Studies on transposable element Tcl in the nematode Caenorhabditis elegans
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The transposable element Tcl is found in all C. elegans strains examined thus far. In most strains it is present in approximately 30 copies per genome at a nearly constant set of genomic sites. In a few strains, there are 200-300 copies per genome. The structure of genomic Tcl elements is highly uniform. Each is 1.6 kb in length, contains an open reading frame, and is bounded by a 54 base pair perfect inverted repeat. Tcl undergoes excision at high frequency in somatic cells. One product of somatic excision is a religated chromosomal empty site. The other (presumed) product is an extra-chromosomal copy of the Tcl element. These two products were studied further.;Extrachromosomal linear, circular, and supercoiled copies of Tcl were detected in DNA preparations of a strain with 200-300 Tcl elements. They are present at a level corresponding to 0.1-1.0 copies per cell, and increase in amount during development. The linear monomer, the predominant species, has well-defined ends corresponding to the ends of integrated genomic elements. In the circularized monomer the two ends were exactly jointed, with the addition of a TA dinucleotide possibly from the insertion site.;The excision products at two chromosomal Tcl insertion sites were examined by DNA sequencing. Eleven restriction fragments containing chromosomal Tcl empty sites were directly cloned from separate worm DNA preparations. DNA sequences from six independent excision events at one chromosomal site are consistent with precise excision. However, the DNA sequences from five independent excision events at a second site showed two patterns; two products resulted from precise excision, whereas three had four extra nucleotides, TGTA, remaining after Tcl excision, indicating an imprecise excision event.;These results indicate that Tcl somatic excision can be either precise or imprecise. The precision and rate of excision depends upon the chromosomal position of Tcl insertion. This observation implies an influence of flanking DNA sequences on the excision mechanism.