蓖麻胚乳表觀調(diào)控與基因組印跡研究
發(fā)布時間：2018-07-17 20:03
【摘要】：植物胚乳發(fā)育的研究一直是植物生殖發(fā)育,表觀遺傳學(xué)和作物遺傳育種關(guān)注的熱點領(lǐng)域和重要科學(xué)前沿。DNA甲基化是一種非常重要的表觀修飾因子,參與異染色質(zhì)的形成,轉(zhuǎn)座子的沉默,基因表達的調(diào)控以及基因組印跡的發(fā)生。越來越多的證據(jù)顯示DNA甲基化和基因組印跡對胚乳發(fā)育和種子大小形成具有重要的調(diào)控作用。目前已經(jīng)在模式植物如擬南芥、水稻和玉米的種子中調(diào)查了DNA甲基化的水平和分布,揭示出胚乳基因組的低甲基化狀態(tài)。但是,關(guān)于胚乳基因組的低甲基化狀態(tài)是如何建立和維持的,是否具有廣泛性以及它在胚乳發(fā)育過程中的作用,目前還不是很清楚。特別是對于大多數(shù)真雙子葉植物包括擬南芥,胚乳組織是瞬時的,隨著種子的發(fā)育逐漸消失,因此在真雙子葉植物種子中研究胚乳DNA甲基化的調(diào)控方式以及DNA甲基化對胚乳發(fā)育和基因組印跡的調(diào)控受到了很大的限制。蓖麻種子是典型的雙子葉胚乳型種子,胚乳在整個種子發(fā)育過程中持續(xù)存在,具有大的體積且易于分離,是種子生物學(xué)研究的模式材料。蓖麻為深入研究表觀調(diào)控因子對胚乳發(fā)育的影響提供了理想的研究系統(tǒng)。本研究以蓖麻品系ZB107的種子為研究材料,結(jié)合全基因組DNA甲基化測序、small RNA測序、mRNA測序以及實驗驗證,全面分析了DNA甲基化的分布規(guī)律、調(diào)控方式和對基因表達的影響。主要結(jié)果如下：1.蓖麻胚乳基因組的低甲基化通過全基因組DNA甲基化測序,我們發(fā)現(xiàn)蓖麻胚乳基因組中CG和CHG甲基化水平分別為30.3%和18.3%,明顯低于胚基因組中CG(40.7%)和CHG(24%)的甲基化水平,與擬南芥、玉米和水稻中的報道一致。但是蓖麻胚乳CHH甲基化水平(11.2%)相對于胚(12.7%)并沒有發(fā)生顯著下降。在檢測的所有甲基化位點中,CHH甲基化類型占了大約68%。在蓖麻種子中絕大部分CG和CHG的甲基化水平維持在90%以上,而CHH的甲基化水平平均分布在30%-100%。而且胚乳基因組廣泛的去甲基化作用導(dǎo)致了胚乳和胚間差異甲基化的形成。2.DNA甲基化的分布規(guī)律以及對基因表達的影響通過調(diào)查DNA甲基化在基因區(qū)域和轉(zhuǎn)座子區(qū)域的分布,我們發(fā)現(xiàn)CG甲基化在整個基因組都有分布,而CHG和CHH甲基化在基因區(qū)很少分布,絕大部分分布在轉(zhuǎn)座子區(qū)域。在基因區(qū)和轉(zhuǎn)座子區(qū),胚乳的DNA甲基化水平均明顯低于胚。通過分析DNA甲基化與基因表達的關(guān)系,我們發(fā)現(xiàn)不同表達程度基因的DNA甲基化水平并沒有發(fā)生明顯的改變,而不表達的基因(RPKM≤1)的DNA甲基化水平最高,表明DNA甲基化的主要作用是抑制基因的表達。而對于胚乳特異表達的基因,DNA甲基化水平,特別是CG和CHG甲基化,在胚乳中發(fā)生了明顯的下降,表明CG和CHG的低甲基化對胚乳特異表達基因的調(diào)控作用。3.24-siRNAs對DNA甲基化的調(diào)控為了進一步解析蓖麻種子中高比例的CHH甲基化,我們調(diào)查了蓖麻胚乳和胚中small RNA以及與DNA甲基化的關(guān)系。small RNA測序結(jié)果顯示,蓖麻種子中包含豐富的24-nt small RNA,且這些24-nt siRNAs與基因組CHG和CHH甲基化的分布和水平顯著相關(guān)。在胚基因組中,基因區(qū)和TE區(qū)24-nt siRNAs的豐度明顯高于胚乳,且在胚和胚乳中,24-nt siRNAs很少在基因上分布,與CHG和CHH甲基化在基因區(qū)的分布一致。另外,我們發(fā)現(xiàn)24-nt siRNAs顯著地富集在CHH的高甲基化區(qū)域；而在CHH低甲基化區(qū)域24-nt siRNAs的豐度發(fā)生了明顯的下降,這些結(jié)果表明蓖麻種子中24-nt siRNAs參與了基因組CHH甲基化的維持。4.蓖麻種子DNA甲基化調(diào)控方式為了揭示蓖麻種子中DNA甲基化分布的潛在機制,我們調(diào)查了DNA甲基化相關(guān)基因在不同組織中的表達。結(jié)果表明,相對于胚組織,DNA甲基轉(zhuǎn)移酶基因RcMET1和RcCMT在胚乳中的表達明顯下降,而且DNA去甲基化酶基因RcDME在胚乳中也表達,共同導(dǎo)致了胚乳CG和CHG甲基化水平的下降;而DNA甲基化酶基因RcDRM3在胚乳中的表達并沒有受到抑制。同時,在蓖麻胚和胚乳中豐富的24-siRNAs以及RdDM途徑的激活維持了蓖麻種子基因組高比例的CHH甲基化�；蚪M印跡是一種典型的表觀遺傳學(xué)現(xiàn)象,主要發(fā)生在開花植物的胚乳中,與胚乳和種子的發(fā)育密切相關(guān)。在本研究中,我們以蓖麻品系ZB107和ZB306為親本進行互交,對獲得的雜交胚乳組織進行了深度mRNA測序和等位基因分‘離分析,調(diào)查和特征化了蓖麻胚乳中的印跡基因。主要結(jié)果如下：1.在蓖麻胚乳中鑒別到大量印跡基因通過全基因組重測序,我們在親本ZB107和ZB306品系間鑒別了1007066個SNPs和100615個indels。結(jié)合這些SNPs和嚴格的篩選,我們在蓖麻胚乳中鑒別到184個母源印跡基因(maternally imprinted genes,MEGs)和9個父源印跡基因(paternally imprinted genes,PEGs)。在挑選的67個印跡基因中,57個得到了實驗驗證,有5個基因表現(xiàn)出品系依賴性印跡。在胚乳的不同發(fā)育階段,我們發(fā)現(xiàn)這些基因表現(xiàn)出動態(tài)的印跡過程。另外,我們也鑒別到14個印跡的long non-coding RNAs,并得到了實驗驗證。在這些驗證的印跡基因中,僅39%的基因在胚乳中特異表達,大部分基因在蓖麻各個組織中均有表達。2.印跡基因的特征化通過印跡基因的聚類分析,發(fā)現(xiàn)僅有少量印跡位點在基因組中發(fā)生了明顯的聚類。GO功能富集分析顯示出這些印跡基因顯著地參與了胚乳的發(fā)育過程。另外,我們發(fā)現(xiàn)TE顯著地富集在這些印跡基因的周圍(上下游4 kb范圍內(nèi)),特別是LTR/Gypsy TE類型。通過比較擬南芥、水稻、玉米和蓖麻中的印跡基因,發(fā)現(xiàn)印跡基因在物種間的保守性比較低,說明印跡基因在物種間發(fā)生了獨立分化,有較快的進化速率。3.DNA甲基化對印跡基因表達的調(diào)控通過對雜交胚和胚乳基因組DNA甲基化測序,我們發(fā)現(xiàn)胚乳的低甲基化區(qū)域顯著地富集在印跡基因周圍(上下游2 kb范圍內(nèi)),且這些低甲基化區(qū)域主要發(fā)生在LTR/Gypsy TE上,表明了TE的去甲基化過程對印跡基因表達的影響。另外,我們檢測到6個MEGs的母源等位基因甲基化水平明顯低于其父源等位基因,表明等位基因甲基化水平的差異對印跡基因的表達調(diào)控作用。
[Abstract]:The research of plant endosperm development has always been plant reproductive development. Epigenetics and crop genetics and breeding focus on the hot areas and important scientific frontiers.DNA methylation is a very important apparent modifier. It participates in the formation of heterochromatin, transposon silence, gene expression regulation and the occurrence of genomic imprinting. Many evidence shows that DNA methylation and genomic imprinting have important regulatory effects on the development of endosperm and the formation of seed size. The level and distribution of DNA methylation in the seeds of model plants, such as Arabidopsis, rice and corn, have been investigated, and the low methylation status of the endosperm genome is revealed. However, the low endosperm genome is low. How the methylation state is established and maintained, whether it is extensive and its role in the development of the endosperm, is not yet clear. Especially for most of the true dicotyledonous plants, including Arabidopsis, endosperm tissue is instantaneous, with the gradual loss of seed development, so the endosperm DN is studied in the seeds of true dicotyledonous plants. The regulation of A methylation and the regulation of DNA methylation on the development of endosperm and genomic imprinting are greatly restricted. The castor seed is a typical dicotyledonous endosperm seed. The endosperm persists in the whole process of seed development. It has large volume and is easy to separate. It is a model material for seed biological research. The effects of apparent regulatory factors on the endosperm development provided an ideal research system. This study used the seeds of ZB107 of Ricinus ricinus as the research material, combined with the whole genome DNA methylation sequencing, small RNA sequencing, mRNA sequencing and experimental verification, to comprehensively analyze the distribution of DNA methylation, the mode of regulation and the effect on the gene expression. The main results are as follows: 1. the methylation of the genomes of the castor plant endosperm through full genome DNA methylation sequencing, we found that the level of CG and CHG methylation in the endosperm genome of castor bean was 30.3% and 18.3%, respectively, significantly lower than the level of methylation of CG (40.7%) and CHG (24%) in the embryo genome, but it was consistent with the reports in Arabidopsis, corn and rice. The level of CHH methylation (11.2%) of the castor endosperm (12.7%) did not decrease significantly. In all the methylation sites, the CHH methylation type accounted for about 68%. over 90% of the methylation level of CG and CHG in Castor seeds, while the methylation level of CHH was distributed evenly in 30%-100%. and in the endosperm genome. Extensive demethylation leads to the distribution of.2.DNA methylation of differentially methylation in the endosperm and embryo, and the effect on gene expression by investigating the distribution of DNA methylation in the region of the gene and the transposon region. We found that CG methylation is distributed throughout the genome, while CHG and CHH methylation is rarely divided in the gene region. Most of the DNA methylation levels of the endosperm in the gene and transposon areas were significantly lower than those of the embryo. By analyzing the relationship between DNA methylation and gene expression, we found that the level of DNA methylation of different expression levels did not occur obviously, but the DNA methylation of the non expressed gene (RPKM < 1) The main function of DNA methylation is to inhibit the expression of gene, and for the gene of endosperm specific expression, the level of DNA methylation, especially CG and CHG methylation, is obviously decreased in the endosperm, indicating the regulation of CG and CHG low methylation on the specific expression of endosperm, the regulation of.3.24-siRNAs on DNA methylation In order to further analyze the high proportion of CHH methylation in Castor seeds, we investigated the relationship between the endosperm and small RNA in the embryo and the relationship with DNA methylation by.Small RNA sequencing results showed that the rich 24-nt small RNA contained in the Castor seeds, and these 24-nt siRNAs were significantly related to the distribution and level of genomic CHG and methylation. In the genome, the abundance of 24-nt siRNAs in the gene region and the TE region is significantly higher than that in the endosperm, and in the embryo and endosperm, the 24-nt siRNAs is rarely distributed in the gene, which is consistent with the distribution of CHG and CHH methylation in the gene region. In addition, we found that 24-nt siRNAs is significantly enriched in the high methylation region of CHH, while the CHH methylation region is abundant in the abundance of 24-nt. The results showed that the degree of 24-nt siRNAs in castor seed was involved in the DNA methylation of.4. Castor Seeds by genomic CHH methylation in order to reveal the potential mechanism of DNA methylation distribution in Castor seeds. We investigated the expression of DNA methylation related genes in different tissues. The results showed that the expression of DNA methylation related genes in different tissues was relative. The expression of DNA methyltransferase gene RcMET1 and RcCMT decreased in the endosperm, and the DNA demethylation gene RcDME was also expressed in the endosperm, which resulted in the decrease in the level of CG and CHG methylation in the endosperm, while the expression of the DNA methylation gene RcDRM3 in the endosperm was not suppressed. The activation of the rich 24-siRNAs and RdDM pathway maintains the high proportion of CHH methylation in the castor seed genome. Genomic imprinting is a typical epigenetic phenomenon, mainly occurring in the endosperm of flowering plants, closely related to the development of the endosperm and seeds. In this study, we use the castor strain ZB107 and ZB306 as parents. Cross intercross, deep mRNA sequencing and allele segregation analysis were carried out to investigate and characterize the imprinting genes in the endosperm of castor bean. The main results were as follows: 1. in the castor endosperm, a large number of imprinted genes were identified by whole genome re sequencing, and 1007066 of our parents were identified between the parent ZB107 and ZB306 lines. Combining these SNPs and 100615 indels. with these SNPs and strict screening, we identified 184 parent imprinting genes (maternally imprinted genes, MEGs) and 9 parent source imprinted genes (paternally imprinted genes, PEGs) in the castor endosperm. 57 of the 67 imprinted genes selected were tested with 5 gene expression lines. In the different stages of endosperm, we found that these genes showed a dynamic imprinting process. In addition, we also identified 14 imprinted long non-coding RNAs, which were verified by experiments. In these imprinted genes, only 39% of the genes were specifically expressed in the endosperm, and most of the genes were in the various tissues of castor. The.2. imprinting gene was characterized by the clustering analysis of the imprinted gene. It was found that only a small number of imprinted loci had a distinct clustering.GO enrichment analysis in the genome, which showed that these imprinted genes were significantly involved in the development of the endosperm. In addition, we found that TE was significantly enriched around these imprinted genes. (4 kb in the upper and lower reaches), especially the LTR/Gypsy TE type. By comparing the imprinted genes in Arabidopsis, rice, corn and castor, it is found that the conservatism of imprinted genes is relatively low among species, indicating that the imprinted gene has been independently differentiated in the species, and the rapid evolution rate of.3.DNA methylation regulates the expression of imprinted genes through the regulation DNA methylation sequencing of the hybrid embryo and endosperm genome, we found that the hypomethylation region of the endosperm is significantly enriched around the imprinted gene (2 kb in the upper and lower reaches), and these low methylation regions mainly occur on LTR/Gypsy TE, indicating the effect of TE demethylation on the expression of imprinted genes. In addition, we detected 6 MEGs The methylation level of maternal allele was significantly lower than that of its parent allele, indicating that the difference of allele methylation level played an important role in regulating the expression of imprinted genes.
【學(xué)位授予單位】：云南大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：Q943.2
本文編號：2130785
[Abstract]:The research of plant endosperm development has always been plant reproductive development. Epigenetics and crop genetics and breeding focus on the hot areas and important scientific frontiers.DNA methylation is a very important apparent modifier. It participates in the formation of heterochromatin, transposon silence, gene expression regulation and the occurrence of genomic imprinting. Many evidence shows that DNA methylation and genomic imprinting have important regulatory effects on the development of endosperm and the formation of seed size. The level and distribution of DNA methylation in the seeds of model plants, such as Arabidopsis, rice and corn, have been investigated, and the low methylation status of the endosperm genome is revealed. However, the low endosperm genome is low. How the methylation state is established and maintained, whether it is extensive and its role in the development of the endosperm, is not yet clear. Especially for most of the true dicotyledonous plants, including Arabidopsis, endosperm tissue is instantaneous, with the gradual loss of seed development, so the endosperm DN is studied in the seeds of true dicotyledonous plants. The regulation of A methylation and the regulation of DNA methylation on the development of endosperm and genomic imprinting are greatly restricted. The castor seed is a typical dicotyledonous endosperm seed. The endosperm persists in the whole process of seed development. It has large volume and is easy to separate. It is a model material for seed biological research. The effects of apparent regulatory factors on the endosperm development provided an ideal research system. This study used the seeds of ZB107 of Ricinus ricinus as the research material, combined with the whole genome DNA methylation sequencing, small RNA sequencing, mRNA sequencing and experimental verification, to comprehensively analyze the distribution of DNA methylation, the mode of regulation and the effect on the gene expression. The main results are as follows: 1. the methylation of the genomes of the castor plant endosperm through full genome DNA methylation sequencing, we found that the level of CG and CHG methylation in the endosperm genome of castor bean was 30.3% and 18.3%, respectively, significantly lower than the level of methylation of CG (40.7%) and CHG (24%) in the embryo genome, but it was consistent with the reports in Arabidopsis, corn and rice. The level of CHH methylation (11.2%) of the castor endosperm (12.7%) did not decrease significantly. In all the methylation sites, the CHH methylation type accounted for about 68%. over 90% of the methylation level of CG and CHG in Castor seeds, while the methylation level of CHH was distributed evenly in 30%-100%. and in the endosperm genome. Extensive demethylation leads to the distribution of.2.DNA methylation of differentially methylation in the endosperm and embryo, and the effect on gene expression by investigating the distribution of DNA methylation in the region of the gene and the transposon region. We found that CG methylation is distributed throughout the genome, while CHG and CHH methylation is rarely divided in the gene region. Most of the DNA methylation levels of the endosperm in the gene and transposon areas were significantly lower than those of the embryo. By analyzing the relationship between DNA methylation and gene expression, we found that the level of DNA methylation of different expression levels did not occur obviously, but the DNA methylation of the non expressed gene (RPKM < 1) The main function of DNA methylation is to inhibit the expression of gene, and for the gene of endosperm specific expression, the level of DNA methylation, especially CG and CHG methylation, is obviously decreased in the endosperm, indicating the regulation of CG and CHG low methylation on the specific expression of endosperm, the regulation of.3.24-siRNAs on DNA methylation In order to further analyze the high proportion of CHH methylation in Castor seeds, we investigated the relationship between the endosperm and small RNA in the embryo and the relationship with DNA methylation by.Small RNA sequencing results showed that the rich 24-nt small RNA contained in the Castor seeds, and these 24-nt siRNAs were significantly related to the distribution and level of genomic CHG and methylation. In the genome, the abundance of 24-nt siRNAs in the gene region and the TE region is significantly higher than that in the endosperm, and in the embryo and endosperm, the 24-nt siRNAs is rarely distributed in the gene, which is consistent with the distribution of CHG and CHH methylation in the gene region. In addition, we found that 24-nt siRNAs is significantly enriched in the high methylation region of CHH, while the CHH methylation region is abundant in the abundance of 24-nt. The results showed that the degree of 24-nt siRNAs in castor seed was involved in the DNA methylation of.4. Castor Seeds by genomic CHH methylation in order to reveal the potential mechanism of DNA methylation distribution in Castor seeds. We investigated the expression of DNA methylation related genes in different tissues. The results showed that the expression of DNA methylation related genes in different tissues was relative. The expression of DNA methyltransferase gene RcMET1 and RcCMT decreased in the endosperm, and the DNA demethylation gene RcDME was also expressed in the endosperm, which resulted in the decrease in the level of CG and CHG methylation in the endosperm, while the expression of the DNA methylation gene RcDRM3 in the endosperm was not suppressed. The activation of the rich 24-siRNAs and RdDM pathway maintains the high proportion of CHH methylation in the castor seed genome. Genomic imprinting is a typical epigenetic phenomenon, mainly occurring in the endosperm of flowering plants, closely related to the development of the endosperm and seeds. In this study, we use the castor strain ZB107 and ZB306 as parents. Cross intercross, deep mRNA sequencing and allele segregation analysis were carried out to investigate and characterize the imprinting genes in the endosperm of castor bean. The main results were as follows: 1. in the castor endosperm, a large number of imprinted genes were identified by whole genome re sequencing, and 1007066 of our parents were identified between the parent ZB107 and ZB306 lines. Combining these SNPs and 100615 indels. with these SNPs and strict screening, we identified 184 parent imprinting genes (maternally imprinted genes, MEGs) and 9 parent source imprinted genes (paternally imprinted genes, PEGs) in the castor endosperm. 57 of the 67 imprinted genes selected were tested with 5 gene expression lines. In the different stages of endosperm, we found that these genes showed a dynamic imprinting process. In addition, we also identified 14 imprinted long non-coding RNAs, which were verified by experiments. In these imprinted genes, only 39% of the genes were specifically expressed in the endosperm, and most of the genes were in the various tissues of castor. The.2. imprinting gene was characterized by the clustering analysis of the imprinted gene. It was found that only a small number of imprinted loci had a distinct clustering.GO enrichment analysis in the genome, which showed that these imprinted genes were significantly involved in the development of the endosperm. In addition, we found that TE was significantly enriched around these imprinted genes. (4 kb in the upper and lower reaches), especially the LTR/Gypsy TE type. By comparing the imprinted genes in Arabidopsis, rice, corn and castor, it is found that the conservatism of imprinted genes is relatively low among species, indicating that the imprinted gene has been independently differentiated in the species, and the rapid evolution rate of.3.DNA methylation regulates the expression of imprinted genes through the regulation DNA methylation sequencing of the hybrid embryo and endosperm genome, we found that the hypomethylation region of the endosperm is significantly enriched around the imprinted gene (2 kb in the upper and lower reaches), and these low methylation regions mainly occur on LTR/Gypsy TE, indicating the effect of TE demethylation on the expression of imprinted genes. In addition, we detected 6 MEGs The methylation level of maternal allele was significantly lower than that of its parent allele, indicating that the difference of allele methylation level played an important role in regulating the expression of imprinted genes.
【學(xué)位授予單位】：云南大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：Q943.2
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