The X element, a novel LINE transposable element from Drosophila melanogaster
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O R I GI N A L P A P E R
M. Tudor á A. J. Davis á M. Feldman M. Grammatikaki á K. O'Hare
The X element, a novel LINE transposable element from Drosophila melanogaster Received: 28 July 2000 / Accepted: 5 December 2000 / Published online: 21 February 2001 Ó Springer-Verlag 2001
Abstract Whilst analysing the nature of repeated DNA sequences in the transition zone between euchromatin and heterochromatin at the base of the X chromosome of Drosophila melanogaster, we discovered a novel transposable element of the LINE class that we have named the X element. Several apparently complete elements have been cloned and analysed, and one has been sequenced. It is 4740 bp long, with a polyadenylation sequence and a run of A residues at one end. It contains two ORFs: the 5¢ ORF is related to the retroviral gag gene and encodes a protein with cysteine-rich motifs that are thought to form a ``zinc-knuckle'' in a nucleic-acid binding protein; the 3¢ ORF encodes a putative reverse transcriptase that includes the conserved domains found in reverse transcriptases from other LINEs and retroviruses. The DNA sequence and the sequences of the predicted gene products are most similar to other LINEs from D. melanogaster, such as the F, jockey, Doc and BS elements. Southern analysis suggests that there are at least 30 copies in the genome and that some elements are polymorphic between dierent strains. Analysis of the DNA sequence of the euchromatic arms of the Drosophila genome identi®ed ®ve full-length elements and a similar number of elements that were intact at the 3¢ end but had variable 5¢ truncations. Sequences ¯anking two dierent insertion sites were used to design PCR primers to assess the occupancy of sites in wild-type ¯ies of dierent geographical origins. Flies that lacked each of the insertions were found, suggesting that the element is an active transposon.
Communicated by D. Gubb M. Tudor á A. J. Davis á M. Feldman á M. Grammatikaki K. O'Hare (&) Department of Biochemistry, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK E-mail: [email protected] Tel.: +44-207-5945292 Fax: +44-207-5945207
Key words Drosophila LINE á Non-LTR retrotransposon
Introduction In the course of studying the euchromatin/heterochromatin transition region at the base of the Drosophila melanogaster X chromosome, we mapped repeated DNA sequences around the most proximal known gene [su(f)], the suppressor of forked locus (Mitchelson et al. 1993; Tudor et al. 1996). As part of our analysis of these sequences, we have characterised homologous sequences from elsewhere in the genome by Southern hybridisation and cloning (Tudor 1994). These studies have led to the discovery of a transposable element whose DNA sequence shows that it is a LINE element, a retrotransposon that lacks long terminal repeats (LTRs). It has all the features of this class of transposable element (Hutchison et al. 1989): one end is characterised by a polyadenylation signal and a poly(A) or A-rich region; duplications that vary in size from 8 to 12 bp are foun
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