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Novel genetic tools for probing individual H3 molecules in each nucleosome

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Abstract

In eukaryotes, genomic DNA is packaged into the nucleus together with histone proteins, forming chromatin. The fundamental repeating unit of chromatin is the nucleosome, a naturally symmetric structure that wraps DNA and is the substrate for numerous regulatory post-translational modifications. However, the biological significance of nucleosomal symmetry until recently had been unexplored. To investigate this issue, we developed an obligate pair of histone H3 heterodimers, a novel genetic tool that allowed us to modulate modification sites on individual H3 molecules within nucleosomes in vivo. We used these constructs for molecular genetic studies, for example demonstrating that H3K36 methylation on a single H3 molecule per nucleosome in vivo is sufficient to restrain cryptic transcription. We also used asymmetric nucleosomes for mass spectrometric analysis of dependency relationships among histone modifications. Furthermore, we extended this system to the centromeric H3 isoform (Cse4/CENP-A), gaining insights into centromeric nucleosomal symmetry and structure. In this review, we summarize our findings and discuss the utility of this novel approach.

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Acknowledgements

This work was supported by NIH grants R01GM100164 (PDK and Oliver J. Rando) and R35GM127035 (PDK).

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Authors and Affiliations

  1. Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA

    Paul D. Kaufman

  2. Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan

    Yuichi Ichikawa

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  1. Yuichi Ichikawa
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  2. Paul D. Kaufman
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Correspondence to Paul D. Kaufman.

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Communicated by M. Kupiec.

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Ichikawa, Y., Kaufman, P.D. Novel genetic tools for probing individual H3 molecules in each nucleosome. Curr Genet 65, 371–377 (2019). https://doi.org/10.1007/s00294-018-0910-0

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