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High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression

Author

Listed:
  • G. Veggiani

    (The Anvil Institute
    Louisiana State University)

  • R. Villaseñor

    (Ludwig-Maximilians-University
    University of Zurich)

  • G. D. Martyn

    (The Anvil Institute
    University of Waterloo)

  • J. Q. Tang

    (The Anvil Institute
    University of Waterloo)

  • M. W. Krone

    (University of North Carolina at Chapel Hill, CB 3290)

  • J. Gu

    (The Anvil Institute)

  • C. Chen

    (The Anvil Institute)

  • M. L. Waters

    (University of North Carolina at Chapel Hill, CB 3290)

  • K. H. Pearce

    (University of North Carolina at Chapel Hill)

  • T. Baubec

    (University of Zurich
    Utrecht University)

  • S. S. Sidhu

    (The Anvil Institute
    University of Waterloo)

Abstract

Histone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies on the use of antibodies, but these suffer from lot-to-lot variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and develop a general strategy for enhancing the affinity of chromodomains of the human Cbx protein family. Our strategy allows us to develop powerful probes for genome-wide binding analysis and live-cell imaging. Furthermore, we use optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.

Suggested Citation

  • G. Veggiani & R. Villaseñor & G. D. Martyn & J. Q. Tang & M. W. Krone & J. Gu & C. Chen & M. L. Waters & K. H. Pearce & T. Baubec & S. S. Sidhu, 2022. "High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34269-7
    DOI: 10.1038/s41467-022-34269-7
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    References listed on IDEAS

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    1. Cristiana Lungu & Sabine Pinter & Julian Broche & Philipp Rathert & Albert Jeltsch, 2017. "Modular fluorescence complementation sensors for live cell detection of epigenetic signals at endogenous genomic sites," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    2. Mike V. Van & Taihei Fujimori & Lacramioara Bintu, 2021. "Nanobody-mediated control of gene expression and epigenetic memory," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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