生命的各個領(lǐng)域環(huán)形RNAs廣泛存在,包括真核生物、細(xì)菌、古生菌和病毒。最近的研究表明環(huán)形RNAs的形成機(jī)制和功能具有多樣性,例如有外顯子環(huán)化、內(nèi)含子環(huán)化、細(xì)菌基因組環(huán)化等。多種形成機(jī)制造成了多樣性的環(huán)形RNAs,具有了多種多樣的功能,它能夠作為miRNA海綿、RBP海綿、翻譯蛋白等。環(huán)形RNA以多種形式存在與自然界中,例如真核生物中外顯子后向剪接的產(chǎn)物、病毒或類病毒的基因組、古生菌中tRNA和rRNA內(nèi)含子的剪切產(chǎn)物環(huán)形RNAs沒有可供核苷酸外切酶識別的3'端,所以能夠抵制核苷酸外切酶的降解。穩(wěn)定、保守,成熟環(huán)形RNA在細(xì)胞質(zhì)中大量存在。能夠作為miRNAs海綿,典型的例子是miR-7海綿。結(jié)合RBP合成RNA-protein合成物,或者調(diào)解基因轉(zhuǎn)錄。由于環(huán)形RNA對RNA酶具有拮抗能力,有較強(qiáng)的穩(wěn)定性,在分化成熟的細(xì)胞中可以緩慢積累,故其可以作為生物分子標(biāo)記作用于臨床、科研。此外有研究表明,環(huán)形RNA有可能與microRNA(miRNA)分子、外源性病毒能結(jié)合,抑制這些分子的功能。環(huán)形RNA可能具有巨大的生物學(xué)意義,目前對環(huán)形RNA的研究還很欠缺,特別是內(nèi)含子來源的環(huán)形RNA方面。本課題以擬南芥為研究對象,依照環(huán)形RNA這類RNA的特點(diǎn),對內(nèi)含子分支點(diǎn)、內(nèi)含子來源的環(huán)形RNA進(jìn)行識別及分析。本課題首先進(jìn)行實(shí)驗(yàn):核苷酸外切酶(RnaseR酶)處理的實(shí)驗(yàn)組及不做任何處理的對照組,共2組4次重復(fù)8個樣本,然后將試驗(yàn)樣本進(jìn)行高通量測序。根據(jù)分支點(diǎn)特點(diǎn)在內(nèi)含子中識別分支點(diǎn),并通過分析分支點(diǎn)的保守性、位點(diǎn)等探索其特征。計(jì)算8個樣本的基因表達(dá)水平,通過對基因表達(dá)水平進(jìn)行聚類、離散方式,分析2組樣本間的差異。此外通過標(biāo)準(zhǔn)化表達(dá)公式對內(nèi)含子的表達(dá)進(jìn)行計(jì)算。依據(jù)內(nèi)含子表達(dá)水平篩選內(nèi)含子來源的環(huán)形RNA,選擇具有代表性的顯著上調(diào)的環(huán)形RNA。比較基因與內(nèi)含子在2組的差異,側(cè)重對內(nèi)含子進(jìn)行分析。通過長度等特征來對環(huán)形RNA進(jìn)行分析。本課題對環(huán)形RNA特征及實(shí)驗(yàn)數(shù)據(jù)進(jìn)行細(xì)致而認(rèn)真的分析,做出如下成果:1)識別出4080個分支點(diǎn);2)發(fā)現(xiàn)分支點(diǎn)核苷酸具有高度保守性,在3'剪切位點(diǎn)上游19-37nt區(qū)域等特征;3)由擬南芥(對照組與實(shí)驗(yàn)組)經(jīng)過RNA酶處理的高通量序列數(shù)據(jù),識別出9227個內(nèi)含子來源環(huán)形RNA;4)通過差異性分析找到172個實(shí)驗(yàn)組相對對照組顯著上調(diào)的環(huán)形RNA;5)環(huán)形RNA長度一般在400bp,比正常內(nèi)含子長度要更長;綜上,本課題分別識別出擬南芥中套索分支點(diǎn)及內(nèi)含子來源環(huán)形RNA,并進(jìn)一步分析其特征。希望能夠?yàn)橹髷M南芥或環(huán)形RNA的研究提供幫助。
[Abstract]:Annular RNAs (rRNAs) are circular non-coding RNA transcripts with different structures from common linear RNA. Circular RNAs exists widely in various fields of life, including eukaryotes. Recent studies have shown that the formation mechanisms and functions of circular RNAs are diverse, such as exon cyclization and intron cyclization. Bacterial genome cyclization and so on. A variety of formation mechanisms led to a variety of ring RNas, with a variety of functions, it can be used as miRNA sponge RBP sponge. Circular RNA exists in many forms with exon backward splicing products in nature, such as eukaryotes, viruses or virus-like genomes. The cleavage product of tRNA and rRNA intron in Archaea has no 3 'end that can be recognized by nucleotide exonuclease, so it can resist the degradation of nucleotide exonuclease and is stable and conservative. Mature ring RNA is abundant in cytoplasm. It can be used as a miRNAs sponge. The typical example is miR-7 sponge. It combines with RBP to synthesize RNA-protein compound. Or mediate gene transcription. Because ring RNA has antagonistic ability to RNA enzyme and has strong stability, it can accumulate slowly in differentiated mature cells, so it can act as biomolecular marker in clinic. In addition, some studies have shown that ring RNA may bind to microRNAs (miRNAs) molecules, foreign viruses can bind. Inhibition of the function of these molecules. Ring RNA may have great biological significance, the current research on circular RNA is still very scarce. Especially the ring RNA of intron origin. In this paper, we take Arabidopsis thaliana as the research object, according to the characteristics of RNA such as ring RNA, branch point of intron. The ring RNA from intron was identified and analyzed. Firstly, the experiment was carried out: the experimental group treated with nucleotide exonuclease (RnaseR) and the control group without any treatment. Eight samples were repeated in 2 groups and 4 times, and then high-throughput sequencing was carried out. According to the characteristics of branch points, branch points were identified in introns, and the conservation of branch points was analyzed. The gene expression level of 8 samples was calculated, and the gene expression level was clustered and discretized. The differences between the two groups were analyzed. In addition, the expression of intron was calculated by standardized expression formula. Ring RNA from intron source was screened according to the expression level of intron. Select the representative significantly up-regulated ring RNA. compare the difference between the gene and intron in the two groups. Focus on the intron analysis. Through length and other characteristics to analyze the annular RNA. This topic on the ring RNA characteristics and experimental data for careful and careful analysis. Make the following result: 1) identify 4080 branch points; 2) it was found that the branched nucleotides were highly conserved, with 19-37 NT region upstream of the 3 'cleavage site. 3) 9227 intron origin annular RNAs were identified from high-throughput sequence data of Arabidopsis thaliana (control group and experimental group) treated with RNA enzyme. 4) based on the difference analysis, 172 experimental groups were found to be significantly up-regulated ring RNAs compared with the control group. 5) the length of annular RNA is generally at 400bp, which is longer than that of normal intron. In summary, we identify the noose branch points and intron origin ring RNAs in Arabidopsis thaliana, and further analyze the characteristics of ring RNAs in Arabidopsis thaliana, and hope to provide some help for the research of Arabidopsis or annular RNA.
【學(xué)位授予單位】：昆明理工大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2017
【分類號】：Q943.2
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本文編號：1390141