玉米核小体定位与基因转录及DNA甲基化的关系

发布时间：2018-03-29 06:33

  本文选题：核小体　切入点：基因转录　出处：《中国农业大学》2016年博士论文

【摘要】：核小体是构成真核生物染色质的基本结构单元,其在基因组上的位置变化可以调节DNA对于转录元件的可接近性。因此,核小体定位在基因表达调控中起着重要的作用,但确切的功能仍然不清楚。此外,也有很多的证据表明核小体定位可以影响DNA甲基化,可是目前对于核小体是如何影响DNA甲基化的也还没有定论。玉米是世界上最重要的作物之一,同时也是植物基因组学研究中广泛使用的模式作物。本研究以玉米幼苗和胚乳为材料,通过对微球菌核酸酶酶切染色质所产生的单核小体片段进行高通量测序,获得了全基因组范围内的核小体定位数据。幼苗中相邻核小体间的距离约比胚乳长3个核苷酸。比较幼苗和胚乳中的核小体定位差异,显示基因表达激活的过程伴随着启动子区核小体的缺失,以及转录起始位点下游第一个核小体(+1核小体)和转录终止位点上游第一个核小体(-1核小体)的移动。另外,我们发现内在序列决定的核小体定位与基因的组织表达特异性相关。与组织特异表达基因相比,组成型表达基因的5’和3’端具有更显著的核小体缺失区域,另外+1和-1核小体距转录起始位点和转录终止位点的距离也更远。这些特征也有助于基因高表达,但组成型表达基因的翻译效率却显著低于组织特异表达基因,说明最终的翻译水平不能反映核小体对基因表达水平的影响。总的来说,这些结果说明内在序列决定的核小体定位的主要功能不是调解基因表达水平,而可能是决定基因的组织表达特异性。结合全基因组范围的DNA甲基化数据,我们也探究了核小体定位与DNA甲基化之间的关系。总体而言,核小体核心DNA和侧翼DNA上的甲基化水平正相关。CHG和CHH背景的甲基化一般偏好发生于核小体侧翼区。另外,与水稻和拟南芥中CG背景的甲基化偏好发生于核小体侧翼区不同,玉米中CG背景下核小体中心区域的甲基化水平高于核小体侧翼序列。有意思的是,CG序列背景下,部分核小体中心位点两侧的甲基化水平存在显著区别,并且这类核小体显著富集于非转座子区。这表明单核小体范围内的DNA甲基化状态的不同具有非常重要的作用。此外,我们还发现玉米幼苗与胚乳之间DNA甲基化差异区两侧存在明显的核小体缺失,并且核小体的缺失程度与两个组织间DNA甲基化水平的差异程度正相关。这意味着核小体定位可能参与影响了DNA去甲基化过程。本研究还分析了不同发育时期的玉米胚、胚乳以及完整籽粒样品的转录组数据,发现至少有26,105个基因参与了玉米籽粒发育过程,其中包括1,614个转录因子。结合已发表的玉米转录组数据,我们还鉴定到1,258个籽粒特异表达基因,包括418个在籽粒不同亚区特异表达的基因。这为深入阐释玉米籽粒发育过程中的基因调控机制提供了重要基础。
[Abstract]:Nucleosome is the basic structural unit of eukaryote chromatin, whose position change in genome can regulate the accessibility of DNA to transcription elements. Therefore, nucleosome localization plays an important role in gene expression regulation. But the exact function is still unclear. In addition, there is a lot of evidence that nucleosome localization can affect DNA methylation. But how nucleosomes affect DNA methylation is still unclear. Corn is one of the most important crops in the world. In this study, maize seedlings and endosperm were used as materials, and high throughput sequencing of mononuclear fragments from chromatin digested by microsphere ribozyme was carried out. The nucleosome localization data in the whole genome were obtained. The distance between adjacent nucleosomes in seedlings was about 3 nucleotides longer than that in endosperm. The difference of nucleosome localization between seedling and endosperm was compared. The activation of gene expression is accompanied by the deletion of the promoter nucleosome and the movement of the first nucleosome downstream of the transcription initiation site (1 nucleosome) and the first nucleosome 1 nucleosome 1 upstream of the transcriptional termination site. We found that the nucleosome localization determined by the intrinsic sequence was related to the tissue expression specificity of the gene, and that the 5 'and 3' nucleosome deletion regions of the constitutive expression gene were more significant than those of the tissue specific expression gene. In addition, nucleosomes 1 and 1 were further away from the initiation and termination sites of transcription. These characteristics also contributed to the high expression of genes, but the translation efficiency of constitutive expression genes was significantly lower than that of tissue-specific expression genes. These results suggest that the final translation level does not reflect the effect of nucleosomes on gene expression. In general, these results suggest that the primary function of nucleosome localization determined by internal sequences is not to mediate gene expression levels. We also looked at the relationship between nucleosome localization and DNA methylation in general, combined with genome-wide DNA methylation data. The methylation level of nucleosome core DNA and flanking DNA is positively correlated with that of CHH background. The methylation preference of nucleosome background occurs in the nucleosome flanking region. In addition, the methylation preference of CG background in rice and Arabidopsis is different from that in the nucleosome flanking region. In maize, the methylation level of nucleosome central region in CG background is higher than that of nucleosome flanking sequence. Moreover, these nucleosomes are significantly enriched in the non-transposon region. This indicates that different DNA methylation states in the monosome range play a very important role. We also found significant nucleosome deletion on both sides of the DNA methylation difference region between maize seedlings and endosperm. The degree of deletion of nucleosome was positively correlated with the difference of DNA methylation level between the two tissues, which suggested that nucleosome localization might be involved in the process of DNA demethylation. Transcriptome data from endosperm and intact grain samples showed that at least 26105 genes were involved in maize grain development, including 1614 transcription factors. We also identified 1258 kernel-specific genes, including 418 genes specifically expressed in different kernel subregions, which provided an important basis for further elucidation of gene regulation mechanisms in maize grain development.
【学位授予单位】：中国农业大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：S513
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本文编号：1679970