Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1
- Netherlands Cancer Institute, Netherlands
- VU University Medical Center, Netherlands
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
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.
Reviewing Editor
- Cynthia Wolberger, Johns Hopkins University, United States
Version history
- Received: June 17, 2016
- Accepted: December 2, 2016
- Accepted Manuscript published: December 6, 2016 (version 1)
- Version of Record published: December 22, 2016 (version 2)
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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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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Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
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