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Multiplexed bioluminescence-mediated tracking of DNA double-strand break repairs in vitro and in vivo

Nature Protocols volume 16, pages 3933–3953 (2021)Cite this article

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Abstract

The dynamics of DNA double-strand break (DSB) repairs including homology-directed repair and nonhomologous end joining play an important role in diseases and therapies. However, investigating DSB repair is typically a low-throughput and cross-sectional process, requiring disruption of cells and organisms for subsequent nuclease-, sequencing- or reporter-based assays. In this protocol, we provide instructions for establishing a bioluminescent repair reporter system using engineered Gaussia and Vargula luciferases for noninvasive tracking of homology-directed repair and nonhomologous end joining, respectively, induced by SceI meganuclease, SpCas9 or SpCas9 D10A nickase-mediated editing. We also describe complementation with orthogonal DSB repair assays and omics analyses to validate the reporter readouts. The bioluminescent repair reporter system provides longitudinal and rapid readout (~seconds per sample) to accurately and efficiently measure the efficacy of genome-editing tools and small-molecule modulators on DSB repair. This protocol takes ~2–4 weeks to establish, and as little as 2 h to complete the assay. The entire bioluminescent repair reporter procedure can be performed by one person with standard molecular biology expertise and equipment. However, orthogonal DNA repair assays would require a specialized facility that performs Sanger sequencing or next-generation sequencing.

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Fig. 1: BLRR reporter design.
Fig. 2: Potential applications of the BLRR assay.
Fig. 3: Multiplexed applications of the BLRR assay.
Fig. 4: Overview of the BLRR assay procedure.
Fig. 5: Expected results from BLRR assays and orthogonal assays using Cas9 D10A nickase, trGluc and ssDNA as donor templates.

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Acknowledgements

We thank members of the Lai Lab and the Badr Lab for the very helpful discussions. This work was supported by the Ministry of Science and Technology (MOST) grants (104-2320-B-007-005-MY2, 106-2320-B-007-004-MY3, 109-2628-B-001-017 to C.P.-K.L.), Academia Sinica Innovative Materials and Analysis Technology Exploration (i-MATE) Program (AS-iMATE-107-33 to C.P.-K.L.), Academia Sinica Career Development Award (AS-CDA-109-M04 C.P.-K.L.), the National Institutes of Health (K22CA197053 and R01NS113822 to C.E.B.) and the American Brain Tumor Association (ABTA) Discovery Grant supported by the Uncle Kory Foundation to C.E.B.

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Author notes

  1. These authors contributed equally: Christian E. Badr, Charles P. Lai.

Authors and Affiliations

  1. Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan

    Jasper Che-Yung Chien & Charles Pin-Kuang Lai

  2. Department of Neurology, Massachusetts General Hospital, Boston, MA, USA

    Christian E. Badr

  3. Neuroscience Program, Harvard Medical School, Boston, MA, USA

    Christian E. Badr

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  1. Jasper Che-Yung Chien
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  3. Charles Pin-Kuang Lai
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Contributions

C.P.-K.L. and C.E.B. conceived and designed the study. J.C.C. conducted the in vitro experiments and developed the procedures. C.E.B developed the in vivo procedures. The manuscript was written by J.C.C., C.E.B. and C.P.-K.L. with input from all authors.

Corresponding authors

Correspondence to Christian E. Badr or Charles Pin-Kuang Lai.

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A provisional patent application on the BLRR reporter has been submitted.

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Chien, J. C. et al. Nucleic Acids Res. 48, e100 (2020): https://doi.org/10.1093/nar/gkaa669

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Chien, J.CY., Badr, C.E. & Lai, C.PK. Multiplexed bioluminescence-mediated tracking of DNA double-strand break repairs in vitro and in vivo. Nat Protoc 16, 3933–3953 (2021). https://doi.org/10.1038/s41596-021-00564-8

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