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Pol θ-mediated end-joining uses microhomologies containing mismatches

Author

Listed:
  • Yuzhen Li

    (MD Anderson Cancer Center)

  • Ngoc K. Dang

    (MD Anderson Cancer Center)

  • Wei He

    (MD Anderson Cancer Center)

  • Mark Returan

    (MD Anderson Cancer Center)

  • Denisse Carvajal-Maldonado

    (MD Anderson Cancer Center)

  • Adele T. Guerin

    (MD Anderson Cancer Center)

  • Han Xu

    (MD Anderson Cancer Center)

  • Bin Liu

    (MD Anderson Cancer Center)

  • Richard D. Wood

    (MD Anderson Cancer Center)

Abstract

DNA polymerase theta (Pol θ) initiates repair of DNA double-strand breaks by pairing single strands at short “microhomologies”. It is important to understand microhomology selection, as some cancer cells rely on Pol θ for survival. Here, we investigate end-joining by purified human Pol θ, employing DNA sequencing of products generated from oligonucleotide libraries having diverse 3′ ends. Pol θ overwhelmingly selects short internal microhomologies found within 15 nucleotides of the terminus of single-stranded DNAs, restricting deletion size during end-joining. Significantly, we find that the selected microhomologies are usually interrupted by mismatches and that base pairing within 6 nucleotides of the 3′ end is important for determining microhomology choice. Bidirectional synthesis is not necessary to initiate end-joining. The preference for mismatched microhomologies suggests a revision of the definition of microhomology to account for the unique properties of Pol θ. This could advance the analysis of mutations in cancer genomes.

Suggested Citation

  • Yuzhen Li & Ngoc K. Dang & Wei He & Mark Returan & Denisse Carvajal-Maldonado & Adele T. Guerin & Han Xu & Bin Liu & Richard D. Wood, 2025. "Pol θ-mediated end-joining uses microhomologies containing mismatches," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61258-3
    DOI: 10.1038/s41467-025-61258-3
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    1. Ludmil B. Alexandrov & Jaegil Kim & Nicholas J. Haradhvala & Mi Ni Huang & Alvin Wei Tian Ng & Yang Wu & Arnoud Boot & Kyle R. Covington & Dmitry A. Gordenin & Erik N. Bergstrom & S. M. Ashiqul Islam , 2020. "The repertoire of mutational signatures in human cancer," Nature, Nature, vol. 578(7793), pages 94-101, February.
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    3. Pedro A. Mateos-Gomez & Fade Gong & Nidhi Nair & Kyle M. Miller & Eros Lazzerini-Denchi & Agnel Sfeir, 2015. "Mammalian polymerase θ promotes alternative NHEJ and suppresses recombination," Nature, Nature, vol. 518(7538), pages 254-257, February.
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