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Gómez de Cedrón M, Moreno Palomares R, Ramírez de Molina A. Metabolo-epigenetic interplay provides targeted nutritional interventions in chronic diseases and ageing. Front Oncol 2023; 13:1169168. [PMID: 37404756 PMCID: PMC10315663 DOI: 10.3389/fonc.2023.1169168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/24/2023] [Indexed: 07/06/2023] Open
Abstract
Epigenetic modifications are chemical modifications that affect gene expression without altering DNA sequences. In particular, epigenetic chemical modifications can occur on histone proteins -mainly acetylation, methylation-, and on DNA and RNA molecules -mainly methylation-. Additional mechanisms, such as RNA-mediated regulation of gene expression and determinants of the genomic architecture can also affect gene expression. Importantly, depending on the cellular context and environment, epigenetic processes can drive developmental programs as well as functional plasticity. However, misbalanced epigenetic regulation can result in disease, particularly in the context of metabolic diseases, cancer, and ageing. Non-communicable chronic diseases (NCCD) and ageing share common features including altered metabolism, systemic meta-inflammation, dysfunctional immune system responses, and oxidative stress, among others. In this scenario, unbalanced diets, such as high sugar and high saturated fatty acids consumption, together with sedentary habits, are risk factors implicated in the development of NCCD and premature ageing. The nutritional and metabolic status of individuals interact with epigenetics at different levels. Thus, it is crucial to understand how we can modulate epigenetic marks through both lifestyle habits and targeted clinical interventions -including fasting mimicking diets, nutraceuticals, and bioactive compounds- which will contribute to restore the metabolic homeostasis in NCCD. Here, we first describe key metabolites from cellular metabolic pathways used as substrates to "write" the epigenetic marks; and cofactors that modulate the activity of the epigenetic enzymes; then, we briefly show how metabolic and epigenetic imbalances may result in disease; and, finally, we show several examples of nutritional interventions - diet based interventions, bioactive compounds, and nutraceuticals- and exercise to counteract epigenetic alterations.
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Affiliation(s)
- Marta Gómez de Cedrón
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- Cell Metabolism Unit, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
| | - Rocío Moreno Palomares
- Molecular Oncology Group, IMDEA Food Institute, CEI UAM, CSIC, Madrid, Spain
- FORCHRONIC S.L, Avda. Industria, Madrid, Spain
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2
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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3
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Di Nisio E, Danovska S, Condemi L, Cirigliano A, Rinaldi T, Licursi V, Negri R. H3 Lysine 4 Methylation Is Required for Full Activation of Genes Involved in α-Ketoglutarate Availability in the Nucleus of Yeast Cells after Diauxic Shift. Metabolites 2023; 13:metabo13040507. [PMID: 37110165 PMCID: PMC10146420 DOI: 10.3390/metabo13040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
We show that in S. cerevisiae the metabolic diauxic shift is associated with a H3 lysine 4 tri-methylation (H3K4me3) increase which involves a significant fraction of transcriptionally induced genes which are required for the metabolic changes, suggesting a role for histone methylation in their transcriptional regulation. We show that histone H3K4me3 around the start site correlates with transcriptional induction in some of these genes. Among the methylation-induced genes are IDP2 and ODC1, which regulate the nuclear availability of α-ketoglutarate, which, as a cofactor for Jhd2 demethylase, regulates H3K4 tri-methylation. We propose that this feedback circuit could be used to regulate the nuclear α-ketoglutarate pool concentration. We also show that yeast cells adapt to the absence of Jhd2 by decreasing Set1 methylation activity.
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4
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Scott V, Dey D, Kuwik J, Hinkelman K, Waldman M, Islam K. Allele-Specific Chemical Rescue of Histone Demethylases Using Abiotic Cofactors. ACS Chem Biol 2022; 17:3321-3330. [PMID: 34496208 DOI: 10.1021/acschembio.1c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Closely related protein families evolved from common ancestral genes present a significant hurdle in developing member- and isoform-specific chemical probes, owing to their similarity in fold and function. In this piece of work, we explore an allele-specific chemical rescue strategy to activate a "dead" variant of a wildtype protein using synthetic cofactors and demonstrate its successful application to the members of the alpha-ketoglutarate (αKG)-dependent histone demethylase 4 (KDM4) family. We show that a mutation at a specific residue in the catalytic site renders the variant inactive toward the natural cosubstrate. In contrast, αKG derivatives bearing appropriate stereoelectronic features endowed the mutant with native-like demethylase activity while remaining refractory to a set of wild type dioxygenases. The orthogonal enzyme-cofactor pairs demonstrated site- and degree-specific lysine demethylation on a full-length chromosomal histone in the cellular milieu. Our work offers a strategy to modulate a specific histone demethylase by identifying and engineering a conserved phenylalanine residue, which acts as a gatekeeper in the KDM4 subfamily, to sensitize the enzyme toward a novel set of αKG derivatives. The orthogonal pairs developed herein will serve as probes to study the role of degree-specific lysine demethylation in mammalian gene expression. Furthermore, this approach to overcome active site degeneracy is expected to have general application among all human αKG-dependent dioxygenases.
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Affiliation(s)
- Valerie Scott
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Debasis Dey
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Jordan Kuwik
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kathryn Hinkelman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Megan Waldman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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5
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LSD1 is required for euchromatic origin firing and replication timing. Signal Transduct Target Ther 2022; 7:102. [PMID: 35414135 PMCID: PMC9005705 DOI: 10.1038/s41392-022-00927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/31/2022] [Accepted: 02/13/2022] [Indexed: 11/08/2022] Open
Abstract
The chromatin-based rule governing the selection and activation of replication origins remains to be elucidated. It is believed that DNA replication initiates from open chromatin domains; thus, replication origins reside in open and active chromatin. However, we report here that lysine-specific demethylase 1 (LSD1), which biochemically catalyzes H3K4me1/2 demethylation favoring chromatin condensation, interacts with the DNA replication machinery in human cells. We find that LSD1 level peaks in early S phase, when it is required for DNA replication by facilitating origin firing in euchromatic regions. Indeed, euchromatic zones enriched in H3K4me2 are the preferred sites for the pre-replicative complex (pre-RC) binding. Remarkably, LSD1 deficiency leads to a genome-wide switch of replication from early to late. We show that LSD1-engaged DNA replication is mechanistically linked to the loading of TopBP1-Interacting Checkpoint and Replication Regulator (TICRR) onto the pre-RC and subsequent recruitment of CDC45 during origin firing. Together, these results reveal an unexpected role for LSD1 in euchromatic origin firing and replication timing, highlighting the importance of epigenetic regulation in the activation of replication origins. As selective inhibitors of LSD1 are being exploited as potential cancer therapeutics, our study supports the importance of leveraging an appropriate level of LSD1 to curb the side effects of anti-LSD1 therapy.
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Fu J, Zhang J, Yang L, Ding N, Yue L, Zhang X, Lu D, Jia X, Li C, Guo C, Yin Z, Jiang X, Zhao Y, Chen F, Zhou D. Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:418-434. [PMID: 34214662 PMCID: PMC9684165 DOI: 10.1016/j.gpb.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/19/2021] [Accepted: 06/11/2021] [Indexed: 01/05/2023]
Abstract
Klebsiella pneumoniae (K. pneumoniae) is an important pathogen that can cause severe hospital- and community-acquired infections. To systematically investigate its methylation features, we determined the whole-genome sequences of 14 K. pneumoniae strains covering varying serotypes, multilocus sequence types, clonal groups, viscosity/virulence, and drug resistance. Their methylomes were further characterized using Pacific Biosciences single-molecule real-time and bisulfite technologies. We identified 15 methylation motifs [13 N6-methyladenine (6mA) and two 5-methylcytosine (5mC) motifs], among which eight were novel. Their corresponding DNA methyltransferases were also validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distribution patterns of some hemi-/un-methylated GATC motifs, which tend to be located within intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slow methylation of the GATC motifs in the replication origin (oriC) regions and IGRs implicates the epigenetic regulation of replication initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumoniae at single-base resolution, and provide a useful reference to better understand epigenetic regulation in this and other bacterial species.
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Affiliation(s)
- Jing Fu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,Department of Oncology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou 450001, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Li Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Xiangli Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Lu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinmiao Jia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Chongye Guo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yongliang Zhao
- University of Chinese Academy of Sciences, Beijing 100049, China,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China,Corresponding authors.
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China,Corresponding authors.
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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8
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Chong SY, Cutler S, Lin JJ, Tsai CH, Tsai HK, Biggins S, Tsukiyama T, Lo YC, Kao CF. H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress. Nat Commun 2020; 11:809. [PMID: 32041946 PMCID: PMC7010754 DOI: 10.1038/s41467-020-14595-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/16/2020] [Indexed: 12/11/2022] Open
Abstract
Transcription-replication conflicts (TRCs) occur when intensive transcriptional activity compromises replication fork stability, potentially leading to gene mutations. Transcription-deposited H3K4 methylation (H3K4me) is associated with regions that are susceptible to TRCs; however, the interplay between H3K4me and TRCs is unknown. Here we show that H3K4me aggravates TRC-induced replication failure in checkpoint-defective cells, and the presence of methylated H3K4 slows down ongoing replication. Both S-phase checkpoint activity and H3K4me are crucial for faithful DNA synthesis under replication stress, especially in highly transcribed regions where the presence of H3K4me is highest and TRCs most often occur. H3K4me mitigates TRCs by decelerating ongoing replication, analogous to how speed bumps slow down cars. These findings establish the concept that H3K4me defines the transcriptional status of a genomic region and defends the genome from TRC-mediated replication stress and instability. Transcription-replication conflicts (TRC) can contribute to genome instability. Here the authors reveal that under replication stress H3K4 methylation can play a role in TRC prevention.
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Affiliation(s)
- Shin Yen Chong
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.,Graduate Institute of Food Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Sam Cutler
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jing-Jer Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Cheng-Hung Tsai
- Institute of Information Science, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Huai-Kuang Tsai
- Institute of Information Science, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Sue Biggins
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.,Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei, 10617, Taiwan.
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
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9
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Wagner S, Waldman M, Arora S, Wang S, Scott V, Islam K. Allele-Specific Inhibition of Histone Demethylases. Chembiochem 2019; 20:1133-1138. [PMID: 30618116 DOI: 10.1002/cbic.201800756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Indexed: 12/21/2022]
Abstract
Histone demethylases play a critical role in mammalian gene expression by removing methyl groups from lysine residues in degree- and site-specific manner. To specifically interrogate members and isoforms of this class of enzymes, we have developed demethylase variants with an expanded active site. The mutant enzymes are capable of performing lysine demethylation with wild-type proficiency, but are sensitive to inhibition by cofactor-competitive molecules embellished with a complementary steric "bump". The selected inhibitors show more than 20-fold selectivity over the wild-type demethylase, thus overcoming issues typical to pharmacological and genetic approaches. The mutant-inhibitor pairs are shown to act on a physiologically relevant full-length substrate. By engineering a conserved amino acid to achieve member-specific perturbation, this study provides a general approach for studying histone demethylases in diverse cellular processes.
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Affiliation(s)
- Shana Wagner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Megan Waldman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Simran Arora
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sinan Wang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Valerie Scott
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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10
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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11
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Islam K. The Bump-and-Hole Tactic: Expanding the Scope of Chemical Genetics. Cell Chem Biol 2018; 25:1171-1184. [PMID: 30078633 PMCID: PMC6195450 DOI: 10.1016/j.chembiol.2018.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/13/2018] [Accepted: 07/02/2018] [Indexed: 12/15/2022]
Abstract
Successful mapping of the human genome has sparked a widespread interest in deciphering functional information encoded in gene sequences. However, because of the high degree of conservation in sequences along with topological and biochemical similarities among members of a protein superfamily, uncovering physiological role of a particular protein has been a challenging task. Chemical genetic approaches have made significant contributions toward understanding protein function. One such effort, dubbed the bump-and-hole approach, has convincingly demonstrated that engineering at the protein-small molecule interface constitutes a powerful method for elucidating the function of a specific gene product. By manipulating the steric component of protein-ligand interactions in a complementary manner, an orthogonal system is developed to probe a specific enzyme-cofactor pair without interference from related members. This article outlines current efforts to expand the approach for diverse protein classes and their applications. Potential future innovations to address contemporary biological problems are highlighted as well.
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Affiliation(s)
- Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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12
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Voichek Y, Mittelman K, Gordon Y, Bar-Ziv R, Lifshitz Smit D, Shenhav R, Barkai N. Epigenetic Control of Expression Homeostasis during Replication Is Stabilized by the Replication Checkpoint. Mol Cell 2018; 70:1121-1133.e9. [PMID: 29910110 DOI: 10.1016/j.molcel.2018.05.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/22/2018] [Accepted: 05/11/2018] [Indexed: 11/24/2022]
Abstract
DNA replication introduces a dosage imbalance between early and late replicating genes. In budding yeast, buffering gene expression against this imbalance depends on marking replicated DNA by H3K56 acetylation (H3K56ac). Whether additional processes are required for suppressing transcription from H3K56ac-labeled DNA remains unknown. Here, using a database-guided candidate screen, we find that COMPASS, the H3K4 methyltransferase, and its upstream effector, PAF1C, act downstream of H3K56ac to buffer expression. Replicated genes show reduced abundance of the transcription activating mark H3K4me3 and accumulate the transcription inhibitory mark H3K4me2 near transcription start sites. Notably, in hydroxyurea-exposed cells, the S phase checkpoint stabilizes H3K56ac and becomes essential for buffering. We suggest that H3K56ac suppresses transcription of replicated genes by interfering with post-replication recovery of epigenetic marks and assign a new function for the S phase checkpoint in stabilizing this mechanism during persistent dosage imbalance.
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Affiliation(s)
- Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Karin Mittelman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yulia Gordon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Lifshitz Smit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rom Shenhav
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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13
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Adam C, Guérois R, Citarella A, Verardi L, Adolphe F, Béneut C, Sommermeyer V, Ramus C, Govin J, Couté Y, Borde V. The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes. PLoS Genet 2018; 14:e1007223. [PMID: 29444071 PMCID: PMC5828529 DOI: 10.1371/journal.pgen.1007223] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 02/27/2018] [Accepted: 01/25/2018] [Indexed: 11/18/2022] Open
Abstract
Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals. Meiotic recombination is initiated by programmed double-strand break (DSB) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethylation. This histone modification is recognized by Spp1, a PHD finger containing protein that belongs to the conserved histone H3K4 methyltransferase Set1 complex. During meiosis, Spp1 binds H3K4me3 and interacts with a DSB protein, Mer2, to promote DSB formation close to gene promoters. How Set1 complex- and Mer2- related functions of Spp1 are connected is not clear. Here, combining genome-wide localization analyses, biochemical approaches and the use of separation of function mutants, we show that Spp1 is present within two distinct complexes in meiotic cells, the Set1 and the Mer2 complexes. Disrupting the Spp1-Set1 interaction mildly decreases H3K4me3 levels and does not affect meiotic recombination initiation. Conversely, the Spp1-Mer2 interaction is required for normal meiotic recombination initiation, but dispensable for Set1 complex-mediated histone H3K4 methylation. Finally, we provide evidence that Spp1 preserves normal H3K4me3 levels independently of the Set1 complex. We propose a model where Spp1 works in three ways to promote recombination initiation: first by depositing histone H3K4 methylation (Set1 complex), next by “reading” and protecting histone H3K4 methylation, and finally by making the link with the chromosome axis (Mer2-Spp1 complex). This work deciphers the precise roles of Spp1 in meiotic recombination and opens perspectives to study its functions in other organisms where H3K4me3 is also present at recombination hotspots. Meiotic recombination is a conserved pathway of sexual reproduction that is required to faithfully segregate homologous chromosomes and produce viable gametes. Recombination events between homologous chromosomes are triggered by the programmed formation of DNA breaks, which occur preferentially at places called hotspots. In many organisms, these hotspots are located close to a particular chromatin modification, the methylation of lysine 4 of histone H3 (H3K4me3). It was previously shown in the budding yeast model that one protein, Spp1, plays an important function in this process. We further explored the functional link between Spp1 and its interacting partners, and show that Spp1 shows genetically separable functions, by depositing the H3K4me3 mark on the chromatin, “reading” and protecting it, and linking it to the recombination proteins. We provide evidence that Spp1 is in distinct complexes to perform these functions. This work opens perspectives for understanding the process in other eukaryotes such as mammals, where most of the proteins involved are conserved.
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Affiliation(s)
- Céline Adam
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Anna Citarella
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Laura Verardi
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Florine Adolphe
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Claire Béneut
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Vérane Sommermeyer
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
| | - Claire Ramus
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Jérôme Govin
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, BIG-BGE, Grenoble, France
| | - Valérie Borde
- Institut Curie, PSL Research University, CNRS, UMR3244, Paris, France
- Université Pierre et Marie Curie (UPMC), Paris, France
- * E-mail:
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14
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Voichek Y, Bar-Ziv R, Barkai N. A role for Rtt109 in buffering gene-dosage imbalance during DNA replication. Nucleus 2017; 7:375-81. [PMID: 27485376 DOI: 10.1080/19491034.2016.1216743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Chromatin can function as an integrator of DNA-related processes, allowing communication, for example, between DNA replication and gene transcription. Such communication is needed to overcome the gene-dosage imbalance introduced during DNA replication, when certain genes are replicated prior to others. Increased transcription of early replicating genes could alter regulatory balances. This does not occur, suggesting a mechanism that suppresses expression from newly replicated DNA. Critical to this buffering is Rtt109, which acetylates the internal K56 residue of newly synthesized histone H3 prior to incorporation onto DNA. H3K56ac distinguishes replicated from non-replicated DNA, communicating this information to the transcription machinery to ensure expression homeostasis during S phase.
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Affiliation(s)
- Yoav Voichek
- a Department of Molecular Genetics , Weizmann Institute of Science , Rehovot , Israel
| | - Raz Bar-Ziv
- a Department of Molecular Genetics , Weizmann Institute of Science , Rehovot , Israel
| | - Naama Barkai
- a Department of Molecular Genetics , Weizmann Institute of Science , Rehovot , Israel
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15
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Sharma U, Rando OJ. Metabolic Inputs into the Epigenome. Cell Metab 2017; 25:544-558. [PMID: 28273477 DOI: 10.1016/j.cmet.2017.02.003] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/14/2016] [Accepted: 01/07/2017] [Indexed: 12/30/2022]
Abstract
A number of molecular pathways play key roles in transmitting information in addition to the genomic sequence-epigenetic information-from one generation to the next. However, so-called epigenetic marks also impact an enormous variety of physiological processes, even under circumstances that do not result in heritable consequences. Perhaps inevitably, the epigenetic regulatory machinery is highly responsive to metabolic cues, as, for example, central metabolites are the substrates for the enzymes that catalyze the deposition of covalent modifications on histones, DNA, and RNA. Interestingly, in addition to the effects that metabolites exert over biological regulation in somatic cells, over the past decade multiple studies have shown that ancestral nutrition can alter the metabolic phenotype of offspring, raising the question of how metabolism regulates the epigenome of germ cells. Here, we review the widespread links between metabolism and epigenetic modifications, both in somatic cells and in the germline.
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Affiliation(s)
- Upasna Sharma
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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16
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17
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Bar-Ziv R, Voichek Y, Barkai N. Chromatin dynamics during DNA replication. Genome Res 2016; 26:1245-56. [PMID: 27225843 PMCID: PMC5052047 DOI: 10.1101/gr.201244.115] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 05/23/2016] [Indexed: 01/21/2023]
Abstract
Chromatin is composed of DNA and histones, which provide a unified platform for regulating DNA-related processes, mostly through their post-translational modification. During DNA replication, histone arrangement is perturbed, first to allow progression of DNA polymerase and then during repackaging of the replicated DNA. To study how DNA replication influences the pattern of histone modification, we followed the cell-cycle dynamics of 10 histone marks in budding yeast. We find that histones deposited on newly replicated DNA are modified at different rates: While some marks appear immediately upon replication (e.g., H4K16ac, H3K4me1), others increase with transcription-dependent delays (e.g., H3K4me3, H3K36me3). Notably, H3K9ac was deposited as a wave preceding the replication fork by ∼5–6 kb. This replication-guided H3K9ac was fully dependent on the acetyltransferase Rtt109, while expression-guided H3K9ac was deposited by Gcn5. Further, topoisomerase depletion intensified H3K9ac in front of the replication fork and in sites where RNA polymerase II was trapped, suggesting supercoiling stresses trigger H3K9 acetylation. Our results assign complementary roles for DNA replication and gene expression in defining the pattern of histone modification.
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Affiliation(s)
- Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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18
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Tu X, Wang Y, Zhang M, Wu J. Using Formal Concept Analysis to Identify Negative Correlations in Gene Expression Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:380-391. [PMID: 27045834 DOI: 10.1109/tcbb.2015.2443805] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recently, many biological studies reported that two groups of genes tend to show negatively correlated or opposite expression tendency in many biological processes or pathways. The negative correlation between genes may imply an important biological mechanism. In this study, we proposed a FCA-based negative correlation algorithm (NCFCA) that can effectively identify opposite expression tendency between two gene groups in gene expression data. After applying it to expression data of cell cycle-regulated genes in yeast, we found that six minichromosome maintenance family genes showed the opposite changing tendency with eight core histone family genes. Furthermore, we confirmed that the negative correlation expression pattern between these two families may be conserved in the cell cycle. Finally, we discussed the reasons underlying the negative correlation of six minichromosome maintenance (MCM) family genes with eight core histone family genes. Our results revealed that negative correlation is an important and potential mechanism that maintains the balance of biological systems by repressing some genes while inducing others. It can thus provide new understanding of gene expression and regulation, the causes of diseases, etc.
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19
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Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep 2015; 16:1620-39. [PMID: 26564907 PMCID: PMC4687429 DOI: 10.15252/embr.201541113] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023] Open
Abstract
Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes.
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Affiliation(s)
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
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20
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Ferrari P, Strubin M. Uncoupling histone turnover from transcription-associated histone H3 modifications. Nucleic Acids Res 2015; 43:3972-85. [PMID: 25845593 PMCID: PMC4417181 DOI: 10.1093/nar/gkv282] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/21/2015] [Indexed: 11/14/2022] Open
Abstract
Transcription in eukaryotes is associated with two major changes in chromatin organization. Firstly, nucleosomal histones are continuously replaced by new histones, an event that in yeast occurs predominantly at transcriptionally active promoters. Secondly, histones become modified post-translationally at specific lysine residues. Some modifications, including histone H3 trimethylation at lysine 4 (H3K4me3) and acetylation at lysines 9 (H3K9ac) and 14 (H3K14ac), are specifically enriched at active promoters where histones exchange, suggesting a possible causal relationship. Other modifications accumulate within transcribed regions and one of them, H3K36me3, is thought to prevent histone exchange. Here we explored the relationship between these four H3 modifications and histone turnover at a few selected genes. Using lysine-to-arginine mutants and a histone exchange assay, we found that none of these modifications plays a major role in either promoting or preventing histone turnover. Unexpectedly, mutation of H3K56, whose acetylation occurs prior to chromatin incorporation, had an effect only when introduced into the nucleosomal histone. Furthermore, we used various genetic approaches to show that histone turnover can be experimentally altered with no major consequence on the H3 modifications tested. Together, these results suggest that transcription-associated histone turnover and H3 modification are two correlating but largely independent events.
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Affiliation(s)
- Paolo Ferrari
- Department of Microbiology and Molecular Medicine, University Medical Centre (C.M.U.), Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Michel Strubin
- Department of Microbiology and Molecular Medicine, University Medical Centre (C.M.U.), Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
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21
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Rondinelli B, Schwerer H, Antonini E, Gaviraghi M, Lupi A, Frenquelli M, Cittaro D, Segalla S, Lemaitre JM, Tonon G. H3K4me3 demethylation by the histone demethylase KDM5C/JARID1C promotes DNA replication origin firing. Nucleic Acids Res 2015; 43:2560-74. [PMID: 25712104 PMCID: PMC4357704 DOI: 10.1093/nar/gkv090] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
DNA replication is a tightly regulated process that initiates from multiple replication origins and leads to the faithful transmission of the genetic material. For proper DNA replication, the chromatin surrounding origins needs to be remodeled. However, remarkably little is known on which epigenetic changes are required to allow the firing of replication origins. Here, we show that the histone demethylase KDM5C/JARID1C is required for proper DNA replication at early origins. JARID1C dictates the assembly of the pre-initiation complex, driving the binding to chromatin of the pre-initiation proteins CDC45 and PCNA, through the demethylation of the histone mark H3K4me3. Fork activation and histone H4 acetylation, additional early events involved in DNA replication, are not affected by JARID1C downregulation. All together, these data point to a prominent role for JARID1C in a specific phase of DNA replication in mammalian cells, through its demethylase activity on H3K4me3.
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Affiliation(s)
- Beatrice Rondinelli
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy Molecular Medicine PhD Program, Vita-Salute San Raffaele University, Via Olgettina 58, 20132, Milan, Italy
| | - Hélène Schwerer
- Laboratory of Stem Cell and Genome Plasticity in Development and Aging, Institute of Regenerative Medicine and Biotherapies, INSERM U1183, Montpellier University, Montpellier, France
| | - Elena Antonini
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy
| | - Marco Gaviraghi
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy Molecular Medicine PhD Program, Vita-Salute San Raffaele University, Via Olgettina 58, 20132, Milan, Italy
| | - Alessio Lupi
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy Molecular Medicine PhD Program, Vita-Salute San Raffaele University, Via Olgettina 58, 20132, Milan, Italy
| | - Michela Frenquelli
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy
| | - Davide Cittaro
- Centre for Translational Genomics and Bioinformatics, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Simona Segalla
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy
| | - Jean-Marc Lemaitre
- Laboratory of Stem Cell and Genome Plasticity in Development and Aging, Institute of Regenerative Medicine and Biotherapies, INSERM U1183, Montpellier University, Montpellier, France
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), San Raffaele Scientific Institute, Via Olgettina 60, 20132 Milan, Italy
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22
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Howe FS, Boubriak I, Sale MJ, Nair A, Clynes D, Grijzenhout A, Murray SC, Woloszczuk R, Mellor J. Lysine acetylation controls local protein conformation by influencing proline isomerization. Mol Cell 2014; 55:733-44. [PMID: 25127513 PMCID: PMC4157579 DOI: 10.1016/j.molcel.2014.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 05/15/2014] [Accepted: 07/02/2014] [Indexed: 11/09/2022]
Abstract
Gene transcription responds to stress and metabolic signals to optimize growth and survival. Histone H3 (H3) lysine 4 trimethylation (K4me3) facilitates state changes, but how levels are coordinated with the environment is unclear. Here, we show that isomerization of H3 at the alanine 15-proline 16 (A15-P16) peptide bond is influenced by lysine 14 (K14) and controls gene-specific K4me3 by balancing the actions of Jhd2, the K4me3 demethylase, and Spp1, a subunit of the Set1 K4 methyltransferase complex. Acetylation at K14 favors the A15-P16trans conformation and reduces K4me3. Environmental stress-induced genes are most sensitive to the changes at K14 influencing H3 tail conformation and K4me3. By contrast, ribosomal protein genes maintain K4me3, required for their repression during stress, independently of Spp1, K14, and P16. Thus, the plasticity in control of K4me3, via signaling to K14 and isomerization at P16, informs distinct gene regulatory mechanisms and processes involving K4me3. H3K14 acetylation influences cis-trans isomerization at the H3A15-P16 peptide bond H3A15-P16trans is associated with H3K14ac and reduced global H3K4me3 A15-P16cis-trans isomerization balances K4me3 (Set1/Spp1) and demethylation (Jhd2) K4me3 on RPGs is largely Spp1- and K14/P16-insensitive while ESR genes are dependent
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Affiliation(s)
- Françoise S Howe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ivan Boubriak
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Matthew J Sale
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anitha Nair
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - David Clynes
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Anne Grijzenhout
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Struan C Murray
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ronja Woloszczuk
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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23
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Zheng Y, Tipton JD, Thomas PM, Kelleher NL, Sweet SMM. Site-specific human histone H3 methylation stability: fast K4me3 turnover. Proteomics 2014; 14:2190-9. [PMID: 24826939 DOI: 10.1002/pmic.201400060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/11/2014] [Accepted: 05/09/2014] [Indexed: 12/16/2022]
Abstract
We employ stable-isotope labeling and quantitative mass spectrometry to track histone methylation stability. We show that H3 trimethyl K9 and K27 are slow to be established on new histones and slow to disappear from old histones, with half-lives of multiple cell divisions. By contrast, the transcription-associated marks K4me3 and K36me3 turn over far more rapidly, with half-lives of 6.8 h and 57 h, respectively. Inhibition of demethylases increases K9 and K36 methylation, with K9 showing the largest and most robust increase. We interpret different turnover rates in light of genome-wide localization data and transcription-dependent nucleosome rearrangements proximal to the transcription start site.
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Affiliation(s)
- Yupeng Zheng
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
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25
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Rizzardi LF, Dorn ES, Strahl BD, Cook JG. DNA replication origin function is promoted by H3K4 di-methylation in Saccharomyces cerevisiae. Genetics 2012; 192:371-84. [PMID: 22851644 PMCID: PMC3454870 DOI: 10.1534/genetics.112.142349] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/18/2012] [Indexed: 12/18/2022] Open
Abstract
DNA replication is a highly regulated process that is initiated from replication origins, but the elements of chromatin structure that contribute to origin activity have not been fully elucidated. To identify histone post-translational modifications important for DNA replication, we initiated a genetic screen to identify interactions between genes encoding chromatin-modifying enzymes and those encoding proteins required for origin function in the budding yeast Saccharomyces cerevisiae. We found that enzymes required for histone H3K4 methylation, both the histone methyltransferase Set1 and the E3 ubiquitin ligase Bre1, are required for robust growth of several hypomorphic replication mutants, including cdc6-1. Consistent with a role for these enzymes in DNA replication, we found that both Set1 and Bre1 are required for efficient minichromosome maintenance. These phenotypes are recapitulated in yeast strains bearing mutations in the histone substrates (H3K4 and H2BK123). Set1 functions as part of the COMPASS complex to mono-, di-, and tri-methylate H3K4. By analyzing strains lacking specific COMPASS complex members or containing H2B mutations that differentially affect H3K4 methylation states, we determined that these replication defects were due to loss of H3K4 di-methylation. Furthermore, histone H3K4 di-methylation is enriched at chromosomal origins. These data suggest that H3K4 di-methylation is necessary and sufficient for normal origin function. We propose that histone H3K4 di-methylation functions in concert with other histone post-translational modifications to support robust genome duplication.
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Affiliation(s)
- Lindsay F. Rizzardi
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Elizabeth S. Dorn
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Brian D. Strahl
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, and
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, and
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599
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26
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Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet 2012; 8:e1002911. [PMID: 22927830 PMCID: PMC3426549 DOI: 10.1371/journal.pgen.1002911] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 07/04/2012] [Indexed: 11/19/2022] Open
Abstract
In plants, multiple detached tissues are capable of forming a pluripotent cell mass, termed callus, when cultured on media containing appropriate plant hormones. Recent studies demonstrated that callus resembles the root-tip meristem, even if it is derived from aerial organs. This finding improves our understanding of the regeneration process of plant cells; however, the molecular mechanism that guides cells of different tissue types to form a callus still remains elusive. Here, we show that genome-wide reprogramming of histone H3 lysine 27 trimethylation (H3K27me3) is a critical step in the leaf-to-callus transition. The Polycomb Repressive Complex 2 (PRC2) is known to function in establishing H3K27me3. By analyzing callus formation of mutants corresponding to different histone modification pathways, we found that leaf blades and/or cotyledons of the PRC2 mutants curly leaf swinger (clf swn) and embryonic flower2 (emf2) were defective in callus formation. We identified the H3K27me3-covered loci in leaves and calli by a ChIP-chip assay, and we found that in the callus H3K27me3 levels decreased first at certain auxin-pathway genes. The levels were then increased at specific leaf genes but decreased at a number of root-regulatory genes. Changes in H3K27me3 levels were negatively correlated with expression levels of the corresponding genes. One possible role of PRC2-mediated H3K27me3 in the leaf-to-callus transition might relate to elimination of leaf features by silencing leaf-regulatory genes, as most leaf-preferentially expressed regulatory genes could not be silenced in the leaf explants of clf swn. In contrast to the leaf explants, the root explants of both clf swn and emf2 formed calli normally, possibly because the root-to-callus transition bypasses the leaf gene silencing process. Furthermore, our data show that PRC2-mediated H3K27me3 and H3K27 demethylation act in parallel in the reprogramming of H3K27me3 during the leaf-to-callus transition, suggesting a general mechanism for cell fate transition in plants.
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27
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He C, Chen X, Huang H, Xu L. Reprogramming of H3K27me3 is critical for acquisition of pluripotency from cultured Arabidopsis tissues. PLoS Genet 2012. [PMID: 22927830 DOI: 10.1371/journal.pgen.1002911pgenetics-d-12-00157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
In plants, multiple detached tissues are capable of forming a pluripotent cell mass, termed callus, when cultured on media containing appropriate plant hormones. Recent studies demonstrated that callus resembles the root-tip meristem, even if it is derived from aerial organs. This finding improves our understanding of the regeneration process of plant cells; however, the molecular mechanism that guides cells of different tissue types to form a callus still remains elusive. Here, we show that genome-wide reprogramming of histone H3 lysine 27 trimethylation (H3K27me3) is a critical step in the leaf-to-callus transition. The Polycomb Repressive Complex 2 (PRC2) is known to function in establishing H3K27me3. By analyzing callus formation of mutants corresponding to different histone modification pathways, we found that leaf blades and/or cotyledons of the PRC2 mutants curly leaf swinger (clf swn) and embryonic flower2 (emf2) were defective in callus formation. We identified the H3K27me3-covered loci in leaves and calli by a ChIP-chip assay, and we found that in the callus H3K27me3 levels decreased first at certain auxin-pathway genes. The levels were then increased at specific leaf genes but decreased at a number of root-regulatory genes. Changes in H3K27me3 levels were negatively correlated with expression levels of the corresponding genes. One possible role of PRC2-mediated H3K27me3 in the leaf-to-callus transition might relate to elimination of leaf features by silencing leaf-regulatory genes, as most leaf-preferentially expressed regulatory genes could not be silenced in the leaf explants of clf swn. In contrast to the leaf explants, the root explants of both clf swn and emf2 formed calli normally, possibly because the root-to-callus transition bypasses the leaf gene silencing process. Furthermore, our data show that PRC2-mediated H3K27me3 and H3K27 demethylation act in parallel in the reprogramming of H3K27me3 during the leaf-to-callus transition, suggesting a general mechanism for cell fate transition in plants.
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Affiliation(s)
- Chongsheng He
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Weiner A, Chen HV, Liu CL, Rahat A, Klien A, Soares L, Gudipati M, Pfeffner J, Regev A, Buratowski S, Pleiss JA, Friedman N, Rando OJ. Systematic dissection of roles for chromatin regulators in a yeast stress response. PLoS Biol 2012; 10:e1001369. [PMID: 22912562 PMCID: PMC3416867 DOI: 10.1371/journal.pbio.1001369] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 06/20/2012] [Indexed: 01/05/2023] Open
Abstract
Systematic functional and mapping studies of histone modifications in yeast show that most chromatin regulators are more important for dynamic transcriptional reprogramming than for steady-state gene expression. Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 gene deletion mutants, on induction/repression dynamics of 170 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We followed up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during multiple stresses, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and identify a significant role for the “activating” mark H3K4me3 in gene repression. Chromatin packaging of eukaryotic genomes has wideranging, yet poorly understood, effects on gene regulation. Curiously, many histone modifications occur on the majority of genes, yet their loss typically affects a small subset of those genes. Here, we examine gene expression defects in 200 chromatin-related mutants during a stress response, finding that chromatin regulators have far greater effects on the dynamics of gene expression than on the steady-state transcription. By grouping mutants according to their shared defects in the stress response, we systematically recover known chromatin-related complexes and pathways, and predict several novel pathways. Finally, by integrating genome-wide changes in the locations of five prominent histone modifications during the stress response with our functional data, we uncover a novel role for the “activating” histone modification H3K4me3 in gene repression. Surprisingly, H3K4 methylation appears to act in conjunction with H3S10 phosphorylation in the repression of ribosomal biosynthesis genes. Repression of ribosomal protein genes and ribosomal RNA maturation genes occur via distinct pathways. Our results show that steady-state studies miss a great deal of important chromatin biology, and identify a surprising role for H3K4 methylation in ribosomal gene repression in yeast.
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Affiliation(s)
- Assaf Weiner
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Hsiuyi V. Chen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Chih Long Liu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ayelet Rahat
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Avital Klien
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Luis Soares
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mohanram Gudipati
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Jenna Pfeffner
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stephen Buratowski
- Department of Biochemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jeffrey A. Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
- * E-mail: (NF); (OJR)
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (NF); (OJR)
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Owen-Hughes T, Gkikopoulos T. Making sense of transcribing chromatin. Curr Opin Cell Biol 2012; 24:296-304. [PMID: 22410403 PMCID: PMC3432231 DOI: 10.1016/j.ceb.2012.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 11/03/2022]
Abstract
Eukaryotic cells package their genomes into a nucleoprotein form called chromatin. The basic unit of chromatin is the nucleosome, formed by the wrapping of ∼147bp of DNA around an octameric complex of core histones. Advances in genomic technologies have enabled the locations of nucleosomes to be mapped across genomes. This has revealed a striking organisation with respect to transcribed genes in a diverse range of eukaryotes. This consists of a nucleosome depleted region upstream of promoters, with an array of well spaced nucleosomes extending into coding regions. This observation reinforces the links between chromatin organisation and transcription. Central to this is the paradox that while chromatin is required by eukaryotes to restrict inappropriate access to DNA, this must be overcome in order for genetic information to be expressed. This conundrum is at its most flagrant when considering the need for nucleic acid polymerase's to transit 1000's of based pairs of DNA wrapped as arrays of nucleosomes.
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Affiliation(s)
- Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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Vermeulen M, Timmers HTM. Grasping trimethylation of histone H3 at lysine 4. Epigenomics 2012; 2:395-406. [PMID: 22121900 DOI: 10.2217/epi.10.11] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Post-translational modifications of chromatin have become a 'booming' area of biomedical research. One particularly interesting modification that is important for eukaryotic gene expression is trimethylation of histone H3 lysine 4 (H3K4me3), which is almost exclusively associated with active promoters of RNA polymerase II. In this article, we highlight the recent progress related to the biochemistry and biology of this histone mark, including its relevant 'writers' and 'readers'. We also outline the complex regulatory mechanisms that are involved in establishing H3K4me3 in health and disease. Further understanding of H3K4me3 regulation will offer both more insight into chromatin-based mechanisms of gene regulation and provide opportunities for epigenetic intervention of the diseased state.
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Affiliation(s)
- Michiel Vermeulen
- Department of Physiological Chemistry, University Medical Centre Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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31
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Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 2012; 13:233-45. [PMID: 22392219 DOI: 10.1038/nrg3163] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Promoters are crucial for gene regulation. They vary greatly in terms of associated regulatory elements, sequence motifs, the choice of transcription start sites and other features. Several technologies that harness next-generation sequencing have enabled recent advances in identifying promoters and their features, helping researchers who are investigating functional categories of promoters and their modes of regulation. Additional features of promoters that are being characterized include types of histone modifications, nucleosome positioning, RNA polymerase pausing and novel small RNAs. In this Review, we discuss recent findings relating to metazoan promoters and how these findings are leading to a revised picture of what a gene promoter is and how it works.
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32
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Sarkies P, Sale JE. Propagation of histone marks and epigenetic memory during normal and interrupted DNA replication. Cell Mol Life Sci 2012; 69:697-716. [PMID: 21964926 PMCID: PMC11114753 DOI: 10.1007/s00018-011-0824-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 09/02/2011] [Accepted: 09/12/2011] [Indexed: 11/30/2022]
Abstract
Although all nucleated cells within a multicellular organism contain a complete copy of the genome, cell identity relies on the expression of a specific subset of genes. Therefore, when cells divide they must not only copy their genome to their daughters, but also ensure that the pattern of gene expression present before division is restored. While the carrier of this epigenetic memory has been a topic of much research and debate, post-translational modifications of histone proteins have emerged in the vanguard of candidates. In this paper we examine the mechanisms by which histone post-translational modifications are propagated through DNA replication and cell division, and we critically examine the evidence that they can also act as vectors of epigenetic memory. Finally, we consider ways in which epigenetic memory might be disrupted by interfering with the mechanisms of DNA replication.
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Affiliation(s)
- Peter Sarkies
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Julian E. Sale
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
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Radman-Livaja M, Verzijlbergen KF, Weiner A, van Welsem T, Friedman N, Rando OJ, van Leeuwen F. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. PLoS Biol 2011; 9:e1001075. [PMID: 21666805 PMCID: PMC3110181 DOI: 10.1371/journal.pbio.1001075] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 04/22/2011] [Indexed: 11/18/2022] Open
Abstract
Tracking of ancestral histone proteins over multiple generations of genome
replication in yeast reveals that old histones move along genes from 3′
toward 5′ over time, and that maternal histones move up to around 400 bp
during genomic replication. Replicating chromatin involves disruption of histone-DNA contacts and subsequent
reassembly of maternal histones on the new daughter genomes. In bulk, maternal
histones are randomly segregated to the two daughters, but little is known about
the fine details of this process: do maternal histones re-assemble at preferred
locations or close to their original loci? Here, we use a recently developed
method for swapping epitope tags to measure the disposition of ancestral histone
H3 across the yeast genome over six generations. We find that ancestral H3 is
preferentially retained at the 5′ ends of most genes, with strongest
retention at long, poorly transcribed genes. We recapitulate these observations
with a quantitative model in which the majority of maternal histones are
reincorporated within 400 bp of their pre-replication locus during replication,
with replication-independent replacement and transcription-related retrograde
nucleosome movement shaping the resulting distributions of ancestral histones.
We find a key role for Topoisomerase I in retrograde histone movement during
transcription, and we find that loss of Chromatin Assembly Factor-1 affects
replication-independent turnover. Together, these results show that specific
loci are enriched for histone proteins first synthesized several generations
beforehand, and that maternal histones re-associate close to their original
locations on daughter genomes after replication. Our findings further suggest
that accumulation of ancestral histones could play a role in shaping histone
modification patterns. It is widely believed that chromatin, the nucleoprotein packaged state of
eukaryotic genomes, can carry epigenetic information and thus transmit gene
expression patterns to replicating cells. However, the inheritance of genomic
packaging status is subject to mechanistic challenges that do not confront the
inheritance of genomic DNA sequence. Most notably, histone proteins must at
least transiently dissociate from the maternal genome during replication, and it
is unknown whether or not maternal proteins re-associate with daughter genomes
near the sequence they originally occupied on the maternal genome. Here, we use
a novel method for tracking old proteins to determine where histone proteins
accumulate after 1, 3, or 6 generations of growth in yeast. To our surprise,
ancestral histones accumulate near the 5′ end of long, relatively inactive
genes. Using a mathematical model, we show that our results can be explained by
the combined effects of histone replacement, histone movement along genes from
3′ towards 5′ ends, and histone spreading during replication. Our
results show that old histones do move but stay relatively close to their
original location (within around 400 base-pairs), which places important
constraints on how chromatin could potentially carry epigenetic information. Our
findings also suggest that accumulation of the ancestral histones that are
inherited can influence histone modification patterns.
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Affiliation(s)
- Marta Radman-Livaja
- Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts Medical School, Worcester,
Massachusetts, United States of America
| | - Kitty F. Verzijlbergen
- Division of Gene Regulation, Netherlands
Cancer Institute, and Netherlands Proteomics Center, Amsterdam, The
Netherlands
| | - Assaf Weiner
- School of Computer Science and Engineering,
The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life
Sciences, The Hebrew University, Jerusalem, Israel
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands
Cancer Institute, and Netherlands Proteomics Center, Amsterdam, The
Netherlands
| | - Nir Friedman
- School of Computer Science and Engineering,
The Hebrew University, Jerusalem, Israel
- Alexander Silberman Institute of Life
Sciences, The Hebrew University, Jerusalem, Israel
- * E-mail: (NF); (OJR); (FVL)
| | - Oliver J. Rando
- Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts Medical School, Worcester,
Massachusetts, United States of America
- * E-mail: (NF); (OJR); (FVL)
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands
Cancer Institute, and Netherlands Proteomics Center, Amsterdam, The
Netherlands
- * E-mail: (NF); (OJR); (FVL)
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Dorn ES, Cook JG. Nucleosomes in the neighborhood: new roles for chromatin modifications in replication origin control. Epigenetics 2011; 6:552-9. [PMID: 21364325 DOI: 10.4161/epi.6.5.15082] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The importance of local chromatin structure in regulating replication initiation has become increasingly apparent. Most recently, histone methylation and nucleosome positioning have been added to the list of modifications demonstrated to regulate origins. In particular, the methylation states of H3K4, H3K36 and H4K20 have been associated with establishing active, repressed or poised origins depending on the timing and extent of methylation. The stability and precise positioning of nucleosomes has also been demonstrated to affect replication efficiency. Although it is not yet clear how these modifications alter the behavior of specific replication factors, ample evidence establishes their role in maintaining coordinated replication. This review will summarize recent advances in understanding these aspects of chromatin structure in DNA replication origin control.
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Affiliation(s)
- Elizabeth Suzanne Dorn
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
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35
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Abstract
The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investigate regulatory mechanisms underlying long-lasting changes in neurons, with direct implications for the study of brain function, behaviour and diseases.
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Affiliation(s)
- Catherine Dulac
- Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
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