普通野生稻miRNA的鉴定与分析
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摘要
MicroRNA(miRNA)是一类调节基因转录后表达中起重要作用的非编码RNA。普通野生稻(Oryza rufipogon Griff.)是栽培稻的近缘祖先,是改良栽培稻的重要种质资源。为了揭示普通野生稻向栽培稻驯化过程中miRNA的变化,并克隆普通野生稻中的miRNA,本研究利用Illumina测序技术对海南万宁普通野生稻小RNA文库进行了分离、鉴定及表达分析,对本项研究中发现的只在普通野生稻中出现的miRNA构建植物表达载体,转化水稻品种日本晴,为普通野生稻中miRNA的功能分析打下基础。主要研究结果如下:
1.小RNA文库高通量测序数据分析
利用Illumina高通量测序平台,分析了普通野生稻小RNA文库,共得到高质量序列8558370个,共2307484种;通过对所有的sRNA序列Blastn比对miRNA数据库(miRBase15.0)中已知的miRNA,在普通野生稻中发现了属于25个家族的104种保守的miRNAs,对比了它们在栽培稻中表达情况的异同;对普通野生稻测到次数最多的前四位:miR156,miR168,miR528,miR166,不同于水稻高通量测序的保守miRNA家族的前四位:miR169, miR156, miR168, miR172;发现215个水稻中特异的miRNA,属于78个家族;经UNAFOLD分析预测,353个小RNA对应的水稻基因组序列能形成发卡环二级结构,进一步通过是否有互补链miRNA*存在及二级结构自由能分析,得到了23个新的miRNA;对23个新的miRNA进行靶基因预测,共发现11个新的miRNA有17个靶基因。
2.候选新miRNA的实验鉴定
提取普通野生稻小分子量RNA,利用改进的茎环引物反转录PCR进一步对能形成发卡环二级结构的353个预测的小RNA序列进行了表达分析,结果发现除了确定的有互补链miRNA*存在23个新的miRNA,还有32个序列通过茎环引物反转录之后PCR扩增,连接到克隆载体,测序得到了目的序列片段,说明这32个序列在普通野生稻中有表达,可能也是新的miRNA。对这32个可能的新miRNA进行靶基因预测,23个预测到了靶基因序列。
3.新miRNA的表达分析及转化栽培稻日本晴
利用RT-PCR检测了CWR-miR28,CWR-miR61,CWR-miR64,CWR-miR68,CWR-miR153,CWR-miR200,CWR-miR264,CWR-miR308在普通野生稻中的表达情况。所有的检测对象在所有部位都有表达,CWR-miR28,CWR-miR153,CWR-miR264在根,茎,叶中表达量相当。其它的在不同部位表达有差异。将23个新的miRNA构建过表达载体,通过农杆菌介导法转化栽培稻日本晴,得到了抗性愈伤,为进一步功能分析打下了基础。
MicroRNA(miRNA) are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Common wild rice (Oryza rufipogon Griff.) is considered to be the ancestor of Asian cultivated rice species, Oryza sativa L. And it is also a important germplasm for cultivated rice modification. In order to reveal the variation of miRNA during the domestication of cultivated rice and, hopefully, clone common wild rice specific miRNA, we use Illumina sequencing approach to characterize, identify and do expression analysis of sRNA cDNA library. Over expression vector harboring precursor of miRNA which were found to be specific to common wild rice were constructed and transferred into cultivated rice variety Nipponbare via Agrobaterium-nediated method, setting the stage for studying the function of those miRNA. The main results were as follows:
Dada analysis of small RNA library for Illumina sequencing
Using Illumina sequencing technology, we analyze the common wild rice sRNA cDNA library and obtain High quality reads 8558370 consisting of 2307484 unique sequences; Through Aligning small RNA to the miRNA precursor of Oryza sativa in miRBase14.0 we identify 104 miRNA belonging to 25 conserved miRNA families; According to the miRNA count in our study and previously reports the most highly expressed conserved miRNA in common wild rice ranked from high to low is miR156,miR168,miR528,miR166,miR167, while in cultivated rice is miR169, miR156, miR168, miR 172;Besides the conserved miRNAs, we also found 215 Rice specific miRNA belonging to 78 families; Using UNAFOLD we found 353 sRNA sequences seemed to be able to generate fold-back secondary structure, further analysis including the existence of miRNA* and the free energy of the harpin, we identified 23 novel miRNA; 17 target genes of 11 new miRNA were predicted by way of bioinformatics approach.
Validation of new miRNA
After extracted small RNA, we use Stem-loop RT-PCR for detecting the expression of 353 small RNA sequences which were predicted to be able to generate fold-back secondary structure. Among those, by sequencing, we got 32 75bp PCR product containing 21nt small RNA except for 23 new miRNA which have miRNA*. Suggesting those 32 sequences are expressed so they are candidate new miRNA. Using on line software--miRU: Plant miRNA Potential Target Find, 23 out of 32 candidate have predicted targets.
Expression patterns of newly identified miRNA and vector construction and transformation of cultivated rice
Knowledge about the expression of miRNA might provide clues about their functions. We did Semi-quantitative PCR for CWR-miR28 , CWR-miR61 , CWR-miR64 , CWR-miR68 ,CWR-miR153,CWR-miR200,CWR-miR264,CWR-miR308 and found all of them expressed in common wild rice, and all of them show different expression level in root, stem and leaf except for CWR-miR28,CWR-miR153,CWR-miR264,.
In order for further study of functions of new miRNAs, we constructed 23 over expression vector harboring precursor of new miRNAs and transferred them into cultivated rice variety Nipponbare via Agrobaterium-mediated method. Now 2 of them are in the differentiation stage.
1.小RNA文库高通量测序数据分析
利用Illumina高通量测序平台,分析了普通野生稻小RNA文库,共得到高质量序列8558370个,共2307484种;通过对所有的sRNA序列Blastn比对miRNA数据库(miRBase15.0)中已知的miRNA,在普通野生稻中发现了属于25个家族的104种保守的miRNAs,对比了它们在栽培稻中表达情况的异同;对普通野生稻测到次数最多的前四位:miR156,miR168,miR528,miR166,不同于水稻高通量测序的保守miRNA家族的前四位:miR169, miR156, miR168, miR172;发现215个水稻中特异的miRNA,属于78个家族;经UNAFOLD分析预测,353个小RNA对应的水稻基因组序列能形成发卡环二级结构,进一步通过是否有互补链miRNA*存在及二级结构自由能分析,得到了23个新的miRNA;对23个新的miRNA进行靶基因预测,共发现11个新的miRNA有17个靶基因。
2.候选新miRNA的实验鉴定
提取普通野生稻小分子量RNA,利用改进的茎环引物反转录PCR进一步对能形成发卡环二级结构的353个预测的小RNA序列进行了表达分析,结果发现除了确定的有互补链miRNA*存在23个新的miRNA,还有32个序列通过茎环引物反转录之后PCR扩增,连接到克隆载体,测序得到了目的序列片段,说明这32个序列在普通野生稻中有表达,可能也是新的miRNA。对这32个可能的新miRNA进行靶基因预测,23个预测到了靶基因序列。
3.新miRNA的表达分析及转化栽培稻日本晴
利用RT-PCR检测了CWR-miR28,CWR-miR61,CWR-miR64,CWR-miR68,CWR-miR153,CWR-miR200,CWR-miR264,CWR-miR308在普通野生稻中的表达情况。所有的检测对象在所有部位都有表达,CWR-miR28,CWR-miR153,CWR-miR264在根,茎,叶中表达量相当。其它的在不同部位表达有差异。将23个新的miRNA构建过表达载体,通过农杆菌介导法转化栽培稻日本晴,得到了抗性愈伤,为进一步功能分析打下了基础。
MicroRNA(miRNA) are a class of non-coding RNAs involved in post-transcriptional control of gene expression, either via degradation or translational inhibition of target mRNAs. Common wild rice (Oryza rufipogon Griff.) is considered to be the ancestor of Asian cultivated rice species, Oryza sativa L. And it is also a important germplasm for cultivated rice modification. In order to reveal the variation of miRNA during the domestication of cultivated rice and, hopefully, clone common wild rice specific miRNA, we use Illumina sequencing approach to characterize, identify and do expression analysis of sRNA cDNA library. Over expression vector harboring precursor of miRNA which were found to be specific to common wild rice were constructed and transferred into cultivated rice variety Nipponbare via Agrobaterium-nediated method, setting the stage for studying the function of those miRNA. The main results were as follows:
Dada analysis of small RNA library for Illumina sequencing
Using Illumina sequencing technology, we analyze the common wild rice sRNA cDNA library and obtain High quality reads 8558370 consisting of 2307484 unique sequences; Through Aligning small RNA to the miRNA precursor of Oryza sativa in miRBase14.0 we identify 104 miRNA belonging to 25 conserved miRNA families; According to the miRNA count in our study and previously reports the most highly expressed conserved miRNA in common wild rice ranked from high to low is miR156,miR168,miR528,miR166,miR167, while in cultivated rice is miR169, miR156, miR168, miR 172;Besides the conserved miRNAs, we also found 215 Rice specific miRNA belonging to 78 families; Using UNAFOLD we found 353 sRNA sequences seemed to be able to generate fold-back secondary structure, further analysis including the existence of miRNA* and the free energy of the harpin, we identified 23 novel miRNA; 17 target genes of 11 new miRNA were predicted by way of bioinformatics approach.
Validation of new miRNA
After extracted small RNA, we use Stem-loop RT-PCR for detecting the expression of 353 small RNA sequences which were predicted to be able to generate fold-back secondary structure. Among those, by sequencing, we got 32 75bp PCR product containing 21nt small RNA except for 23 new miRNA which have miRNA*. Suggesting those 32 sequences are expressed so they are candidate new miRNA. Using on line software--miRU: Plant miRNA Potential Target Find, 23 out of 32 candidate have predicted targets.
Expression patterns of newly identified miRNA and vector construction and transformation of cultivated rice
Knowledge about the expression of miRNA might provide clues about their functions. We did Semi-quantitative PCR for CWR-miR28 , CWR-miR61 , CWR-miR64 , CWR-miR68 ,CWR-miR153,CWR-miR200,CWR-miR264,CWR-miR308 and found all of them expressed in common wild rice, and all of them show different expression level in root, stem and leaf except for CWR-miR28,CWR-miR153,CWR-miR264,.
In order for further study of functions of new miRNAs, we constructed 23 over expression vector harboring precursor of new miRNAs and transferred them into cultivated rice variety Nipponbare via Agrobaterium-mediated method. Now 2 of them are in the differentiation stage.
引文
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