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Nucleic Acids Research, 2003, Vol. 31, No. 15 4531-4540
© 2003 Oxford University Press

Patterns of sequence conservation at termini of long terminal repeat (LTR) retrotransposons and DNA transposons in the human genome: lessons from phage Mu

Insuk Lee* and Rasika M. Harshey

Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA

*To whom correspondence should be addressed. Tel: +1 512 232 3919; Fax: +1 512 232 3432; Email: lee-micro{at}mail.utexas.edu

Long terminal repeat (LTR) retrotransposons and DNA transposons are transposable elements (TEs) that perform cleavage and transfer at precise DNA positions. Here, we present statistical analyses of sequences found at the termini of precise TEs in the human genome. The results show that the terminal di- and trinucleotides of these TEs are highly conserved. 5'TG...CA3' occurs most frequently at the termini of LTR retrotransposons, while 5'CAG...CTG3' occurs most frequently in DNA transposons. Interestingly, these sequences are the most flexible base pair steps in DNA. Both the sequence preference and the degree of conservation of each position within the human LTR dinucleotide termini are remarkably similar to those experimentally demonstrated in transposable phage Mu. We discuss the significance of these observations and their implication for the function of terminal residues in the transposition of precise TEs.


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