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The importance of DNAPKcs for blunt DNA end joining is magnified when XLF is weakened

Author

Listed:
  • Metztli Cisneros-Aguirre

    (Beckman Research Institute of the City of Hope
    Beckman Research Institute of the City of Hope)

  • Felicia Wednesday Lopezcolorado

    (Beckman Research Institute of the City of Hope)

  • Linda Jillianne Tsai

    (Beckman Research Institute of the City of Hope
    Beckman Research Institute of the City of Hope)

  • Ragini Bhargava

    (Beckman Research Institute of the City of Hope
    Beckman Research Institute of the City of Hope
    University of Pittsburgh)

  • Jeremy M. Stark

    (Beckman Research Institute of the City of Hope
    Beckman Research Institute of the City of Hope)

Abstract

Canonical non-homologous end joining (C-NHEJ) factors can assemble into a long-range (LR) complex with DNA ends relatively far apart that contains DNAPKcs, XLF, XRCC4, LIG4, and the KU heterodimer and a short-range (SR) complex lacking DNAPKcs that has the ends positioned for ligation. Since the SR complex can form de novo, the role of the LR complex (i.e., DNAPKcs) for chromosomal EJ is unclear. We have examined EJ of chromosomal blunt DNA double-strand breaks (DSBs), and found that DNAPKcs is significantly less important than XLF for such EJ. However, weakening XLF via disrupting interaction interfaces causes a marked requirement for DNAPKcs, its kinase activity, and its ABCDE-cluster autophosphorylation sites for blunt DSB EJ. In contrast, other aspects of genome maintenance are sensitive to DNAPKcs kinase inhibition in a manner that is not further enhanced by XLF loss (i.e., suppression of homology-directed repair and structural variants, and IR-resistance). We suggest that DNAPKcs is required to position a weakened XLF in an LR complex that can transition into a functional SR complex for blunt DSB EJ, but also has distinct functions for other aspects of genome maintenance.

Suggested Citation

  • Metztli Cisneros-Aguirre & Felicia Wednesday Lopezcolorado & Linda Jillianne Tsai & Ragini Bhargava & Jeremy M. Stark, 2022. "The importance of DNAPKcs for blunt DNA end joining is magnified when XLF is weakened," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31365-6
    DOI: 10.1038/s41467-022-31365-6
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    References listed on IDEAS

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    1. Barbara Corneo & Rebecca L. Wendland & Ludovic Deriano & Xiaoping Cui & Isaac A. Klein & Serre-Yu Wong & Suzzette Arnal & Abigail J. Holub & Geoffrey R. Weller & Bette A. Pancake & Sundeep Shah & Vick, 2007. "Rag mutations reveal robust alternative end joining," Nature, Nature, vol. 449(7161), pages 483-486, September.
    2. Shikang Liang & Sherine E. Thomas & Amanda K. Chaplin & Steven W. Hardwick & Dimitri Y. Chirgadze & Tom L. Blundell, 2022. "Structural insights into inhibitor regulation of the DNA repair protein DNA-PKcs," Nature, Nature, vol. 601(7894), pages 643-648, January.
    3. Ulf Grawunder & Matthias Wilm & Xiantuo Wu & Peter Kulesza & Thomas E. Wilson & Matthias Mann & Michael R. Lieber, 1997. "Activity of DNA ligase IV stimulated by complex formation with XRCC4 protein in mammalian cells," Nature, Nature, vol. 388(6641), pages 492-495, July.
    4. Bailin Zhao & Go Watanabe & Michael J. Morten & Dylan A. Reid & Eli Rothenberg & Michael R. Lieber, 2019. "The essential elements for the noncovalent association of two DNA ends during NHEJ synapsis," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    5. Siyu Chen & Linda Lee & Tasmin Naila & Susan Fishbain & Annie Wang & Alan E. Tomkinson & Susan P. Lees-Miller & Yuan He, 2021. "Structural basis of long-range to short-range synaptic transition in NHEJ," Nature, Nature, vol. 593(7858), pages 294-298, May.
    6. Zhengping Shao & Ryan A. Flynn & Jennifer L. Crowe & Yimeng Zhu & Jialiang Liang & Wenxia Jiang & Fardin Aryan & Patrick Aoude & Carolyn R. Bertozzi & Verna M. Estes & Brian J. Lee & Govind Bhagat & S, 2020. "DNA-PKcs has KU-dependent function in rRNA processing and haematopoiesis," Nature, Nature, vol. 579(7798), pages 291-296, March.
    7. Ragini Bhargava & Manbir Sandhu & Sanychen Muk & Gabriella Lee & Nagarajan Vaidehi & Jeremy M. Stark, 2018. "C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
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