本文選題：豬 + 共調(diào)控��； 參考：《石河子大學(xué)》2017年碩士論文

【摘要】：生物機(jī)體是一個(gè)精美的體系,參與生命活動(dòng)的物質(zhì)環(huán)環(huán)相扣,形成一個(gè)復(fù)雜的網(wǎng)絡(luò)系統(tǒng)。利用網(wǎng)絡(luò)生物學(xué)的技術(shù),提煉高通量基因表達(dá)數(shù)據(jù),已經(jīng)成為研究基因互作及功能機(jī)制的重要方向。本研究旨在利用豬的基因組和轉(zhuǎn)錄組數(shù)據(jù),分析豬的基因表達(dá)特征,解析基因的網(wǎng)絡(luò)調(diào)控模式,為探究豬特有的基因資源信息,提供新思路和新途徑。獲得以下主要結(jié)果:(1)利用豬的RNA-seq數(shù)據(jù)集,鑒定了3,136個(gè)持家基因和1,316個(gè)組織特異性基因;對(duì)比顯示,持家基因結(jié)構(gòu)比組織特異性基因緊湊,受到較強(qiáng)凈化選擇壓力;持家基因啟動(dòng)子區(qū)域比組織特異性基因保守,其表達(dá)調(diào)控的復(fù)雜性低于組織特異性基因,表明持家基因的進(jìn)化緩慢穩(wěn)定,持家基因主要與細(xì)胞的基礎(chǔ)代謝功能相關(guān),組織特異性基因主要與組織分化、發(fā)育、環(huán)境適應(yīng)相關(guān)的特性一致。(2)對(duì)比豬與人的持家基因,發(fā)現(xiàn)二者交集較低,豬持家基因結(jié)構(gòu)顯著長(zhǎng)于人持家基因;然而,功能富集和蛋白活性位點(diǎn)分析,顯示盡管二者持家蛋白之間的同源性低且空間結(jié)構(gòu)有異,但卻具有相似的蛋白質(zhì)活性位點(diǎn)、側(cè)鏈、催化中心或DNA結(jié)合域,表現(xiàn)趨同進(jìn)化。(3)基于權(quán)重基因共表達(dá)網(wǎng)絡(luò)分析技術(shù),利用豬多個(gè)組織的RNA-seq數(shù)據(jù)集,構(gòu)建了24個(gè)基因共表達(dá)模塊;對(duì)模塊進(jìn)行富集分析,發(fā)現(xiàn)模塊具有功能特異性,并且模塊內(nèi)許多基因的啟動(dòng)子含有相似的順式作用元件,顯示模塊內(nèi)的基因呈顯著協(xié)同關(guān)系;此外,模塊具有組織特異性,如與SIX1、PRKAG3等基因相關(guān)的局部網(wǎng)絡(luò)涉及肌肉發(fā)育。(4)利用豬肌肉組織的RNA-seq數(shù)據(jù)集,構(gòu)建了13個(gè)網(wǎng)絡(luò)模塊;功能富集和組織定位分析,顯示大部分模塊都與肌肉組織的分化、發(fā)育和代謝功能相關(guān);調(diào)控模體富集分析,顯示模塊內(nèi)基因的啟動(dòng)子,顯著富集一個(gè)或幾個(gè)的順式作用元件,對(duì)應(yīng)于POU3F3、FOXC2、Sox18等17個(gè)轉(zhuǎn)錄因子結(jié)合位點(diǎn),揭示了轉(zhuǎn)錄因子與其靶基因集的調(diào)控關(guān)系。優(yōu)異基因資源的挖掘是提高豬生產(chǎn)力的有效途徑之一。在轉(zhuǎn)錄組水平上,本研究探索了豬的基因表達(dá)特征,鑒定了持家基因與組織特異基因集,并揭示了持家基因的趨同進(jìn)化模式;所建立的基因共表達(dá)網(wǎng)絡(luò),揭示了許多與功能相關(guān)的候選基因,可為探究中國(guó)地方豬品種特有的基因資源信息、豐富分子育種理論奠定基礎(chǔ)。
[Abstract]:Biological organism is a delicate system. The matter involved in life activities is linked to each other, forming a complex network system. Using network biology technology to extract high throughput gene expression data has become an important research direction in gene interaction and functional mechanism. The purpose of this study was to analyze the gene expression characteristics of pigs by using the genomic and transcriptional data of pigs, and to analyze the network regulation model of genes, so as to provide new ideas and approaches for exploring the information of porcine specific gene resources. The main results were as follows: 1) 3136 housekeeping genes and 136 tissue-specific genes were identified by using RNA-seq data sets of pigs, and the results showed that the housekeeping genes were more compact than tissue specific genes and were under strong pressure of purification and selection. The promoter region of housekeeping gene is more conserved than that of tissue specific gene, and the complexity of its expression regulation is lower than that of tissue specific gene, which indicates that the evolution of housekeeping gene is slow and stable, and the housekeeping gene is mainly related to the basic metabolic function of cell. Tissue specific genes are mainly related to tissue differentiation, development and environmental adaptation. (2) comparing pig and human housekeeping genes, we found that the structure of pig housekeeping genes is significantly longer than that of human housekeeping genes. Functional enrichment and protein activity site analysis showed that although the homology and spatial structure of the two homekeeping proteins were low, they had similar protein active sites, side chains, catalytic centers or DNA binding domains. Based on the technique of weight gene coexpression network analysis, 24 gene coexpression modules were constructed by using RNA-seq data sets of multiple tissues of pigs, and the functional specificity of the modules was found by enrichment analysis. And the promoter of many genes in the module contains similar cis-acting elements, which shows that the genes in the module are significantly synergistic; in addition, the module is tissue specific. For example, the local network related to SIX 1, PRKAG3 and other genes involved in muscle development. (4) using the RNA-seq data set of pig muscle tissue, 13 network modules were constructed, and the function enrichment and tissue localization analysis showed that most of the modules were differentiated with muscle tissue. Regulation motif enrichment analysis showed that the promoter of the gene in the module significantly enriched one or more cis-acting elements corresponding to 17 transcription factor binding sites, such as POU3F3F3FOXC2OX18, etc. The regulatory relationship between transcription factors and their target gene sets was revealed. The mining of excellent genetic resources is one of the effective ways to improve pig productivity. At the transcriptional level, this study explored the gene expression characteristics of pigs, identified housekeeping genes and tissue-specific gene sets, and revealed the convergent evolutionary patterns of housekeeping genes. Many candidate genes related to function are revealed, which can be used to explore the specific genetic resources of Chinese local pig breeds and enrich molecular breeding theory.
【學(xué)位授予單位】：石河子大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：S828;Q78

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