植物LTR反转录转座子的研究进展

反转录转座子是真核生物基因组中普遍存在的一类可移动的遗传因子,它们以RNA为媒介,在基因组中不断自我复制。在高等植物中,反转录转座子是基因组的重要成分之一。反转录转座子可以分为5大类型,其中以长末端重复（LTR）类型报道较多。LTR类型由于其首尾具有长末端重复序列,内部含有PBS、PPT、GAG和POL开放阅读框、TSD等结构,可以采用生物信息学软件进行预测。LTR反转录转座子的活性受到自身甲基化和环境因素的影响,DNA甲基化抑制反转录转座子转座,而外界环境的刺激能够激活转座子,从而影响插入位点周边基因的表达。同时由于LTR反转录转座子在植物中普遍存在,丰富的拷贝数以及多态性为新型分子标记（RBIP、SSAP、IRAP、REMAP）的开发提供了良好的素材。该文对近年来国内外有关植物反转录转座子的类型、结构特征、 LTR反转录转座子的活性及其影响因素、 LTR反转录转座子的预测以及标记开发等方面的研究进展进行综述。     

植物LTR类反转录转座子序列分析识别方法

LTR类反转录转座子(Long terminal repeat retrotransponson)是真核生物中的一类重要转座元件,具有分布广泛、异质性高等特点,在真核生物基因组进化中起着重要作用,现广泛应用于植物的基因功能分析和遗传多样性研究等方面。LTR类反转录转座子的序列识别是其应用的前提条件,因此对LTR类反转录转座子的序列鉴定和分析方法的研究具有重要的理论意义和实际应用价值。LTR类反转录转座子序列的生物信息学分析软件按原理可大致分为序列比对分析和相关序列保守区域识别鉴定两类。比对软件如BLAST、DNAstar等,是一种序列相似性搜索程序,通过与已知的反转录转座子序列比对后的序列相似性来判断未知序列是否是反转录转座子序列,但这类软件不能直接获得具体的LTR等特征序列的相关信息,不能对反转录转座子序列的全长进行识别。识别鉴定软件按原理可分为从头算起法、比较基因组法、同源搜索法和结构基础法4种,如LTR-Finder等基于从头算起法的识别鉴定软件,可对LTR类反转录转座子全序列进行较准确地预测和注释,RepeatMasker等基于同源搜索法的软件,通过与数据库中的序列的相似性比对后发现可能存在的LTR类反转录转座子。文章对不同的LTR类反转录转座子预测方法进行了比较和分析,在此基础上归纳总结出一套分析LTR类反转录转座子序列的操作流程,旨在为LTR类反转录转座子序列的分析提供参考。     

利用iPBS技术克隆牡丹反转录转座子LTR序列

利用iPBS方法从西北牡丹(Paeonia suffruticosa)品种红绣球和中原牡丹品种洛阳红中扩增出相应片段,经回收、克隆及测序,获得了12条来自牡丹LTR类反转录转座子的LTR序列,并用相关生物信息学软件对序列进行分析。结果表明,这些核苷酸序列表现出较高的异质性,主要表现为缺失突变,序列长度变化范围为313–894 bp,同源性从31.1%–65.8%不等。将其氨基酸序列与已登录的不同植物LTR类反转录转座子LTR氨基酸序列进行聚类分析,结果显示与某些植物相应序列具有较高的同源性,表明可能存在LTR类反转录转座子的横向传递关系。根据克隆出的LTR序列设计SSAP引物,对牡丹29个品种进行了SSAP分子标记分析,结果显示具丰富的多态性。实验验证了用iPBS技术分离牡丹LTR序列的适用性,并为牡丹种质资源评价提供了新的技术手段。     

人类基因组中的反转录转座子

人类基因组中有35%以上的序列为转座子序列.反转录转座子是引起人类疾病的潜在病因.人类基因组中的主导转座子——L1反转录转座子内部有二个开放读框,其编码蛋白具有RNA结合蛋白、反转录酶和内切酶活性.L1可能通过靶引物反转录机制整合到染色体中;Alu等非自主性反转录转座子可能利用L1反转录酶的反式互补作用进行转座.     

BB染色体组野生种花生LTR反转录转座子RT基因的多样性分析

利用简并PCR技术从野生花生种(Arachis ipaensis Krapov. et W. C. Greg.)的基因组中扩增分离Ty1-copia类(1类)和Ty3-gypsy类(2类)反转录转座子RT基因,并对其序列特征、多样性、系统进化关系及转录活性进行分析。结果显示:对于1和2类RT基因,目的条带分别约为260和430 bp;分离获得了23和32条序列,长度范围分别为262～266、395～435 bp;AT所占比例分别为61.60%～69.17%和55.79%～61.34%;核苷酸序列间相似性分别为52.5%～98.9%和45.0%～98.8%,氨基酸序列间相似性分别为39.8%～100%和9.0%～97.2%。其中2类基因的异质性高于1类;1类和2类基因分别有3条和15条发生了无义突变,2类的无义突变发生率远高于1类。1类基因的保守基序保守性较高,2类的保守基序呈一定程度的变异。代表序列的蛋白质三级结构基本类似。聚类分析结果显示,1类和2类基因可被分为5个和6个家族。1类和2类基因都有部分序列与其他物种的RT基因序列亲缘关系较近,表明它们之间可能存在两类反转录转座子的横向传...     

高等植物基因组中的反转录转座子

高等植物基因组中的反转录转座子王石平张启发（华中农业大学作物遗传改良国家重点实验室武汉４３００７０）关键词植物,反转录转座子,遗传多样性,转座ＲＥＴＲＯＴＲＡＮＳＰＯＳＯＮＳＩＮＴＨＥＧＥＮＯＭＥＳＯＦＨＩＧＨＥＲＰＬＡＮＴＳＷＡＮＧＳｈｉＰｉｎ...     

植物反转录转座子及其分子标记

反转录转座子（retrotransposon）是真核生物中一类可移动因子,可分为LTR反转录转座子和非LTR反转录转座子。反转录转座子以高拷贝在植物界广泛分布,可以通过纵向和横向分别在世代之间和不同种之间进行传递,同一家族的反转录转座子具有高度的异质性. 在一些生物的和非生物的逆境条件下,反转录转座子的转录可以被激活。由于反转录转座子的特点,使其作为一种分子标记得以应用。S-SAP、IRAP、REMAP和RBIP等分子标记相继发展起来,在基因作图、生物遗传多样性与系统进化、品种鉴定等方面具有广泛的应用前景。     

绿豆Ty1/Copia类反转录转座子逆转录酶序列的克隆和分析

利用Ty1/copia类反转录转座子的保守位点设计简并引物,从绿豆(Vigna radiata(L.)Wilczek)基因组中扩增得到了反转录转座子的逆转录酶序列.对扩增得到的约270bp的片段进行分离和克隆,并随机挑选了40个克隆进行测序,结果得到了36个单独的核酸序列,其中18个含有移码突变或终止子.根据序列比对,这些克隆可分为9组以及单个的9种.这40个克隆中,核酸序列相似性从8%到100%,显示出其核酸序列的高度异质性.将这些克隆的核酸序列与来自其他种植物的相应序列进行谱系分析,发现有些克隆与来自其他种植物的相应序列的亲缘关系比这些克隆之间更为接近.斑点杂交显示Ty1/copia反转录转座子约占绿豆基因组的9.3%.     

植物活性长末端重复序列反转录转座子研究进展

长末端重复序列(Long terminal repeat,LTR)反转录转座子是真核生物基因组中普遍存在的一类可移动的DNA序列,它们以RNA为媒介,通过"复制粘贴"机制在基因组中不断自我复制。在高等植物中,许多活性的LTR反转录转座子已被详尽研究并应用于分子标记技术、基因标签、插入型突变及基因功能等分析。本文对植物活性LTR反转录转座子进行全面的调查,并对其结构、拷贝数和分布以及转座特性进行系统的归纳,分析了植物活性LTR反转录转座子的gag(种属特异抗原)和pol(聚合酶)序列特征,以及LTR序列中顺式调控元件的分布。研究发现自主有活性的LTR反转录转座子必须具备LTR区域以及编码Gag、Pr、Int、Rt和Rh蛋白的基因区。其中两端LTR区域具有高度同源性且富含顺式调控元件;Rt蛋白必备RVT结构域;Rh蛋白必备RNase_H1_RT结构域。这些结果为后续植物活性LTR反转录转座子的鉴定和功能分析奠定了重要基础。     

RetroPred: A tool for prediction, classification and extraction of non-LTR retrotransposons (LINEs & SINEs) from the genome by integrating PALS, PILER, MEME and ANN

The problem of predicting non-long terminal repeats (LTR) like long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs) from the DNA sequence is still an open problem in bioinformatics. To elevate the quality of annotations of LINES and SINEs an automated tool "RetroPred" was developed. The pipeline allowed rapid and thorough annotation of non-LTR retrotransposons. The non-LTR retrotransposable elements were initially predicted by Pairwise Aligner for Long Sequences (PALS) and Parsimonious Inference of a Library of Elementary Repeats (PILER). Predicted non-LTR elements were automatically classified into LINEs and SINEs using ANN based on the position specific probability matrix (PSPM) generated by Multiple EM for Motif Elicitation (MEME). The ANN model revealed a superior model (accuracy = 78.79 +/- 6.86 %, Q(pred) = 74.734 +/- 17.08 %, sensitivity = 84.48 +/- 6.73 %, specificity = 77.13 +/- 13.39 %) using four-fold cross validation. As proof of principle, we have thoroughly annotated the location of LINEs and SINEs in rice and Arabidopsis genome using the tool and is proved to be very useful with good accuracy. Our tool is accessible at http://www.juit.ac.in/RepeatPred/home.html.     

Non-LTR retrotransposons (LINEs) as ubiquitous components of plant genomes

During the course of work aimed at isolating a rice gene from Oryza australiensis by PCR, the oligonucleotide primers used were found to generate a fragment that showed sequence homology to the endonuclease (EN) region of the maize non-LTR retrotransposon (LINE) Cin4. We carried out further PCRs using oligonucleotide primers that hybridized to these sequences, and found that they amplified several fragments, each with homology to the EN regions, from Oryza sativa cv. Nipponbare as well as O. australiensis. We mapped the approximate locations of two rice LINE homologues by screening clones in a YAC library made from a rice (O. sativa) genome, and found that each homologue was present in a low copy number apparently at nonspecific regions on rice chromosomes. We then carried out PCR using degenerate oligonucleotide primers which hybridized to the rice LINE homologues and Cin4 to ascertain whether LINE homologues are present in a variety of members of the plant kingdom, including angiosperms, gymnosperms, bracken, horsetail and liverwort. Cloning and nucleotide sequencing revealed that 53 clones obtained from 27 out of 33 plant species contained LINE homologues. In addition to these homologues, we identified four homologues with EN regions in the Arabidopsis thaliana genome by a computer search of databases. The nucleotide sequences of almost all the LINE homologues were greatly diverged, but the derived amino acid sequences were well conserved, and all contained glutamic acid and tyrosine residues at almost the same relative positions as in the the active site regions of AP (apurinic/apyrimidinic)-endonucleases. The EN regions in the LINE homologues from closely related plant species show a closer phylogenetic relationship, indicating that sequence divergence during vertical transmission has been a major influence upon the evolution of plant LINEs. Received: 13 July 1998 / Accepted: 13 October 1998     

Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs.

Some previously unidentified short interspersed repetitive elements (SINEs) and long interspersed repetitive element (LINEs) were isolated from various higher elasmobranchs (sharks, skates, and rays) and characterized. These SINEs, members of the HE1 SINE family, were tRNA-derived and were widespread in higher elasmobranches. The 3'-tail region of this SINE family was strongly conserved among elasmobranchs. The LINEs, members of the HER1 LINE family, encoded an amino acid sequence similar to that encoded by the chicken CR1 LINE family, and they contained a strongly conserved 3'-tail region in the 3' untranslated region. This tail region of the HER1 LINE family was almost identical to that of the HE1 SINE family. Thus, the HE1 SINE family and the HER1 LINE family provide a clear example of a pair of SINEs and LINEs that share the same tail region. Conservation of the secondary structures of the tail regions, as well as of the nucleotide sequences, between the HE1 SINE family and HER1 LINE family during evolution suggests that SINEs utilize the enzymatic machinery for retroposition of LINEs through the recognition of higher-order structures of the conserved 3'-tail region. A discussion is presented of the parasitism of SINEs on LINEs during the evolution of these retroposons.     

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

Many SINEs and LINEs have been characterized to date, and examples of the SINE and LINE pair that have the same 3' end sequence have also increased. We report the phylogenetic relationships of nearly all known LINEs from which SINEs are derived, including a new example of a SINE/LINE pair identified in the salmon genome. We also use several biological examples to discuss the impact and significance of SINEs and LINEs in the evolution of vertebrate genomes.