1. Chromosomes and Gene Expression

An asymmetric centromeric nucleosome

  1. Yuichi Ichikawa
  2. Noriko Saitoh
  3. Paul D Kaufman  Is a corresponding author
  1. University of Massachusetts Medical School, United States
  2. The Cancer Institute of JFCR, Japan
https://doi.org/10.7554/eLife.37911
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  1. Yuichi Ichikawa
  2. Noriko Saitoh
  3. Paul D Kaufman
(2018)
An asymmetric centromeric nucleosome
eLife 7:e37911.
https://doi.org/10.7554/eLife.37911
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Abstract

Nucleosomes contain two copies of each core histone, held together by a naturally symmetric, homodimeric histone H3-H3 interface. This symmetry has complicated efforts to determine the regulatory potential of this architecture. Through molecular design and in vivo selection, we recently generated obligately heterodimeric H3s, providing a powerful tool for discovery of the degree to which nucleosome symmetry regulates chromosomal functions in living cells (Ichikawa et al., 2017). We now have extended this tool to the centromeric H3 isoform (Cse4/CENP-A) in budding yeast. These studies indicate that a single Cse4 N- or C-terminal extension per pair of Cse4 molecules is sufficient for kinetochore function, and validate previous experiments indicating that an octameric centromeric nucleosome is required for viability in this organism. These data also support the generality of the H3 asymmetric interface for probing general questions in chromatin biology.

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All data generated or analysed during this study are included in the manuscript and supporting files.

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Author details

  1. Yuichi Ichikawa

    Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6773-2455

  2. Noriko Saitoh

    Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.

  3. Paul D Kaufman

    Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, United States
    For correspondence
    paul.kaufman1@umassmed.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3089-313X

Funding

National Institutes of Health (R01GM100164)

  • Paul D Kaufman

National Institutes of Health (R35GM127035)

  • Paul D Kaufman

Japan Society for the Promotion of Science (JSPS KAKENHI 18H05531)

  • Noriko Saitoh

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2018, Ichikawa et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Yuichi Ichikawa
  2. Noriko Saitoh
  3. Paul D Kaufman
(2018)
An asymmetric centromeric nucleosome
eLife 7:e37911.
https://doi.org/10.7554/eLife.37911

Share this article

https://doi.org/10.7554/eLife.37911

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Further reading

    1. Chromosomes and Gene Expression

    A synthetic biology approach to probing nucleosome symmetry

    Yuichi Ichikawa, Caitlin F Connelly ... Paul D Kaufman
    Tools and Resources Updated

    The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell.