A programmable seekRNA guides target selection by IS1111 and IS110 type insertion sequences

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 find 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 are used to demonstrate that the NCR determines a short seeker RNA (seekRNA) that co-purified with the transposase. The seekRNA is 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 are present in the seekRNA but their order in IS 1111 and IS 110 family IS is reversed. Reprogramming the seekRNA and donor flank to target a different site is demonstrated, indicating future biotechnological potential for these systems. Here the authors show that a seekRNA derived from the non-coding region of IS 1111 and IS family insertion sequences is required for insertion sequence movement from and to a specific target site. The seekRNA is bound to the transposase, recognises the target and is programmable.