Molecular mechanism of the diversification of genome by retroposons

CR1元件是一个反转录子家族。它们被归类为长穿插元件（LINEs）或非长末端重复（non-long terminal repeat, non-LTR）反转录转座子，在许多脊椎动物的基因组中都发现了它们。然而，它们仅被部分表征，并且仅对鸡CR1 3'端的2 kbp区域进行了测序。在本研究中，我们确定了海龟基因组中CR1元件的完整共识序列，命名为PsCR1。PsCR1的第一个开放阅读框（ORF1）有两个不寻常的Cys残基排列。其中包括一个锌指motif， CX_2CX_<14>CX_2C。假定的锌指具有与物种特异性转录起始因子SL1和TIF-IB中发现的相同间距和相似氨基酸组成的半胱氨酸残基。PsCR1的5'-非翻译区（5' UTR）包含一个类似于人类L1启动子的部分序列，L1位点a，以及真核基因中发现的几种顺式元件。在大约500 bp的区域内，有9个“E盒”，即被基本螺旋-环-螺旋（bHLH）蛋白家族识别的顺式元件。这一观察结果提出了一种可能性，即结合这些序列的细胞转录因子可能协同作用来调节PsCR1的表达。在ORF2中，cr1的3′UTR在物种间的序列分化程度低于每个位点的非同义替换率，表明该区域一定存在严格的功能约束。这一结果强烈提示CR1保守的3′端序列是CR1逆转录酶的识别位点。讨论了CR1元件整合的可能机制，以及SINEs逆转录的可能的逆转录酶募集。

CR1 elements are a family of retroposons. They are classified as long interspersed elements (LINEs) or non-long terminal repeat (non-LTR) retrotransposons, and they have been found in the genomes of many vertebrates. However, they have been only partially characterized and only a 2-kbp region of the 3' end of chicken CR1 has been sequenced. In the present study, we determined the entire consensus sequence of CR1 elements in the turtle genome, designated PsCR1.The first open reading frame (ORF1) of PsCR1 has two unusual arrangements of Cys residues. One of them includes a zinc finger motif, CX_2CX_<14>CX_2C.The putative zinc finger has cysteine residues with identical spacing and a similar amino acid composition to those found in the species-specific transcription initiation factors, SL1 and TIF-IB.The 5'-untranslated region (5' UTR) of PsCR1 contains a sequence similar to part of the human L1 promoter, L1 site A, and several cis elements of the type found in eukaryotic genes. Within a region of about 500 bp, there are nine "E boxes", cis elements that are recognized by the basic helix-loop-helix (bHLH) family of proteins. This observation raises the possibility that cellular transcription factors that bind to these sequences might act in concert to regulate the expression of PsCR1.The extent of the sequence divergence of the 3' UTR of CR1-between species was found to be lower than the rate of nonsynonymous substitutions per site in ORF2, suggesting that a strict functional constraint must exist for this region. This result strongly suggests that the conserved 3'-end sequence of CR1 is the recognition site for the reverse transcriptase of CR1. A discussion is presented of a possible mechanism for the integration of CR1 elements and, also, of the intriguing possible recruitment of the reverse transcriptase for the retroposition of SINEs.