Kojima Kenji K, Fujiwara Haruhiko
Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo.
Mol Biol Evol. 2004 Feb;21(2):207-17. doi: 10.1093/molbev/msg235. Epub 2003 Aug 29.
Although most LINEs (long interspersed nuclear elements), which are autonomous non-long-terminal-repeat retrotransposons, are inserted throughout the host genome, three groups of LINEs, the early-branched group, the Tx group, and the R1 clade, are inserted into specific sites within the target sequence. We previously characterized the sequence specificity of the R1 clade elements. In this study, we screened the other two groups of sequence-specific LINEs from public DNA databases, reconstructed elements from fragmented sequences, identified their target sequences, and analyzed them phylogenetically. We characterized 13 elements in the early-branched group and 13 in the Tx group. In the early-branched group, we identified R2 elements from sea squirts and zebrafish in this study, although R2 has not been characterized outside the arthropod group to date. This is the first evidence of cross-phylum distribution of sequence-specific LINEs. The Dong element also occurs across phyla, among arthropods and mollusks. In the Tx group, we characterized five novel sequence-specific families: Kibi for TC repeats, Koshi for TTC repeats, Keno for the U2 snRNA gene, Dewa for the tRNA tandem arrays, and Mutsu for the 5S rRNA gene. Keno and Mutsu insert into the highly conserved region within small RNA genes and destroy the targets. Several copies of Dewa insert different positions of tRNA tandem array, which indicates a certain "site specifier" other than sequence-specific endonuclease. In all three groups, LINEs specific for the rRNA genes or microsatellites can occur as multiple families in one organism. This indicates that the copy number of a target sequence is the primary factor to restrict the variety of sequence specificity of LINEs.
虽然大多数长散在核元件（LINEs）是自主的非长末端重复逆转座子，可插入宿主基因组各处，但有三组LINEs，即早期分支组、Tx组和R1进化枝，会插入目标序列内的特定位点。我们之前已对R1进化枝元件的序列特异性进行了表征。在本研究中，我们从公共DNA数据库中筛选了另外两组具有序列特异性的LINEs，从片段化序列中重建元件，确定它们的目标序列，并进行了系统发育分析。我们表征了早期分支组中的13个元件和Tx组中的13个元件。在早期分支组中，我们在本研究中鉴定出了来自海鞘和斑马鱼的R2元件，尽管迄今为止在节肢动物类群之外尚未对R2进行过表征。这是序列特异性LINEs跨门分布的首个证据。董元件也跨门出现，存在于节肢动物和软体动物中。在Tx组中，我们表征了五个新的序列特异性家族：针对TC重复序列的木更津（Kibi）、针对TTC重复序列的小田原（Koshi）、针对U2 snRNA基因的气仙沼（Keno）、针对tRNA串联阵列的出羽（Dewa）以及针对5S rRNA基因的陆奥（Mutsu）。气仙沼和陆奥插入小RNA基因内的高度保守区域并破坏目标。出羽的几个拷贝插入tRNA串联阵列的不同位置，这表明除了序列特异性内切核酸酶之外还有某种“位点特异性因子”。在所有这三组中，对rRNA基因或微卫星具有特异性的LINEs在一个生物体中可以作为多个家族出现。这表明目标序列的拷贝数是限制LINEs序列特异性多样性的主要因素。
