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De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens

Author

Listed:
  • Wei He

    (The University of Texas MD Anderson Cancer Center)

  • Liang Zhang

    (The University of Texas MD Anderson Cancer Center)

  • Oscar D. Villarreal

    (The University of Texas MD Anderson Cancer Center)

  • Rongjie Fu

    (The University of Texas MD Anderson Cancer Center)

  • Ella Bedford

    (The University of Texas MD Anderson Cancer Center)

  • Jingzhuang Dou

    (The University of Texas MD Anderson Cancer Center)

  • Anish Y. Patel

    (The University of Texas MD Anderson Cancer Center)

  • Mark T. Bedford

    (The University of Texas MD Anderson Cancer Center
    The University of Texas MD Anderson Cancer Center)

  • Xiaobing Shi

    (Van Andel Research Institute)

  • Taiping Chen

    (The University of Texas MD Anderson Cancer Center
    The University of Texas MD Anderson Cancer Center)

  • Blaine Bartholomew

    (The University of Texas MD Anderson Cancer Center
    The University of Texas MD Anderson Cancer Center)

  • Han Xu

    (The University of Texas MD Anderson Cancer Center
    The University of Texas MD Anderson Cancer Center
    The University of Texas MD Anderson Cancer Center)

Abstract

High-throughput CRISPR-Cas9 knockout screens using a tiling-sgRNA design permit in situ evaluation of protein domain function. Here, to facilitate de novo identification of essential protein domains from such screens, we propose ProTiler, a computational method for the robust mapping of CRISPR knockout hyper-sensitive (CKHS) regions, which refer to the protein regions associated with a strong sgRNA dropout effect in the screens. Applied to a published CRISPR tiling screen dataset, ProTiler identifies 175 CKHS regions in 83 proteins. Of these CKHS regions, more than 80% overlap with annotated Pfam domains, including all of the 15 known drug targets in the dataset. ProTiler also reveals unannotated essential domains, including the N-terminus of the SWI/SNF subunit SMARCB1, which is validated experimentally. Surprisingly, the CKHS regions are negatively correlated with phosphorylation and acetylation sites, suggesting that protein domains and post-translational modification sites have distinct sensitivities to CRISPR-Cas9 mediated amino acids loss.

Suggested Citation

  • Wei He & Liang Zhang & Oscar D. Villarreal & Rongjie Fu & Ella Bedford & Jingzhuang Dou & Anish Y. Patel & Mark T. Bedford & Xiaobing Shi & Taiping Chen & Blaine Bartholomew & Han Xu, 2019. "De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12489-8
    DOI: 10.1038/s41467-019-12489-8
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    Cited by:

    1. Luke Hoberecht & Pirunthan Perampalam & Aaron Lun & Jean-Philippe Fortin, 2022. "A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies," Nature Communications, Nature, vol. 13(1), pages 1-20, December.

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