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Groth B, Huang CC, Lin SJ. The histone deacetylases Rpd3 and Hst1 antagonistically regulate de novo NAD + metabolism in the budding yeast Saccharomyces cerevisiae. J Biol Chem 2022; 298:102410. [PMID: 36007612 PMCID: PMC9486569 DOI: 10.1016/j.jbc.2022.102410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/05/2022] Open
Abstract
NAD+ is a cellular redox cofactor involved in many essential processes. The regulation of NAD+ metabolism and the signaling networks reciprocally interacting with NAD+-producing metabolic pathways are not yet fully understood. The NAD+-dependent histone deacetylase (HDAC) Hst1 has been shown to inhibit de novo NAD+ synthesis by repressing biosynthesis of nicotinic acid (BNA) gene expression. Here, we alternatively identify HDAC Rpd3 as a positive regulator of de novo NAD+ metabolism in the budding yeast Saccharomyces cerevisiae. We reveal that deletion of RPD3 causes marked decreases in the production of de novo pathway metabolites, in direct contrast to deletion of HST1. We determined the BNA expression profiles of rpd3Δ and hst1Δ cells to be similarly opposed, suggesting the two HDACs may regulate the BNA genes in an antagonistic fashion. Our chromatin immunoprecipitation analysis revealed that Rpd3 and Hst1 mutually influence each other’s binding distribution at the BNA2 promoter. We demonstrate Hst1 to be the main deacetylase active at the BNA2 promoter, with hst1Δ cells displaying increased acetylation of the N-terminal tail lysine residues of histone H4, H4K5, and H4K12. Conversely, we show that deletion of RPD3 reduces the acetylation of these residues in an Hst1-dependent manner. This suggests that Rpd3 may function to oppose spreading of Hst1-dependent heterochromatin and represents a unique form of antagonism between HDACs in regulating gene expression. Moreover, we found that Rpd3 and Hst1 also coregulate additional targets involved in other branches of NAD+ metabolism. These findings help elucidate the complex interconnections involved in effecting the regulation of NAD+ metabolism.
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Affiliation(s)
- Benjamin Groth
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Chi-Chun Huang
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA
| | - Su-Ju Lin
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, California, USA.
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2
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Jethmalani Y, Tran K, Negesse MY, Sun W, Ramos M, Jaiswal D, Jezek M, Amos S, Garcia EJ, Park D, Green EM. Set4 regulates stress response genes and coordinates histone deacetylases within yeast subtelomeres. Life Sci Alliance 2021; 4:e202101126. [PMID: 34625508 PMCID: PMC8507492 DOI: 10.26508/lsa.202101126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
The yeast chromatin protein Set4 is a member of the Set3-subfamily of SET domain proteins which play critical roles in the regulation of gene expression in diverse developmental and environmental contexts. We previously reported that Set4 promotes survival during oxidative stress and regulates expression of stress response genes via stress-dependent chromatin localization. In this study, global gene expression analysis and investigation of histone modification status identified a role for Set4 in maintaining gene repressive mechanisms within yeast subtelomeres under both normal and stress conditions. We show that Set4 works in a partially overlapping pathway to the SIR complex and the histone deacetylase Rpd3 to maintain proper levels of histone acetylation and expression of stress response genes encoded in subtelomeres. This role for Set4 is particularly critical for cells under hypoxic conditions, where the loss of Set4 decreases cell fitness and cell wall integrity. These findings uncover a new regulator of subtelomeric chromatin that is key to stress defense pathways and demonstrate a function for Set4 in regulating repressive, heterochromatin-like environments.
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Affiliation(s)
- Yogita Jethmalani
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Khoa Tran
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Maraki Y Negesse
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Winny Sun
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Mark Ramos
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Deepika Jaiswal
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Shandon Amos
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Eric Joshua Garcia
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
| | - DoHwan Park
- Department of Mathematics and Statistics, University of Maryland Baltimore County, Baltimore, MD, USA
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, USA
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3
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Kleinschmidt RA, Lyon LM, Smith SL, Rittenberry J, Lawless KM, Acosta AA, Donze D. Genetic screen for suppressors of increased silencing in rpd3 mutants in Saccharomyces cerevisiae identifies a potential role for H3K4 methylation. G3 GENES|GENOMES|GENETICS 2021; 11:6371869. [PMID: 34534290 PMCID: PMC8527511 DOI: 10.1093/g3journal/jkab309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022]
Abstract
Several studies have identified the paradoxical phenotype of increased heterochromatic gene silencing at specific loci that results from deletion or mutation of the histone deacetylase (HDAC) gene RPD3. To further understand this phenomenon, we conducted a genetic screen for suppressors of this extended silencing phenotype at the HMR locus in Saccharomyces cerevisiae. Most of the mutations that suppressed extended HMR silencing in rpd3 mutants without completely abolishing silencing were identified in the histone H3 lysine 4 methylation (H3K4me) pathway, specifically in SET1, BRE1, and BRE2. These second-site mutations retained normal HMR silencing, therefore, appear to be specific for the rpd3Δ extended silencing phenotype. As an initial assessment of the role of H3K4 methylation in extended silencing, we rule out some of the known mechanisms of Set1p/H3K4me mediated gene repression by HST1, HOS2, and HST3 encoded HDACs. Interestingly, we demonstrate that the RNA Polymerase III complex remains bound and active at the HMR-tDNA in rpd3 mutants despite silencing extending beyond the normal barrier. We discuss these results as they relate to the interplay among different chromatin-modifying enzyme functions and the importance of further study of this enigmatic phenomenon.
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Affiliation(s)
| | - Laurie M Lyon
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Samantha L Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jonah Rittenberry
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - K Maeve Lawless
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Anabelle A Acosta
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - David Donze
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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4
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Acetyl-CoA Metabolism and Histone Acetylation in the Regulation of Aging and Lifespan. Antioxidants (Basel) 2021; 10:antiox10040572. [PMID: 33917812 PMCID: PMC8068152 DOI: 10.3390/antiox10040572] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/16/2022] Open
Abstract
Acetyl-CoA is a metabolite at the crossroads of central metabolism and the substrate of histone acetyltransferases regulating gene expression. In many tissues fasting or lifespan extending calorie restriction (CR) decreases glucose-derived metabolic flux through ATP-citrate lyase (ACLY) to reduce cytoplasmic acetyl-CoA levels to decrease activity of the p300 histone acetyltransferase (HAT) stimulating pro-longevity autophagy. Because of this, compounds that decrease cytoplasmic acetyl-CoA have been described as CR mimetics. But few authors have highlighted the potential longevity promoting roles of nuclear acetyl-CoA. For example, increasing nuclear acetyl-CoA levels increases histone acetylation and administration of class I histone deacetylase (HDAC) inhibitors increases longevity through increased histone acetylation. Therefore, increased nuclear acetyl-CoA likely plays an important role in promoting longevity. Although cytoplasmic acetyl-CoA synthetase 2 (ACSS2) promotes aging by decreasing autophagy in some peripheral tissues, increased glial AMPK activity or neuronal differentiation can stimulate ACSS2 nuclear translocation and chromatin association. ACSS2 nuclear translocation can result in increased activity of CREB binding protein (CBP), p300/CBP-associated factor (PCAF), and other HATs to increase histone acetylation on the promoter of neuroprotective genes including transcription factor EB (TFEB) target genes resulting in increased lysosomal biogenesis and autophagy. Much of what is known regarding acetyl-CoA metabolism and aging has come from pioneering studies with yeast, fruit flies, and nematodes. These studies have identified evolutionary conserved roles for histone acetylation in promoting longevity. Future studies should focus on the role of nuclear acetyl-CoA and histone acetylation in the control of hypothalamic inflammation, an important driver of organismal aging.
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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Abstract
The budding yeast, Saccharomyces cerevisiae, has been widely used for genetic studies of fundamental cellular functions. The isolation and analysis of yeast mutants is a commonly used and powerful technique to identify the genes that are involved in a process of interest. Furthermore, natural genetic variation among wild yeast strains has been studied for analysis of polygenic traits by quantitative trait loci mapping. Whole-genome sequencing, often combined with bulk segregant analysis, is a powerful technique that helps determine the identity of mutations causing a phenotype. Here, we describe protocols for the construction of libraries for S. cerevisiae whole-genome sequencing. We also present a bioinformatic pipeline to determine the genetic variants in a yeast strain using whole-genome sequencing data. This pipeline can also be used for analyzing Schizosaccharomyces pombe mutants. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of haploid spores for bulk segregant analysis Basic Protocol 2: Extraction of genomic DNA from yeast cells Basic Protocol 3: Shearing of genomic DNA for library preparation Basic Protocol 4: Construction and amplification of DNA libraries Support Protocol 1: Annealing oligonucleotides for forming Y-adapters Support Protocol 2: Size selection and cleanup using SPRI beads Basic Protocol 5: Identification of genomic variants from sequencing data.
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Affiliation(s)
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
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Chakraborty U, Mackenroth B, Shalloway D, Alani E. Chromatin Modifiers Alter Recombination Between Divergent DNA Sequences. Genetics 2019; 212:1147-1162. [PMID: 31221666 PMCID: PMC6707472 DOI: 10.1534/genetics.119.302395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Recombination between divergent DNA sequences is actively prevented by heteroduplex rejection mechanisms. In baker's yeast, such antirecombination mechanisms can be initiated by the recognition of DNA mismatches in heteroduplex DNA by MSH proteins, followed by recruitment of the Sgs1-Top3-Rmi1 helicase-topoisomerase complex to unwind the recombination intermediate. We previously showed that the repair/rejection decision during single-strand annealing recombination is temporally regulated by MSH (MutShomolog) protein levels and by factors that excise nonhomologous single-stranded tails. These observations, coupled with recent studies indicating that mismatch repair (MMR) factors interact with components of the histone chaperone machinery, encouraged us to explore roles for epigenetic factors and chromatin conformation in regulating the decision to reject vs. repair recombination between divergent DNA substrates. This work involved the use of an inverted repeat recombination assay thought to measure sister chromatid repair during DNA replication. Our observations are consistent with the histone chaperones CAF-1 and Rtt106, and the histone deacetylase Sir2, acting to suppress heteroduplex rejection and the Rpd3, Hst3, and Hst4 deacetylases acting to promote heteroduplex rejection. These observations, and double-mutant analysis, have led to a model in which nucleosomes located at DNA lesions stabilize recombination intermediates and compete with MMR factors that mediate heteroduplex rejection.
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Affiliation(s)
- Ujani Chakraborty
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Beata Mackenroth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
| | - Eric Alani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703
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Vlaming H, McLean CM, Korthout T, Alemdehy MF, Hendriks S, Lancini C, Palit S, Klarenbeek S, Kwesi‐Maliepaard EM, Molenaar TM, Hoekman L, Schmidlin TT, Altelaar AFM, van Welsem T, Dannenberg J, Jacobs H, van Leeuwen F. Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. EMBO J 2019; 38:e101564. [PMID: 31304633 PMCID: PMC6627229 DOI: 10.15252/embj.2019101564] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
DOT1L methylates histone H3K79 and is aberrantly regulated in MLL-rearranged leukemia. Inhibitors have been developed to target DOT1L activity in leukemia, but cellular mechanisms that regulate DOT1L are still poorly understood. We have identified the histone deacetylase Rpd3 as a negative regulator of budding yeast Dot1. At its target genes, the transcriptional repressor Rpd3 restricts H3K79 methylation, explaining the absence of H3K79me3 at a subset of genes in the yeast genome. Similar to the crosstalk in yeast, inactivation of the murine Rpd3 homolog HDAC1 in thymocytes led to an increase in H3K79 methylation. Thymic lymphomas that arise upon genetic deletion of Hdac1 retained the increased H3K79 methylation and were sensitive to reduced DOT1L dosage. Furthermore, cell lines derived from Hdac1Δ/Δ thymic lymphomas were sensitive to a DOT1L inhibitor, which induced apoptosis. In summary, we identified an evolutionarily conserved crosstalk between HDAC1 and DOT1L with impact in murine thymic lymphoma development.
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Affiliation(s)
- Hanneke Vlaming
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMAUSA
| | - Chelsea M McLean
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tessy Korthout
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mir Farshid Alemdehy
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Hendriks
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Cesare Lancini
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sander Palit
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Thom M Molenaar
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Thierry T Schmidlin
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
- Proteomics FacilityNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tibor van Welsem
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jan‐Hermen Dannenberg
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Genmab B.V.Antibody SciencesUtrechtThe Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Fred van Leeuwen
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
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McCullough LL, Pham TH, Parnell TJ, Connell Z, Chandrasekharan MB, Stillman DJ, Formosa T. Establishment and Maintenance of Chromatin Architecture Are Promoted Independently of Transcription by the Histone Chaperone FACT and H3-K56 Acetylation in Saccharomyces cerevisiae. Genetics 2019; 211:877-892. [PMID: 30679261 PMCID: PMC6404263 DOI: 10.1534/genetics.118.301853] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/14/2019] [Indexed: 12/16/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription/Transactions) is a histone chaperone that can destabilize or assemble nucleosomes. Acetylation of histone H3-K56 weakens a histone-DNA contact that is central to FACT activity, suggesting that this modification could affect FACT functions. We tested this by asking how mutations of H3-K56 and FACT affect nucleosome reorganization activity in vitro, and chromatin integrity and transcript output in vivo Mimics of unacetylated or permanently acetylated H3-K56 had different effects on FACT activity as expected, but the same mutations had surprisingly similar effects on global transcript levels. The results are consistent with emerging models that emphasize FACT's importance in establishing global chromatin architecture prior to transcription, promoting transitions among different states as transcription profiles change, and restoring chromatin integrity after it is disturbed. Optimal FACT activity required the availability of both modified and unmodified states of H3-K56. Perturbing this balance was especially detrimental for maintaining repression of genes with high nucleosome occupancy over their promoters and for blocking antisense transcription at the +1 nucleosome. The results reveal a complex collaboration between H3-K56 modification status and multiple FACT functions, and support roles for nucleosome reorganization by FACT before, during, and after transcription.
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Affiliation(s)
- Laura L McCullough
- Department of Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Trang H Pham
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Timothy J Parnell
- Department of Oncological Sciences, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Zaily Connell
- Department of Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
| | - Tim Formosa
- Department of Biochemistry, University of Utah Health Sciences Center, Salt Lake City, Utah 84112
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Janke R, Iavarone AT, Rine J. Oncometabolite D-2-Hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases. eLife 2017; 6. [PMID: 28346139 PMCID: PMC5388528 DOI: 10.7554/elife.22451] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/17/2017] [Indexed: 11/24/2022] Open
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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Affiliation(s)
- Ryan Janke
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
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Schlissel G, Krzyzanowski MK, Caudron F, Barral Y, Rine J. Aggregation of the Whi3 protein, not loss of heterochromatin, causes sterility in old yeast cells. Science 2017; 355:1184-1187. [PMID: 28302853 DOI: 10.1126/science.aaj2103] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/25/2017] [Indexed: 12/21/2022]
Abstract
In yeast, heterochromatin silencing is reported to decline in aging mother cells, causing sterility in old cells. This process is thought to reflect a decrease in the activity of the NAD+ (oxidized nicotinamide adenine dinucleotide)-dependent deacetylase Sir2. We tested whether Sir2 becomes nonfunctional gradually or precipitously during aging. Unexpectedly, silencing of the heterochromatic HML and HMR loci was not lost during aging. Old cells could initiate a mating response; however, they were less sensitive to mating pheromone than were young cells because of age-dependent aggregation of Whi3, an RNA-binding protein controlling S-phase entry. Removing the polyglutamine domain of Whi3 restored the pheromone sensitivity of old cells. We propose that aging phenotypes previously attributed to loss of heterochromatin silencing are instead caused by aggregation of the Whi3 cell cycle regulator.
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Affiliation(s)
- Gavin Schlissel
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | | | - Fabrice Caudron
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,King's College London, London, UK
| | - Yves Barral
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
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