Table 1.
Retrotransposons that integrate adjacent to tRNA genes
| Mobile element | Clade | Hosta | Preferred integration site | Host factors mediating this insertion preference |
|---|---|---|---|---|
| LTR Retrotransposons | ||||
| Ty1 | Ty1-copia | Saccharomyces cerevisiae | ~ 1 kb window upstream of RNA Pol III-transcribed genes, including tRNA and 5S rRNA genes [13, 14, 21] | Ty1-IN interaction with Rpc40 [29] and Ty1-IN interaction with Rpc53, Rpc34, Rpc31 [30] |
| Ty2 | Ty1-copia | Saccharomyces cerevisiae | ~ 1 kb window upstream of RNA Pol III-transcribed genes [21] | |
| Ty3 | Ty3-gypsy | Saccharomyces cerevisiae | 1–4 bp upstream of tRNA TSSb [93] | Ty3-IN interaction with TFIIIB [88, 89] |
| Ty3p | Ty3-gypsy | Saccharomyces paradoxus | ~ 6 bp upstream of tRNA TSS [110] | |
| Ty4 | Ty1-copia | Saccharomyces cerevisiae | ~ 1 kb window upstream of RNA Pol III-transcribed genes [21] | |
| Tj1 | Ty3-gypsy | Schizosaccharomyces japonicus | 1–10 bp upstream of tRNA TSS [121] | |
| Beta/Tca8 | Ty3-gypsy | Candida albicans | 6-30 bp upstream of tRNA MCSc [119] | |
| Tyl3 | Ty3-gypsy | Yarrowia lipolytica | ~ 5 bp upstream of tRNA TSS [116] | |
| Ylt1 | Ty3-gypsy | Yarrowia lipolytica | ~ 5 bp upstream of tRNA TSS [117] | |
| Tyl6 | Ty3-gypsy | Yarrowia lipolytica | ~ 5 bp upstream of tRNA TSS [115] | |
| DGLT-A | Ty3-gypsy | Dictyostelium discoideum | 13–33 bp upstream of tRNA MCS [125] | |
| Skipper-2 | Ty3-gypsy | Dictyostelium discoideum | 8–23 bp downstream of tRNA gene [124, 172] | |
| Non-LTR Retrotransposons | ||||
| TRE5 | L1 | Dictyostelium discoideum | 40–54 bp upstream of tRNA MCS; 37–41 bp upstream of extrachromosomal 5S rRNA genes [125, 134, 135, 174] | TRE5 ORF1 interaction with TFIIIB [132] |
| TRE3 | L1 | Dictyostelium discoideum | 40–150 bp downstream tRNA genes [137, 175] | |
| NLTR-A | L1 | Dictyostelium purpureum | 2–6 bp upstream of tRNA MCS [124] | |
| NLTR-B | L1 | Polysphondylium pallidum | 39–64 bp upstream of tRNA MCS [124] | |
aHost that retrotransposon was first identified in
bTSS refers to the tRNA transcription start site which is ~ 10 bp upstream of the mature tRNA
cMCS refers to the tRNA mature coding sequence