發(fā)布時(shí)間：2018-03-29 06:33

  本文選題：核小體　切入點(diǎn)：基因轉(zhuǎn)錄　出處：《中國農(nóng)業(yè)大學(xué)》2016年博士論文

【摘要】：核小體是構(gòu)成真核生物染色質(zhì)的基本結(jié)構(gòu)單元,其在基因組上的位置變化可以調(diào)節(jié)DNA對(duì)于轉(zhuǎn)錄元件的可接近性。因此,核小體定位在基因表達(dá)調(diào)控中起著重要的作用,但確切的功能仍然不清楚。此外,也有很多的證據(jù)表明核小體定位可以影響DNA甲基化,可是目前對(duì)于核小體是如何影響DNA甲基化的也還沒有定論。玉米是世界上最重要的作物之一,同時(shí)也是植物基因組學(xué)研究中廣泛使用的模式作物。本研究以玉米幼苗和胚乳為材料,通過對(duì)微球菌核酸酶酶切染色質(zhì)所產(chǎn)生的單核小體片段進(jìn)行高通量測序,獲得了全基因組范圍內(nèi)的核小體定位數(shù)據(jù)。幼苗中相鄰核小體間的距離約比胚乳長3個(gè)核苷酸。比較幼苗和胚乳中的核小體定位差異,顯示基因表達(dá)激活的過程伴隨著啟動(dòng)子區(qū)核小體的缺失,以及轉(zhuǎn)錄起始位點(diǎn)下游第一個(gè)核小體(+1核小體)和轉(zhuǎn)錄終止位點(diǎn)上游第一個(gè)核小體(-1核小體)的移動(dòng)。另外,我們發(fā)現(xiàn)內(nèi)在序列決定的核小體定位與基因的組織表達(dá)特異性相關(guān)。與組織特異表達(dá)基因相比,組成型表達(dá)基因的5’和3’端具有更顯著的核小體缺失區(qū)域,另外+1和-1核小體距轉(zhuǎn)錄起始位點(diǎn)和轉(zhuǎn)錄終止位點(diǎn)的距離也更遠(yuǎn)。這些特征也有助于基因高表達(dá),但組成型表達(dá)基因的翻譯效率卻顯著低于組織特異表達(dá)基因,說明最終的翻譯水平不能反映核小體對(duì)基因表達(dá)水平的影響�？偟膩碚f,這些結(jié)果說明內(nèi)在序列決定的核小體定位的主要功能不是調(diào)解基因表達(dá)水平,而可能是決定基因的組織表達(dá)特異性。結(jié)合全基因組范圍的DNA甲基化數(shù)據(jù),我們也探究了核小體定位與DNA甲基化之間的關(guān)系。總體而言,核小體核心DNA和側(cè)翼DNA上的甲基化水平正相關(guān)。CHG和CHH背景的甲基化一般偏好發(fā)生于核小體側(cè)翼區(qū)。另外,與水稻和擬南芥中CG背景的甲基化偏好發(fā)生于核小體側(cè)翼區(qū)不同,玉米中CG背景下核小體中心區(qū)域的甲基化水平高于核小體側(cè)翼序列。有意思的是,CG序列背景下,部分核小體中心位點(diǎn)兩側(cè)的甲基化水平存在顯著區(qū)別,并且這類核小體顯著富集于非轉(zhuǎn)座子區(qū)。這表明單核小體范圍內(nèi)的DNA甲基化狀態(tài)的不同具有非常重要的作用。此外,我們還發(fā)現(xiàn)玉米幼苗與胚乳之間DNA甲基化差異區(qū)兩側(cè)存在明顯的核小體缺失,并且核小體的缺失程度與兩個(gè)組織間DNA甲基化水平的差異程度正相關(guān)。這意味著核小體定位可能參與影響了DNA去甲基化過程。本研究還分析了不同發(fā)育時(shí)期的玉米胚、胚乳以及完整籽粒樣品的轉(zhuǎn)錄組數(shù)據(jù),發(fā)現(xiàn)至少有26,105個(gè)基因參與了玉米籽粒發(fā)育過程,其中包括1,614個(gè)轉(zhuǎn)錄因子。結(jié)合已發(fā)表的玉米轉(zhuǎn)錄組數(shù)據(jù),我們還鑒定到1,258個(gè)籽粒特異表達(dá)基因,包括418個(gè)在籽粒不同亞區(qū)特異表達(dá)的基因。這為深入闡釋玉米籽粒發(fā)育過程中的基因調(diào)控機(jī)制提供了重要基礎(chǔ)。
[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.
【學(xué)位授予單位】：中國農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：S513
，

本文編號(hào)：1679970