本文選題：毛竹 + ChIP-seq　； 參考：《福建農(nóng)林大學(xué)》2017年碩士論文

【摘要】：毛竹是我國(guó)森林資源中產(chǎn)量高、面積大、用處多的竹種,在竹業(yè)加工中占有非常重要的位置。因?yàn)槠渚邆錁O高的經(jīng)濟(jì)價(jià)值、生態(tài)價(jià)值并且與人們的生活緊密相連,所以對(duì)其研究有著非常重要的實(shí)際應(yīng)用價(jià)值。前人對(duì)毛竹的研究主要在形態(tài)學(xué)和生態(tài)學(xué)以及營(yíng)養(yǎng)學(xué)上,而對(duì)其生長(zhǎng)發(fā)育的內(nèi)在分子機(jī)制研究還很少。毛竹冬筍大約是在立秋前后由竹鞭側(cè)芽形成,鞭筍是竹鞭的最先端組織,這兩個(gè)組織在竹竿快速生長(zhǎng)和竹鞭快速延伸過程中具有重要的生物學(xué)意義,因此我們首次構(gòu)建了關(guān)于毛竹筍尖和鞭筍尖組織的染色質(zhì)免疫共沉淀測(cè)序文庫(kù)(ChIP-seq),分析兩種最為常見也是最為重要的組蛋白修飾:H3K4me3和H3K27me3。我們對(duì)整個(gè)文庫(kù)構(gòu)建的步驟進(jìn)行了優(yōu)化,確立了適合毛竹的ChIP實(shí)驗(yàn)方法。通過生物信息學(xué)分析,揭示了毛竹筍尖和鞭筍尖的組蛋白H3K4me3和H3K27me3修飾的全基因組分布特征及差異。對(duì)測(cè)序結(jié)果經(jīng)過Peak-calling之后一共得到了 5379個(gè)測(cè)序峰,將這些峰對(duì)比到毛竹注釋基因數(shù)據(jù)庫(kù)后,經(jīng)過去除相同基因不同修飾位點(diǎn)的情況,最后得到了 3293個(gè)獨(dú)立的被組蛋白修飾基因。這其中鞭筍尖特有的H3K4me3修飾位點(diǎn)基因有219個(gè),H3K27me3修飾位點(diǎn)基因有827個(gè)。竹筍尖特有的H3K4me3修飾位點(diǎn)基因有1105個(gè),H3K27me3修飾位點(diǎn)基因569個(gè)。同時(shí)有2種修飾的基因一共有539個(gè)基因,有3種修飾的基因一共有32個(gè),4種修飾的基因有2個(gè)。這說明組蛋白修飾位點(diǎn)在毛竹筍尖和鞭筍尖的基因組內(nèi)分布具有組織特異性、廣泛性和多樣性。從結(jié)合峰在基因上下游分布來看毛竹鞭筍尖和筍尖H3K4me3的峰值信號(hào)主要分布在轉(zhuǎn)錄起始位點(diǎn)的附近和轉(zhuǎn)錄終止位點(diǎn)的附近,而在基因內(nèi)部很少有修飾。在轉(zhuǎn)錄起始位點(diǎn)附近毛竹鞭筍尖的修飾信號(hào)要強(qiáng)于筍尖的信號(hào),但是在轉(zhuǎn)錄終止位點(diǎn)附近鞭筍尖的信號(hào)要弱于筍尖的信號(hào)。H3K27me3的修飾信號(hào)峰也是出現(xiàn)在轉(zhuǎn)錄起始位點(diǎn)和轉(zhuǎn)錄終止位點(diǎn)附近,而且鞭筍尖的信號(hào)一直強(qiáng)于筍尖的信號(hào)。我們通過用Cytoscape軟件對(duì)毛竹筍尖和鞭筍尖H3K27me3修飾基因進(jìn)行GO分析,構(gòu)建了基因功能富集圖譜。通過對(duì)其功能注釋的研究發(fā)現(xiàn)被H3K27me3修飾的基因大部分在細(xì)胞核中,而且主要參與調(diào)控了 DNA調(diào)控區(qū)域結(jié)合蛋白的轉(zhuǎn)錄,轉(zhuǎn)錄因子的轉(zhuǎn)錄過程及其活性,DNA和RNA介導(dǎo)的轉(zhuǎn)錄調(diào)控過程等。暗示組蛋白修飾可以通過調(diào)控上述基因進(jìn)而實(shí)現(xiàn)對(duì)其他基因的表達(dá)調(diào)控,我們這些前期工作可以為后續(xù)深入研究毛竹的表觀遺傳學(xué)調(diào)控奠定堅(jiān)實(shí)的基礎(chǔ)。
[Abstract]:Phyllostachys pubescens, which has high yield, large area and more use in forest resources in China, occupies a very important position in the processing of bamboo industry. Because of its high economic value, ecological value and closely connected with people's life, it has a very important practical application value for its research. The previous studies on Mao bamboo were mainly in the form. There are few studies on the intrinsic molecular mechanism of its growth and development in science and ecology and nutrition. The bamboo shoots are formed by the lateral buds of the bamboo whip before and after the autumn, and the flagellum is the first end of the bamboo whip. These two tissues have important biological significance in the rapid growth of bamboo and the rapid extension of the bamboo whip. The chromatin immunoprecipitation sequence library (ChIP-seq) was constructed to analyze the two most common and most important histone modification of bamboo shoot tip and whip shoot tip tissue: H3K4me3 and H3K27me3., we optimized the construction steps of the whole library, and established the ChIP experiment method suitable for bamboo. The whole genome distribution characteristics and differences of the histone H3K4me3 and H3K27me3 modified by the bamboo shoot tip and the whip shoot tip were shown. After Peak-calling, 5379 sequence peaks were obtained. After comparing these peaks to the annotation gene database of bamboo, the results were 3293. There are 219 H3K4me3 modified loci and 827 H3K27me3 modifier loci. There are 1105 H3K4me3 modification loci genes specific to bamboo shoot tips, 569 gene modification loci, and 2 modified genes with 539 genes and 3 modified genes. A total of 32 and 4 modified genes have 2 genes. This shows that the histone modification loci have tissue specificity, universality and diversity in the genome of bamboo shoot tips and whip shoot tips. The peak signals of the bamboo shoot tip and the shoot tip H3K4me3 are mainly distributed around and around the transcriptional starting site from the distribution of the peak in the upstream and downstream. In the vicinity of the termination site, there are few modifications within the gene. The modification signal of the bamboo shoot tip near the transcriptional starting site is stronger than the signal of the shoot tip, but the signal of the whip tip near the transcriptional termination site is weaker than the signal.H3K27me3 of the shoot tip and also appears at the transcriptional starting point and the transcriptional termination site. In the vicinity, the signal of the whip shoot tip has been stronger than the signal of the shoot tip. By using the Cytoscape software to analyze the H3K27me3 modified gene of bamboo shoot tip and the whip shoot tip, we construct the gene function enrichment map. Through the study of its functional annotation, we found that most of the H3K27me3 modified genes are in the nucleus and are mainly involved in the regulation and control of the nucleus. DNA regulates the transcription of regional binding proteins, the transcriptional processes and activities of transcription factors, and the transcriptional regulation process mediated by DNA and RNA, suggesting that histone modification can regulate the expression of other genes by regulating the genes mentioned above, and our earlier work can provide a further study on epigenetic regulation of Mao bamboo. A solid foundation.

【學(xué)位授予單位】：福建農(nóng)林大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：S795.7

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