%0 Journal Article
%T Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans
%A Kenji K Kojima
%J Mobile DNA
%D 2010
%I BioMed Central
%R 10.1186/1759-8753-1-17
%X In this study, a method to correctly characterize insertions with short target site duplications (TSDs) is developed and extranucleotides, TSDs and microhomologies (MHs) at junctions were analysed for the three types of insertions. Only 5'-truncated L1 insertions were found to be associated with short TSDs. Both full-length and 5'-truncated retrotransposed sequences in trans, including Alu, SVA and mRNA retrocopies and also full-length and 5'-inverted L1, were not associated with short TSDs, indicating the difference of 5' attachment between retrotransposition in cis and retrotransposition in trans. Target sequence analysis suggested that short TSDs were generated in an L1 endonuclease-dependent manner. The MHs were longer for 5'-inverted L1 than for 5'-truncated L1, indicating less dependence on annealing in 5'-truncated L1 insertions.The results suggest that insertions flanked by short TSDs occur more often coupled with the insertion of 5'-truncated L1 than with those of other types of insertions in vivo. The method used in this study can be used to characterize elements without any apparent boundary structures.Long interspersed nuclear element-1 (LINE-1 or L1) is the only active non-long terminal repeat (non-LTR) retrotransposon family in humans and constitutes one sixth of the human genome [1,2]. It encodes two proteins, open reading frame one protein (ORF1p) and open reading frame two protein (ORF2p). Both these proteins are essential for L1 retrotransposition [3]. ORF2p contains two enzymatic domains: endonuclease (EN) [4] and reverse transcriptase (RT) [5]. Retrotransposition-competent L1 copies are ~6000 bp in length [6,7], but most of the L1 copies on the human genome are severely 5'-truncated [1,8]. In addition, ~10% of the human L1 copies are rearranged to be composed of two segments: 5' inverted and 3' noninverted segments [9,10]. L1 copies are classifiable into three categories: full-length; 5'-truncated; and 5'-inverted insertions.The insertion of L1 i
%U http://www.mobilednajournal.com/content/1/1/17