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A tRNA-derived SINE

In our study of C. elegans tRNA pseudogenes, we discovered a large family of related elements that we believe are likely retrotransposons, dubbed ``tde-1'' for tRNA-Derived repetitive Element-1. An alignment of 52 members of this family is shown in Figures 3.4 and 3.5. We estimate there are over 200 copies of tde-1 in the C. elegans genome. Tde-1 resembles SINE elements found in other metazoans based on its high copy number, apparent derivation from a non-coding RNA (tRNA in this case), and lack of secondary structure conservation. Like other SINES, this element appears to have included flanking sequence, outside the ancestor RNA gene, as part of the mobile element. The 5' 74 nucleotides of tde-1 contain strong primary sequence similarity to tRNA pol-III promoters, but poor tRNA-like secondary structure. 3' to the tRNA-like sequence is an additional 175 nucleotides present in over 100 family members. Careful examination of the tde-1 alignment shows fairly random substitutions throughout the sequence, leading one to believe there is little or no selection for biological function.

Todd M. Lowe