植物反转录转座子功能研究进展
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摘要
反转录转座子(retrotransposon),是一类以RNA为中介,在反转录酶的参与下,进行自我复制并整合到基因组其他位点中的转座元件(transposableelements,TEs).反转录转座子是许多真核生物基因组的主要组成部分,在高等植物如玉米、小麦等作物中含量丰富.这些反转座子的功能及生物学意义一直以来都存在争议,但越来越多研究表明,它们对于邻近基因的表达调控以及整个生物体基因组的进化有着深远的影响.本文主要从反转座子与非编码RNA的联系及其转座过程所产生的基因结构变异、反转座基因等方面,概述了植物中反转座子功能的相关研究进展.
Retrotransposon is a type of transposable elements(TEs), which can replicate itself and move to other loci through the form of DNA→RNA→DNA intermediated with RNA in the genome, and belongs to the class I type transposon. Basically, retrotransposons can be divided into two mainly categories including LTR(long terminal repeat) and nonLTR(non-long terminal repeat). The LTR retrotransposon can be furtherly divided into two main groups including Ty1/copia and Ty3/gypsy, which have a long terminal repeat structure similar to the retrovirus genome. The LTR usually do not encode proteins, but it can serve as regulator for transcription and termination and so on. Non-LTR retrotransposon includes the LINE(Long interspersed nuclear elements) and SINE(Short interspersed nuclear elements). The SINE retrotransposons do not encode the enzymes required for transposition and cannot complete the retrotransposition autonomously. Retrotransposons are the main components in the genome of most eukaryotic, which are also abundant in higher plants. For example, they account for more than 60 percent of the genome sequence in tomatoes, while nearly 80 percent of the genome sequence is made up of retrotransposons in corn and wheat. As early as 1950 s, the famous American geneticist, Barbara McClintock, had discovered the existence of transposon when studying the variation of color spots in corn kernels. However, the function and biological significance of those transposons including retrotransposons have always been controversial. But more and more researches reveal that the retrotransposons play an important role in the regulation of gene expression and evolution of plant genome in recent years. Some activated transcript of retrotransposons can participate the production of non-coding RNAs, such as small RNAs or LncRNAs, and rely on the targeting effect of these non-coding RNAs, and are further involved in the expression regulation of downstream-related genes. The transposition of retrotransposons always influences gene structure and expression of insertion loci and neighborhood. They can act as cis-or trans-acting elements in the upstream or downstream regions of genes, or directly as promoter and terminator and so on to regulate the expression, transcription and function of target genes. Besides, the enzyme system produced by autonomous retrotransposon may also act on the other genes of genome, which may result in the creation of chimeric genes or production of new gene copy. Furthermore, some retrotransposon sequences may have involved in the generation of new functional genes during the long-term evolution of plants. Obviously, they are of great significance to the plants. Moreover, retrotransposon may play a role in physiological changes and stress responses of plants, for instance, the plant growth and development regulation, disease resistance and stress-related response and so on. They can even reprogramming plant cell gene expression or creating a considerable number of natural ecotype variations. Intriguingly, the subtle relationship in the origin and evolution of retrotransposons and retroviruses deserves further exploration. They have too much in common and similarities, which indicate that they must have some evolutionary connections. From the study of retrotransposon, we may obtain some unknown secrets about mammalian retrovirus. In this paper, the function progress of the retrotransposon in plants are briefly summarized from the above aspects, which may lay a good theoretical foundation for further revealing the function and mechanism of retrotransposon in the genome and incite the enthusiasm of researchers to study these elements.
Retrotransposon is a type of transposable elements(TEs), which can replicate itself and move to other loci through the form of DNA→RNA→DNA intermediated with RNA in the genome, and belongs to the class I type transposon. Basically, retrotransposons can be divided into two mainly categories including LTR(long terminal repeat) and nonLTR(non-long terminal repeat). The LTR retrotransposon can be furtherly divided into two main groups including Ty1/copia and Ty3/gypsy, which have a long terminal repeat structure similar to the retrovirus genome. The LTR usually do not encode proteins, but it can serve as regulator for transcription and termination and so on. Non-LTR retrotransposon includes the LINE(Long interspersed nuclear elements) and SINE(Short interspersed nuclear elements). The SINE retrotransposons do not encode the enzymes required for transposition and cannot complete the retrotransposition autonomously. Retrotransposons are the main components in the genome of most eukaryotic, which are also abundant in higher plants. For example, they account for more than 60 percent of the genome sequence in tomatoes, while nearly 80 percent of the genome sequence is made up of retrotransposons in corn and wheat. As early as 1950 s, the famous American geneticist, Barbara McClintock, had discovered the existence of transposon when studying the variation of color spots in corn kernels. However, the function and biological significance of those transposons including retrotransposons have always been controversial. But more and more researches reveal that the retrotransposons play an important role in the regulation of gene expression and evolution of plant genome in recent years. Some activated transcript of retrotransposons can participate the production of non-coding RNAs, such as small RNAs or LncRNAs, and rely on the targeting effect of these non-coding RNAs, and are further involved in the expression regulation of downstream-related genes. The transposition of retrotransposons always influences gene structure and expression of insertion loci and neighborhood. They can act as cis-or trans-acting elements in the upstream or downstream regions of genes, or directly as promoter and terminator and so on to regulate the expression, transcription and function of target genes. Besides, the enzyme system produced by autonomous retrotransposon may also act on the other genes of genome, which may result in the creation of chimeric genes or production of new gene copy. Furthermore, some retrotransposon sequences may have involved in the generation of new functional genes during the long-term evolution of plants. Obviously, they are of great significance to the plants. Moreover, retrotransposon may play a role in physiological changes and stress responses of plants, for instance, the plant growth and development regulation, disease resistance and stress-related response and so on. They can even reprogramming plant cell gene expression or creating a considerable number of natural ecotype variations. Intriguingly, the subtle relationship in the origin and evolution of retrotransposons and retroviruses deserves further exploration. They have too much in common and similarities, which indicate that they must have some evolutionary connections. From the study of retrotransposon, we may obtain some unknown secrets about mammalian retrovirus. In this paper, the function progress of the retrotransposon in plants are briefly summarized from the above aspects, which may lay a good theoretical foundation for further revealing the function and mechanism of retrotransposon in the genome and incite the enthusiasm of researchers to study these elements.
引文
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3 Jr K H,Scott A F.‘Copy and paste’transposable elements in the human genome.J Clin Invest,1993,91:1859-1860
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7 Witte C P,Le Q H,Bureau T,et al.Terminal-repeat retrotransposons in miniature(TRIM)are involved in restructuring plant genomes.Proc Natl Acad Sci USA,2001,98:13778-13783
8 Chen Z W,Wu W R.The plant retrotransposon and application(in Chinese).Hereditas(Beijing),2004,26:122-126[陈志伟,吴为人.植物中的反转录转座子及其应用.遗传,2004,26:122-126]
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10 Vassetzky N S,Kramerov D A.SINEBase:A database and tool for SINE analysis.Nucleic Acids Res,2013,41:D83-D89
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17 Mccue A D,Slotkin R K.Transposable element small RNAs as regulators of gene expression.Trends Genet,2012,28:616-623
18 Chau N C,Kentaro N,Akihiro M,et al.Oligouridylate binding protein 1b plays an integral role in plant heat stress tolerance.Front Plant Sci,2016,7:853-861
19 Creasey K M,Zhai J,Borges F,et al.miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis.Nature,2014,508:411-415
20 Zhang X.Dynamic differential methylation facilitates pathogen stress response in Arabidopsis.Proc Natl Acad Sci USA,2012,109:12842-12843
21 Hsieh L C,Lin S,Shih C C,et al.Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing.Plant Physiol,2010,151:2120-2132
22 Yuan J,Ye Z,Dong J,et al.Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana.BMC Genomics,2016,17:655
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