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BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

Author

Listed:
  • Winston X. Yan

    (Broad Institute of MIT and Harvard
    Graduate Program in Biophysics, Harvard Medical School
    Harvard Medical School)

  • Reza Mirzazadeh

    (Science for Life Laboratory, Karolinska Institutet)

  • Silvano Garnerone

    (Science for Life Laboratory, Karolinska Institutet)

  • David Scott

    (Broad Institute of MIT and Harvard
    McGovern Institute for Brain Research, Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Martin W. Schneider

    (Broad Institute of MIT and Harvard)

  • Tomasz Kallas

    (Science for Life Laboratory, Karolinska Institutet)

  • Joaquin Custodio

    (Science for Life Laboratory, Karolinska Institutet)

  • Erik Wernersson

    (Science for Life Laboratory, Karolinska Institutet)

  • Yinqing Li

    (Broad Institute of MIT and Harvard
    McGovern Institute for Brain Research, Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Linyi Gao

    (Broad Institute of MIT and Harvard
    McGovern Institute for Brain Research, Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Yana Federova

    (Broad Institute of MIT and Harvard
    McGovern Institute for Brain Research, Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Bernd Zetsche

    (Broad Institute of MIT and Harvard
    McGovern Institute for Brain Research, Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Feng Zhang

    (Broad Institute of MIT and Harvard
    McGovern Institute for Brain Research, Massachusetts Institute of Technology
    Massachusetts Institute of Technology
    Massachusetts Institute of Technology)

  • Magda Bienko

    (Science for Life Laboratory, Karolinska Institutet)

  • Nicola Crosetto

    (Science for Life Laboratory, Karolinska Institutet)

Abstract

Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current methods are limited in versatility, sensitivity or practicality. Here we present Breaks Labeling In Situ and Sequencing (BLISS), featuring the following: (1) direct labelling of DSBs in fixed cells or tissue sections on a solid surface; (2) low-input requirement by linear amplification of tagged DSBs by in vitro transcription; (3) quantification of DSBs through unique molecular identifiers; and (4) easy scalability and multiplexing. We apply BLISS to profile endogenous and exogenous DSBs in low-input samples of cancer cells, embryonic stem cells and liver tissue. We demonstrate the sensitivity of BLISS by assessing the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, observing that Cpf1 has higher specificity than Cas9. Our results establish BLISS as a versatile, sensitive and efficient method for genome-wide DSB mapping in many applications.

Suggested Citation

  • Winston X. Yan & Reza Mirzazadeh & Silvano Garnerone & David Scott & Martin W. Schneider & Tomasz Kallas & Joaquin Custodio & Erik Wernersson & Yinqing Li & Linyi Gao & Yana Federova & Bernd Zetsche &, 2017. "BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks," Nature Communications, Nature, vol. 8(1), pages 1-9, August.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms15058
    DOI: 10.1038/ncomms15058
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    Cited by:

    1. Behrouz Eslami-Mossallam & Misha Klein & Constantijn V. D. Smagt & Koen V. D. Sanden & Stephen K. Jones & John A. Hawkins & Ilya J. Finkelstein & Martin Depken, 2022. "A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    2. Jianli Tao & Daniel E. Bauer & Roberto Chiarle, 2023. "Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Péter István Kulcsár & András Tálas & Zoltán Ligeti & Eszter Tóth & Zsófia Rakvács & Zsuzsa Bartos & Sarah Laura Krausz & Ágnes Welker & Vanessza Laura Végi & Krisztina Huszár & Ervin Welker, 2023. "A cleavage rule for selection of increased-fidelity SpCas9 variants with high efficiency and no detectable off-targets," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    4. Guanhua Xun & Zhixin Zhu & Nilmani Singh & Jingxia Lu & Piyush K. Jain & Huimin Zhao, 2024. "Harnessing noncanonical crRNA for highly efficient genome editing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Xiaoguang Pan & Kunli Qu & Hao Yuan & Xi Xiang & Christian Anthon & Liubov Pashkova & Xue Liang & Peng Han & Giulia I. Corsi & Fengping Xu & Ping Liu & Jiayan Zhong & Yan Zhou & Tao Ma & Hui Jiang & J, 2022. "Massively targeted evaluation of therapeutic CRISPR off-targets in cells," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Ye Cai & Huifen Cao & Fang Wang & Yufei Zhang & Philipp Kapranov, 2022. "Complex genomic patterns of abasic sites in mammalian DNA revealed by a high-resolution SSiNGLe-AP method," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    7. Jeonghun Kwon & Minyoung Kim & Seungmin Bae & Anna Jo & Youngho Kim & Jungjoon K. Lee, 2022. "TAPE-seq is a cell-based method for predicting genome-wide off-target effects of prime editor," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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