A programmable seeker RNA guides target selection by IS1111and IS110type insertion sequences

SUMMARY IS 1111 and IS 110 insertion sequence (IS) family members encode an unusual DEDD transposase type and exhibit specific target site selection. The IS 1111 group include identifiable subterminal inverted repeats (sTIR) not found in the IS 110 type [1]. IS in both families include a noncoding region (NCR) of significant length and, as each individual IS or group of closely related IS selects a different site, we had previously proposed that an NCR-derived RNA was involved in target selection [2]. Here, we found that the NCR is usually downstream of the transposase gene in IS 1111 family IS and upstream in the IS 110 type. Four IS 1111 and one IS 110 family members that target different sequences were used to demonstrate that the NCR determines a short seeker RNA (seekRNA) that co-purified with the transposase. The seekRNA was essential for transposition of the IS or a cargo flanked by IS ends from and to the preferred target. Short sequences matching both top and bottom strands of the target were identified in the seekRNA but their order in IS 1111 and IS 110 family IS was reversed. Reprogramming the seekRNA and donor flank to target a different site was demonstrated, indicating future biotechnological potential for these systems.