1. Chromosomes and Gene Expression

Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1

  1. Hanneke Vlaming
  2. Thom M Molenaar
  3. Tibor van Welsem
  4. Deepani W Poramba-Liyanage
  5. Desiree E Smith
  6. Arno Velds
  7. Liesbeth Hoekman
  8. Tessy Korthout
  9. Sjoerd Hendriks
  10. AF Maarten Altelaar
  11. Fred van Leeuwen  Is a corresponding author
  1. Netherlands Cancer Institute, Netherlands
  2. VU University Medical Center, Netherlands
https://doi.org/10.7554/eLife.18919
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Cite this article
  1. Hanneke Vlaming
  2. Thom M Molenaar
  3. Tibor van Welsem
  4. Deepani W Poramba-Liyanage
  5. Desiree E Smith
  6. Arno Velds
  7. Liesbeth Hoekman
  8. Tessy Korthout
  9. Sjoerd Hendriks
  10. AF Maarten Altelaar
  11. Fred van Leeuwen
(2016)
Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1
eLife 5:e18919.
https://doi.org/10.7554/eLife.18919
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Abstract

Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel. Screening of a barcoded yeast knock-out collection for regulators of histone H3K79 methylation by Dot1 identified all known regulators as well as novel players and processes. These include histone deposition, homologous recombination, and adenosine kinase, which influences the methionine cycle. Gcn5, the acetyltransferase within the SAGA complex, was found to regulate histone methylation and H2B ubiquitination. The concept of Epi-ID is widely applicable and can be readily applied to other chromatin features.

Article and author information

Author details

  1. Hanneke Vlaming

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1743-6428

  2. Thom M Molenaar

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  3. Tibor van Welsem

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  4. Deepani W Poramba-Liyanage

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  5. Desiree E Smith

    Department of Clinical Chemistry, Metabolic Laboratory, VU University Medical Center, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  6. Arno Velds

    Central Genomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  7. Liesbeth Hoekman

    Mass Spectrometry/Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  8. Tessy Korthout

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  9. Sjoerd Hendriks

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  10. AF Maarten Altelaar

    Mass Spectrometry/Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
    Competing interests
    No competing interests declared.

  11. Fred van Leeuwen

    Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
    For correspondence
    fred.v.leeuwen@nki.nl
    Competing interests
    Fred van Leeuwen, The Netherlands Cancer Institute and FvL are entitled to royalties that may result from licensing the yeast H2BK123ub-specific monocloncal antibody according to IP policies of the Netherlands Cancer Institute..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7267-7251

Funding

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO-VICI-016.130.627)

  • Fred van Leeuwen

KWF Kankerbestrijding (KWF NKI2014-7232)

  • Fred van Leeuwen

KWF Kankerbestrijding (KWF NKI2009-4511)

  • Fred van Leeuwen

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO-VIDI 723.012.102)

  • AF Maarten Altelaar

National Roadmap Large-scale Research Facilities of The Netherlands (184.032.201)

  • Liesbeth Hoekman
  • AF Maarten Altelaar

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NCI-KIEM-731.013.102)

  • Fred van Leeuwen

Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NCI-LIFT-731.015.405)

  • Fred van Leeuwen

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

Copyright

© 2016, Vlaming 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. Hanneke Vlaming
  2. Thom M Molenaar
  3. Tibor van Welsem
  4. Deepani W Poramba-Liyanage
  5. Desiree E Smith
  6. Arno Velds
  7. Liesbeth Hoekman
  8. Tessy Korthout
  9. Sjoerd Hendriks
  10. AF Maarten Altelaar
  11. Fred van Leeuwen
(2016)
Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1
eLife 5:e18919.
https://doi.org/10.7554/eLife.18919

Share this article

https://doi.org/10.7554/eLife.18919

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