Characterization of Tc6 repetitive DNA sequences in the genome of the nematode Caenorhabditis elegans

Abstract

Four out of approximately 40 repetitive sequences denoted Tc6 elements in the genome of the nematode Caenorhabditis elegans have been cloned and analyzed at the nucleotide level. The genomic organization of the Tc6 repetitive sequence family has been studied through Southern blotting. Tc6 elements are present at different genomic sites in the genomes of closely related C. elegans strains, suggesting that Tc6 elements may have been mobile in the recent past.;The structure of most Tc6 elements is a 1.6 kb palindrome with a small non-palindromic central region. The termini of Tc6 elements are similar to the termini of the C. elegans transposable element Tc1. However, the internal regions of Tc6 and Tc1 are not similar. Unlike Tc1 elements, Tc6 elements do not exhibit strain copy-number differences or undergo somatic excision at a high rate. The termini of Tc6 and Tc1 are similar to a widely distributed class of mobile DNA sequences in both vertebrate and invertebrate species which may include the somatic recombination sites of the vertebrate immunoglobulin gene family. Evidence for nucleotide rearrangements within or flanking Tc6 sequences at 3 Tc6 sites has been analyzed and related to previous studies of spontaneous DNA rearrangements in the genomes of eukaryotic species.;Conserved sequences within the genomes of viroids and viral satellites, small circular RNA molecules which are common plant pathogens, can be aligned with Tc6 sequences. This finding suggests that reverse transcription and integration of a viroid/viral satellite-like molecule may account for the structure of Tc6 elements. Thus, Tc6 elements may represent a new class of eukaryotic transposable elements with similarity to plant viroids and viral satellite RNAs.