Simmen M W, Bird A
Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, Scotland.
Mol Biol Evol. 2000 Nov;17(11):1685-94. doi: 10.1093/oxfordjournals.molbev.a026267.
A systematic search of 1 Mb of genomic sequences from the sea squirt, Ciona intestinalis, revealed the presence of six families of transposable elements. The Cigr-1 retrotransposon contains identical 245-bp long terminal repeats (LTRs) and a 3,630-bp open reading frame (ORF) encoding translation products in the same order as the domains characteristic of gypsy/Ty3-type LTR retrotransposons. The closest homologs of the reverse transcriptase domain were in gypsy elements from Drosophila and the sushi element from the pufferfish. However, the capsid-nucleocapsid region shows the clearest homology to an echinoderm element, Tgr1. Database searches also indicated two classes of non-LTR retrotransposon, named Cili-1 and Cili-2. The Cili-1 sequences show matches to regions of the ORF2 product of mammalian L1 elements. The Cili-2 sequences possess similarity to the RNaseH domain of Lian-Aa1, a mosquito non-LTR retrotransposon. The most abundant element was a short interspersed nucleotide element named Cics-1 with a copy number estimated at 40,000. Cics-1 consists of two conserved domains separated by an A-rich stretch. The 172-bp 5' domain is related to tRNA sequences, whereas the 110-bp 3' domain is unique. Cics-1 is unusual, not just in its modular structure, but also in its lack of a 3' poly(A) tail or direct flanking repeats. A second abundant element, Cimi-1, has an A+T-rich 193-bp consensus sequence and 30-bp terminal inverted repeats (TIRs) and is usually flanked by A+T-rich 2-4-bp putative target site duplications-characteristics of miniature inverted-repeat transposable elements found in plants and insects. A single 2,444-bp foldback element was found, possessing long TIRs containing an A+T-rich internal domain, an array of subrepeats, and a flanking domain at the TIR ends; this is the first example of a chordate foldback element. This study provides the first systematic characterization of the families of transposable elements in a lower chordate.
对海鞘（Ciona intestinalis）1兆碱基的基因组序列进行系统搜索，发现了六个转座元件家族。Cigr-1逆转录转座子包含相同的245碱基对长末端重复序列（LTRs）和一个3630碱基对的开放阅读框（ORF），其编码的翻译产物顺序与gypsy/Ty3型LTR逆转录转座子的特征结构域相同。逆转录酶结构域最接近的同源物存在于果蝇的gypsy元件和河豚的sushi元件中。然而，衣壳-核衣壳区域与棘皮动物元件Tgr1显示出最明显的同源性。数据库搜索还表明存在两类非LTR逆转录转座子，分别命名为Cili-1和Cili-2。Cili-1序列与哺乳动物L1元件的ORF2产物区域匹配。Cili-2序列与蚊子非LTR逆转录转座子Lian-Aa1的RNaseH结构域具有相似性。最丰富的元件是一个名为Cics-1的短散在核苷酸元件，估计拷贝数为40000。Cics-1由两个保守结构域组成，中间由富含A的区域隔开。172碱基对的5'结构域与tRNA序列相关，而110碱基对的3'结构域是独特的。Cics-1不同寻常，不仅在于其模块化结构，还在于其缺乏3'聚腺苷酸尾巴或直接侧翼重复序列。第二个丰富的元件Cimi-1具有富含A+T的193碱基对共有序列和30碱基对的末端反向重复序列（TIRs），并且通常侧翼为富含A+T的2-4碱基对推定靶位点重复序列，这是植物和昆虫中发现的微型反向重复转座元件的特征。发现了一个单一的2444碱基对的回文元件，其具有长的TIRs，包含一个富含A+T的内部结构域、一系列亚重复序列以及TIR末端的侧翼结构域；这是脊索动物回文元件的首个例子。这项研究首次对低等脊索动物中的转座元件家族进行了系统表征。
