Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases

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Abstract

Certain mutations affecting central metabolism cause accumulation of the oncometabolite D-2-hydroxyglutarate which promotes progression of certain tumors. High levels of D-2-hydroxyglutarate inhibit the TET family of DNA demethylases and Jumonji family of histone demethylases and cause epigenetic changes that lead to altered gene expression. The link between inhibition of DNA demethylation and changes in expression is strong in some cancers, but not in others. To determine whether D-2-hydroxyglutarate can affect gene expression through inhibiting histone demethylases, orthologous mutations to those known to cause accumulation of D-2-hydroxyglutarate in tumors were generated in Saccharomyces cerevisiae, which has histone demethylases but not DNA methylases or demethylases. Accumulation of D-2-hydroxyglutarate caused inhibition of several histone demethylases. Inhibition of two of the demethylases that act specifically on histone H3K36me2,3 led to enhanced gene silencing. These observations pinpointed a new mechanism by which this oncometabolite can alter gene expression, perhaps repressing critical inhibitors of proliferation.

DOI: http://dx.doi.org/10.7554/eLife.22451.001

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Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae.

A Goldstein, J H McCusker (1999)

Disruption-deletion cassettes are powerful tools used to study gene function in many organisms, including Saccharomyces cerevisiae. Perhaps the most widely useful of these are the heterologous dominant drug resistance cassettes, which use antibiotic resistance genes from bacteria and fungi as selectable markers. We have created three new dominant drug resistance cassettes by replacing the kanamycin resistance (kan(r)) open reading frame from the kanMX3 and kanMX4 disruption-deletion cassettes (Wach et al., 1994) with open reading frames conferring resistance to the antibiotics hygromycin B (hph), nourseothricin (nat) and bialaphos (pat). The new cassettes, pAG25 (natMX4), pAG29 (patMX4), pAG31 (patMX3), pAG32 (hphMX4), pAG34 (hphMX3) and pAG35 (natMX3), are cloned into pFA6, and so are in all other respects identical to pFA6-kanMX3 and pFA6-kanMX4. Most tools and techniques used with the kanMX plasmids can also be used with the hph, nat and patMX containing plasmids. These new heterologous dominant drug resistance cassettes have unique antibiotic resistance phenotypes and do not affect growth when inserted into the ho locus. These attributes make the cassettes ideally suited for creating S. cerevisiae strains with multiple mutations within a single strain. Copyright 1999 John Wiley & Sons, Ltd.

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New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae.

A Wach, A Brachat, R. Pohlmann … (1994)

We have constructed and tested a dominant resistance module, for selection of S. cerevisiae transformants, which entirely consists of heterologous DNA. This kanMX module contains the known kanr open reading-frame of the E. coli transposon Tn903 fused to transcriptional and translational control sequences of the TEF gene of the filamentous fungus Ashbya gossypii. This hybrid module permits efficient selection of transformants resistant against geneticin (G418). We also constructed a lacZMT reporter module in which the open reading-frame of the E. coli lacZ gene (lacking the first 9 codons) is fused at its 3' end to the S. cerevisiae ADH1 terminator. KanMX and the lacZMT module, or both modules together, were cloned in the center of a new multiple cloning sequence comprising 18 unique restriction sites flanked by Not I sites. Using the double module for constructions of in-frame substitutions of genes, only one transformation experiment is necessary to test the activity of the promotor and to search for phenotypes due to inactivation of this gene. To allow for repeated use of the G418 selection some kanMX modules are flanked by 470 bp direct repeats, promoting in vivo excision with frequencies of 10(-3)-10(-4). The 1.4 kb kanMX module was also shown to be very useful for PCR based gene disruptions. In an experiment in which a gene disruption was done with DNA molecules carrying PCR-added terminal sequences of only 35 bases homology to each target site, all twelve tested geneticin-resistant colonies carried the correctly integrated kanMX module.

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A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast.

U Gueldener (2002)

Heterologous markers are important tools required for the molecular dissection of gene function in many organisms, including Saccharomyces cerevisiae. Moreover, the presence of gene families and isoenzymes often makes it necessary to delete more than one gene. We recently introduced a new and efficient gene disruption cassette for repeated use in budding yeast, which combines the heterologous dominant kan(r) resistance marker with a Cre/loxP-mediated marker removal procedure. Here we describe an additional set of four completely heterologous loxP-flanked marker cassettes carrying the genes URA3 and LEU2 from Kluyveromyces lactis, his5(+) from Schizosaccharomyces pombe and the dominant resistance marker ble(r) from the bacterial transposon Tn5, which confers resistance to the antibiotic phleomycin. All five loxP--marker gene--loxP gene disruption cassettes can be generated using the same pair of oligonucleotides and all can be used for gene disruption with high efficiency. For marker rescue we have created three additional Cre expression vectors carrying HIS3, TRP1 or ble(r) as the yeast selection marker. The set of disruption cassettes and Cre expression plasmids described here represents a significant further development of the marker rescue system, which is ideally suited to functional analysis of the yeast genome.

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Alan G Hinnebusch: Role: Reviewing editor

Journal

Journal ID (nlm-ta): eLife

Journal ID (iso-abbrev): Elife

Journal ID (hwp): eLife

Journal ID (publisher-id): eLife

Title: eLife

Publisher: eLife Sciences Publications, Ltd

ISSN (Electronic): 2050-084X

Publication date (Electronic, pub): 27 March 2017

Publication date Collection: 2017

Volume: 6

Electronic Location Identifier: e22451

Affiliations

[1 ]deptDepartment of Molecular and Cell Biology , University of California, Berkeley , Berkeley, United States

[2 ]deptCalifornia Institute for Quantitative Biosciences , University of California, Berkeley , Berkeley, United States

National Institutes of Health , United States

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jrine@ 123456berkeley.edu

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Ryan Janke http://orcid.org/0000-0002-5755-8019

Jasper Rine http://orcid.org/0000-0003-2297-9814

Article

Publisher ID: 22451

DOI: 10.7554/eLife.22451

PMC ID: 5388528

PubMed ID: 28346139

SO-VID: dcc93284-86a7-4d47-b7b8-fd5a732eeeb7

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

History

Date received : 08 December 2016

Date accepted : 17 March 2017

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;

Award ID: F32 Postdoctoral Fellowship, GM115074

Award Recipient : Ryan Janke

Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;

Award ID: 1S10OD020062-01

Award Recipient : Anthony Iavarone

Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;

Award ID: GM31105

Award Recipient : Jasper Rine

Funded by: FundRef http://dx.doi.org/10.13039/100000002, National Institutes of Health;

Award ID: GM120374

Award Recipient : Jasper Rine

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

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Author impact statement Mutations in budding yeast modeled after cancer-associated isocitrate dehydrogenase mutations lead to stabilization of heterochromatin and enhanced gene silencing through inhibition of specific histone demethylases by the oncometabolite D-2-hydroxyglutarate.

ScienceOpen disciplines: Life sciences

Keywords: heterochromatin,d-2-hydroxyglutarate,isocitrate dehydrogenase,oncometabolite,s. cerevisiae

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ScienceOpen disciplines: Life sciences

Keywords: heterochromatin, d-2-hydroxyglutarate, isocitrate dehydrogenase, oncometabolite, s. cerevisiae

Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases

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Most cited references 26

Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae.

New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae.

A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast.

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