基于ChIP-seq全基因组识别毛竹笋尖与鞭笋尖组蛋白修饰位点

发布时间：2018-05-05 14:10

本文选题：毛竹 + ChIP-seq　；参考：《福建农林大学》2017年硕士论文

【摘要】：毛竹是我国森林资源中产量高、面积大、用处多的竹种,在竹业加工中占有非常重要的位置。因为其具备极高的经济价值、生态价值并且与人们的生活紧密相连,所以对其研究有着非常重要的实际应用价值。前人对毛竹的研究主要在形态学和生态学以及营养学上,而对其生长发育的内在分子机制研究还很少。毛竹冬笋大约是在立秋前后由竹鞭侧芽形成,鞭笋是竹鞭的最先端组织,这两个组织在竹竿快速生长和竹鞭快速延伸过程中具有重要的生物学意义,因此我们首次构建了关于毛竹笋尖和鞭笋尖组织的染色质免疫共沉淀测序文库(ChIP-seq),分析两种最为常见也是最为重要的组蛋白修饰:H3K4me3和H3K27me3。我们对整个文库构建的步骤进行了优化,确立了适合毛竹的ChIP实验方法。通过生物信息学分析,揭示了毛竹笋尖和鞭笋尖的组蛋白H3K4me3和H3K27me3修饰的全基因组分布特征及差异。对测序结果经过Peak-calling之后一共得到了 5379个测序峰,将这些峰对比到毛竹注释基因数据库后,经过去除相同基因不同修饰位点的情况,最后得到了 3293个独立的被组蛋白修饰基因。这其中鞭笋尖特有的H3K4me3修饰位点基因有219个,H3K27me3修饰位点基因有827个。竹笋尖特有的H3K4me3修饰位点基因有1105个,H3K27me3修饰位点基因569个。同时有2种修饰的基因一共有539个基因,有3种修饰的基因一共有32个,4种修饰的基因有2个。这说明组蛋白修饰位点在毛竹笋尖和鞭笋尖的基因组内分布具有组织特异性、广泛性和多样性。从结合峰在基因上下游分布来看毛竹鞭笋尖和笋尖H3K4me3的峰值信号主要分布在转录起始位点的附近和转录终止位点的附近,而在基因内部很少有修饰。在转录起始位点附近毛竹鞭笋尖的修饰信号要强于笋尖的信号,但是在转录终止位点附近鞭笋尖的信号要弱于笋尖的信号。H3K27me3的修饰信号峰也是出现在转录起始位点和转录终止位点附近,而且鞭笋尖的信号一直强于笋尖的信号。我们通过用Cytoscape软件对毛竹笋尖和鞭笋尖H3K27me3修饰基因进行GO分析,构建了基因功能富集图谱。通过对其功能注释的研究发现被H3K27me3修饰的基因大部分在细胞核中,而且主要参与调控了 DNA调控区域结合蛋白的转录,转录因子的转录过程及其活性,DNA和RNA介导的转录调控过程等。暗示组蛋白修饰可以通过调控上述基因进而实现对其他基因的表达调控,我们这些前期工作可以为后续深入研究毛竹的表观遗传学调控奠定坚实的基础。
[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.

【学位授予单位】：福建农林大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S795.7

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