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

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  • Rezwan Siddiquee

    (The University of Sydney)

  • Carol H. Pong

    (The University of Sydney)

  • Ruth M. Hall

    (The University of Sydney)

  • Sandro F. Ataide

    (The University of Sydney)

Abstract

IS1111 and IS110 insertion sequence (IS) family members encode an unusual DEDD transposase type and exhibit specific target site selection. The IS1111 group include identifiable subterminal inverted repeats (sTIR) not found in the IS110 type1. 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 selection2. Here, we find that the NCR is usually downstream of the transposase gene in IS1111 family IS and upstream in the IS110 type. Four IS1111 and one IS110 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 IS1111 and IS110 family IS is reversed. Reprogramming the seekRNA and donor flank to target a different site is demonstrated, indicating future biotechnological potential for these systems.

Suggested Citation

  • Rezwan Siddiquee & Carol H. Pong & Ruth M. Hall & Sandro F. Ataide, 2024. "A programmable seekRNA guides target selection by IS1111 and IS110 type insertion sequences," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49474-9
    DOI: 10.1038/s41467-024-49474-9
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    1. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
    2. Tautvydas Karvelis & Gytis Druteika & Greta Bigelyte & Karolina Budre & Rimante Zedaveinyte & Arunas Silanskas & Darius Kazlauskas & Česlovas Venclovas & Virginijus Siksnys, 2021. "Transposon-associated TnpB is a programmable RNA-guided DNA endonuclease," Nature, Nature, vol. 599(7886), pages 692-696, November.
    3. Kengo Sato & Manato Akiyama & Yasubumi Sakakibara, 2021. "RNA secondary structure prediction using deep learning with thermodynamic integration," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    4. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
    5. Irma Querques & Michael Schmitz & Seraina Oberli & Christelle Chanez & Martin Jinek, 2021. "Target site selection and remodelling by type V CRISPR-transposon systems," Nature, Nature, vol. 599(7885), pages 497-502, November.
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