Non-LTR retrotransposons with unique integration preferences downstream ofDictyostelium discoideum tRNA genes

Retrotransposable elements are genetic entities which move and replicate wi thin host cell genomes. We have previously reported on the structures and g enomic distributions of two non-long terminal repeat (non-LTR) retrotranspo sons, DRE and Tdd-3, in the eukaryotic microorganism Dictyostelium discoide um. DRE elements are found inserted upstream, and Tdd-3 elements downstream , of transfer RNA (tRNA) genes with remarkable position and orientation spe cificities. The data set currently available from the Dictyostelium Genome Project led to the characterisation of two repetitive DNA elements which ar e related to the Dictyostelium non-LTR retrotransposon Tdd-3 in both their structural properties and genomic distributions. It appears from our data t hat in the D. discoideum genome tRNA genes are major targets for the insert ion of mobilised non-LTR retrotransposons. This may be interpreted as the c onsequence of a process of coevolution, allowing a viable population of ret roelements to transpose without being deleterious to the small microbial ho st genome which carries only short intergenic DNA sequences. A new nomencla ture is introduced to designate all tRNA gene-targeted non-LTR retrotranspo sons (TREs) in the D. discoideum genome. TREs inserted 5' and 3' of tRNA ge nes are named TRE5 and TRE3, respectively. According to this nomenclature D RE and Tdd-3 are renamed TRE5-A and TRE3-A, respectively. The new retroelem ents described in this study are named TRE3-B (formerly RED) and TRE3-C.