A TRANSPOSON-BASED STRATEGY FOR SEQUENCING REPETITIVE DNA IN EUKARYOTIC GENOMES

Repetitive DNA is a significant component of eukaryotic genomes. We ha ve developed a strategy to efficiently and accurately sequence repetit ive DNA in the nematode Caenorhabditis elegans using integrated artifi cial transposons and automated fluorescent sequencing. Mapping and ass embly tools represent important components of this strategy and facili tate sequence assembly in complex regions. We have applied the strateg y to several cosmid assembly gaps resulting from repetitive DNA and ha ve accurately recovered the sequences of these regions. Analysis of th ese regions revealed six novel transposon-like repetitive elements, IR -1, IR-2, IR-3, IR-4, IR-5, and TR-1. Each of these elements represent s a middle-repetitive DNA family in C. elegans containing at least 3-1 40 copies per genome. Copies of IR-l, IR-2, IR-4, and IR-5 are located on ail (or most) of the six nematode chromosomes, whereas IR-3 is pre dominantly located on chromosome X. These elements are almost exclusiv ely interspersed between predicted genes or within the predicted intro ns of these genes, with the exception of a single IR-S element, which is located within a predicted exon. IR-1, IR-2, and IR-3 are flanked b y short sequence duplications resembling the target site duplications of transposons. We have established a website database (http://www.wel ch.jhu.edu/similar to devine/RepDNAdb.html) to track and cross-referen ce these transposon-like repetitive elements that contains detailed in formation on individual element copies and provides links to appropria te GenBank records. This set or tools may be used to sequence, track, and study repetitive DNA in model organisms and humans.