1
|
Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
Collapse
Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| |
Collapse
|
2
|
Gurugubelli KR, Ballambattu VB. Perspectives on folate with special reference to epigenetics and neural tube defects. Reprod Toxicol 2024; 125:108576. [PMID: 38479591 DOI: 10.1016/j.reprotox.2024.108576] [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: 12/27/2023] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Folate is a micronutrient essential for DNA synthesis, cell division, fetal growth and development. Folate deficiency leads to genomic instability. Inadequate intake of folate during conception may lead to neural tube defects (NTDs) in the offspring. Folate influences the DNA methylation, histone methylation and homocysteine mediated gene methylation. DNA methylation influences the expression of microRNAs (miRNAs). Folate deficiency may be associated with miRNAs misregulation leading to NTDs. Mitochondrial epigenetics and folate metabolism has proved to be involved in embryogenesis and neural tube development. Folate related genetic variants also cause the occurrence of NTDs. Unmetabolized excessive folate may affect health adversely. Hence estimation of folate levels in the blood plays an important role in high-risk cases.
Collapse
Affiliation(s)
- Krishna Rao Gurugubelli
- Department of Biochemistry, Andhra Medical College (AMC), Visakhapatnam, Andhra Pradesh, India
| | - Vishnu Bhat Ballambattu
- Aarupadai Veedu Medical College & Hospital (AVMC & H), Vinayaka Mission's Research Foundation (DU), Kirumambakkam, Puducherry, India.
| |
Collapse
|
3
|
Kang J, Benjamin DI, Kim S, Salvi JS, Dhaliwal G, Lam R, Goshayeshi A, Brett JO, Liu L, Rando TA. Depletion of SAM leading to loss of heterochromatin drives muscle stem cell ageing. Nat Metab 2024; 6:153-168. [PMID: 38243132 PMCID: PMC10976122 DOI: 10.1038/s42255-023-00955-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/30/2023] [Indexed: 01/21/2024]
Abstract
The global loss of heterochromatin during ageing has been observed in eukaryotes from yeast to humans, and this has been proposed as one of the causes of ageing. However, the cause of this age-associated loss of heterochromatin has remained enigmatic. Here we show that heterochromatin markers, including histone H3K9 di/tri-methylation and HP1, decrease with age in muscle stem cells (MuSCs) as a consequence of the depletion of the methyl donor S-adenosylmethionine (SAM). We find that restoration of intracellular SAM in aged MuSCs restores heterochromatin content to youthful levels and rejuvenates age-associated features, including DNA damage accumulation, increased cell death, and defective muscle regeneration. SAM is not only a methyl group donor for transmethylation, but it is also an aminopropyl donor for polyamine synthesis. Excessive consumption of SAM in polyamine synthesis may reduce its availability for transmethylation. Consistent with this premise, we observe that perturbation of increased polyamine synthesis by inhibiting spermidine synthase restores intracellular SAM content and heterochromatin formation, leading to improvements in aged MuSC function and regenerative capacity in male and female mice. Together, our studies demonstrate a direct causal link between polyamine metabolism and epigenetic dysregulation during murine MuSC ageing.
Collapse
Affiliation(s)
- Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel I Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jayesh S Salvi
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Gurkamal Dhaliwal
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard Lam
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Armon Goshayeshi
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jamie O Brett
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
- Department of Neurology and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Neurology Service, Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
- Department of Neurology and Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
4
|
Fu Y, Yu B, Wang Q, Lu Z, Zhang H, Zhang D, Luo F, Liu R, Wang L, Chu Y. Oxidative stress-initiated one-carbon metabolism drives the generation of interleukin-10-producing B cells to resolve pneumonia. Cell Mol Immunol 2024; 21:19-32. [PMID: 38082147 PMCID: PMC10757717 DOI: 10.1038/s41423-023-01109-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/07/2023] [Indexed: 01/01/2024] Open
Abstract
The metabolic reprogramming underlying the generation of regulatory B cells during infectious diseases remains unknown. Using a Pseudomonas aeruginosa-induced pneumonia model, we reported that IL-10-producing B cells (IL-10+ B cells) play a key role in spontaneously resolving infection-mediated inflammation. Accumulated cytosolic reactive oxygen species (ROS) during inflammation were shown to drive IL-10+ B-cell generation by remodeling one-carbon metabolism. Depletion of the enzyme serine hydroxymethyltransferase 1 (Shmt1) led to inadequate one-carbon metabolism and decreased IL-10+ B-cell production. Furthermore, increased one-carbon flux elevated the levels of the methyl donor S-adenosylmethionine (SAM), altering histone H3 lysine 4 methylation (H3K4me) at the Il10 gene to promote chromatin accessibility and upregulate Il10 expression in B cells. Therefore, the one-carbon metabolism-associated compound ethacrynic acid (EA) was screened and found to potentially treat infectious pneumonia by boosting IL-10+ B-cell generation. Overall, these findings reveal that ROS serve as modulators to resolve inflammation by reprogramming one-carbon metabolism pathways in B cells.
Collapse
Affiliation(s)
- Ying Fu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Baichao Yu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Wang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhou Lu
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Shanghai, China
| | - Hushan Zhang
- Zhaotong Health Vocational College, Zhaotong, Yunnan, China
| | - Dan Zhang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feifei Luo
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ronghua Liu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Luman Wang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- Shanghai Fifth People's Hospital, Fudan University, Shanghai, China.
| | - Yiwei Chu
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
5
|
Soukar I, Amarasinghe A, Pile LA. Coordination of cross-talk between metabolism and epigenetic regulation by the SIN3 complex. Enzymes 2023; 53:33-68. [PMID: 37748836 DOI: 10.1016/bs.enz.2023.06.001] [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] [Indexed: 09/27/2023]
Abstract
Post-translational modifications of histone proteins control the expression of genes. Metabolites from central and one-carbon metabolism act as donor moieties to modify histones and regulate gene expression. Thus, histone modification and gene regulation are connected to the metabolite status of the cell. Histone modifiers, such as the SIN3 complex, regulate genes involved in proliferation and metabolism. The SIN3 complex contains a histone deacetylase and a histone demethylase, which regulate the chromatin landscape and gene expression. In this chapter, we review the cross-talk between metabolic pathways that produce donor moieties, and epigenetic complexes regulating proliferation and metabolic genes. This cross-talk between gene regulation and metabolism is tightly controlled, and disruption of this cross-talk leads to metabolic diseases. We discuss promising therapeutics that directly regulate histone modifiers, and can affect the metabolic status of the cell, alleviating some metabolic diseases.
Collapse
Affiliation(s)
- Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Anjalie Amarasinghe
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States.
| |
Collapse
|
6
|
Schneider V, Visone J, Harris C, Florini F, Hadjimichael E, Zhang X, Gross M, Rhee K, Ben Mamoun C, Kafsack B, Deitsch K. The human malaria parasite Plasmodium falciparum can sense environmental changes and respond by antigenic switching. Proc Natl Acad Sci U S A 2023; 120:e2302152120. [PMID: 37068249 PMCID: PMC10151525 DOI: 10.1073/pnas.2302152120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
The primary antigenic and virulence determinant of the human malaria parasite Plasmodium falciparum is a variant surface protein called PfEMP1. Different forms of PfEMP1 are encoded by a multicopy gene family called var, and switching between active genes enables the parasites to evade the antibody response of their human hosts. var gene switching is key for the maintenance of chronic infections; however, what controls switching is unknown, although it has been suggested to occur at a constant frequency with little or no environmental influence. var gene transcription is controlled epigenetically through the activity of histone methyltransferases (HMTs). Studies in model systems have shown that metabolism and epigenetic control of gene expression are linked through the availability of intracellular S-adenosylmethionine (SAM), the principal methyl donor in biological methylation modifications, which can fluctuate based on nutrient availability. To determine whether environmental conditions and changes in metabolism can influence var gene expression, P. falciparum was cultured in media with altered concentrations of nutrients involved in SAM metabolism. We found that conditions that influence lipid metabolism induce var gene switching, indicating that parasites can respond to changes in their environment by altering var gene expression patterns. Genetic modifications that directly modified expression of the enzymes that control SAM levels similarly led to profound changes in var gene expression, confirming that changes in SAM availability modulate var gene switching. These observations directly challenge the paradigm that antigenic variation in P. falciparum follows an intrinsic, programed switching rate, which operates independently of any external stimuli.
Collapse
Affiliation(s)
- Victoria M. Schneider
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
- Laboratory of Chemical Biology and Microbial Pathogenesis, Rockefeller University, New York, NY 10065
| | - Joseph E. Visone
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Chantal T. Harris
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Francesca Florini
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Evi Hadjimichael
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Mackensie R. Gross
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Kyu Y. Rhee
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Choukri Ben Mamoun
- Section of Infectious Disease, Department of Microbial Pathogenesis, Yale School of Medicine, Yale University New Haven, CT 06510
| | - Björn F. C. Kafsack
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, Ithaca, NY14853
| |
Collapse
|
7
|
Islam A, Shaukat Z, Hussain R, Gregory SL. One-Carbon and Polyamine Metabolism as Cancer Therapy Targets. Biomolecules 2022; 12:biom12121902. [PMID: 36551330 PMCID: PMC9775183 DOI: 10.3390/biom12121902] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer metabolic reprogramming is essential for maintaining cancer cell survival and rapid replication. A common target of this metabolic reprogramming is one-carbon metabolism which is notable for its function in DNA synthesis, protein and DNA methylation, and antioxidant production. Polyamines are a key output of one-carbon metabolism with widespread effects on gene expression and signaling. As a result of these functions, one-carbon and polyamine metabolism have recently drawn a lot of interest for their part in cancer malignancy. Therapeutic inhibitors that target one-carbon and polyamine metabolism have thus been trialed as anticancer medications. The significance and future possibilities of one-carbon and polyamine metabolism as a target in cancer therapy are discussed in this review.
Collapse
Affiliation(s)
- Anowarul Islam
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Zeeshan Shaukat
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Rashid Hussain
- Clinical and Health Sciences, University of South Australia, Adelaide 5001, Australia
| | - Stephen L. Gregory
- College of Medicine and Public Health, Flinders University, Adelaide 5042, Australia
- Correspondence: ; Tel.: +61-0466987583
| |
Collapse
|
8
|
Meneses JAM, Nascimento KB, Galvão MC, Ramírez-Zamudio GD, Gionbelli TRS, Ladeira MM, Duarte MDS, Casagrande DR, Gionbelli MP. Protein Supplementation during Mid-Gestation Alters the Amino Acid Patterns, Hepatic Metabolism, and Maternal Skeletal Muscle Turnover of Pregnant Zebu Beef Cows. Animals (Basel) 2022; 12:ani12243567. [PMID: 36552487 PMCID: PMC9774392 DOI: 10.3390/ani12243567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
From 100 to 200 days of gestation, 52 cows carrying male (n = 30) or female (n = 22) fetuses were assigned to CON (basal diet-5.5% of CP, n = 26) or SUP (basal diet + protein supplement [40% CP, 3.5 g/kg BW]-12% of CP, n = 26) treatments. Glucose concentrations decreased at 200 (p ≤ 0.01; CON = 46.9 and SUP = 54.7 mg/dL) and 270 days (p ≤ 0.05; CON = 48.4 and SUP = 53.3 mg/dL) for CON compared to SUP. The same pattern occurred for insulin (p ≤ 0.01). At parturition, the NEFA concentration was greater (p = 0.01, 0.10 vs. 0.08 mmol/L) for CON than for SUP. Total AA increased in SUP (p ≤ 0.03) at mid- and late-gestation compared to CON. At 200 days, CON dams carrying females had less essential AA (p = 0.01) than cows carrying males. The SUP dams had greater expressions of protein synthesis markers, namely eIf4E and GSK3β (p ≤ 0.04), at day 200 and of MuFR1 (protein degradation marker, p ≤ 0.04) at parturition. Supplemented cows had higher hepatic pyruvate carboxylase expressions (p = 0.02). Therefore, PS alleviates the restriction overload on maternal metabolism.
Collapse
Affiliation(s)
- Javier Andrés Moreno Meneses
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
- Department of Veterinary Medicine and Animal Science, Universidad de Ciencias Aplicadas y Ambientales, Cartagena 130001, Bolivar, Colombia
| | | | | | | | | | - Marcio Machado Ladeira
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
| | | | - Daniel Rume Casagrande
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
| | - Mateus Pies Gionbelli
- Department of Animal Science, Universidade Federal de Lavras, Lavras 37200-900, MG, Brazil
- Correspondence: ; Tel.: +55-(35)-3829-4618
| |
Collapse
|
9
|
Gorica E, Mohammed SA, Ambrosini S, Calderone V, Costantino S, Paneni F. Epi-Drugs in Heart Failure. Front Cardiovasc Med 2022; 9:923014. [PMID: 35911511 PMCID: PMC9326055 DOI: 10.3389/fcvm.2022.923014] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Unveiling the secrets of genome’s flexibility does not only foster new research in the field, but also gives rise to the exploration and development of novel epigenetic-based therapies as an approach to alleviate disease phenotypes. A better understanding of chromatin biology (DNA/histone complexes) and non-coding RNAs (ncRNAs) has enabled the development of epigenetic drugs able to modulate transcriptional programs implicated in cardiovascular diseases. This particularly applies to heart failure, where epigenetic networks have shown to underpin several pathological features, such as left ventricular hypertrophy, fibrosis, cardiomyocyte apoptosis and microvascular dysfunction. Targeting epigenetic signals might represent a promising approach, especially in patients with heart failure with preserved ejection fraction (HFpEF), where prognosis remains poor and breakthrough therapies have yet to be approved. In this setting, epigenetics can be employed for the development of customized therapeutic approaches thus paving the way for personalized medicine. Even though the beneficial effects of epi-drugs are gaining attention, the number of epigenetic compounds used in the clinical practice remains low suggesting that more selective epi-drugs are needed. From DNA-methylation changes to non-coding RNAs, we can establish brand-new regulations for drug targets with the aim of restoring healthy epigenomes and transcriptional programs in the failing heart. In the present review, we bring the timeline of epi-drug discovery and development, thus highlighting the emerging role of epigenetic therapies in heart failure.
Collapse
Affiliation(s)
- Era Gorica
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland
| | | | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Cardiology, University Heart Center, Zurich, Switzerland
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Schlieren, Switzerland.,Department of Cardiology, University Heart Center, Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| |
Collapse
|
10
|
Dietary folic acid supplementation improves semen quality and spermatogenesis through altering autophagy and histone methylation in the testis of aged broiler breeder roosters. Theriogenology 2021; 181:8-15. [PMID: 34998023 DOI: 10.1016/j.theriogenology.2021.12.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 12/21/2022]
Abstract
The aging phenomenon often exerts a significant reduction in the reproduction performance of aged animals. The objective of this project was to investigate the effects of dietary Folic acid (FA) supplementation on the reproductive performance of aged broiler breeder roosters. A total of 16 aged ROSS 308 broiler breeder roosters (50-week-old) were randomly divided into two groups. The treatments were basal diet (CON), a basal diet supplemented with 10 mg/kg Folic acid (FAS) for four weeks. At the end of the experiment, semen quality, histopathological studies, serum concentrations of testosterone and relative mRNA and protein expressions of testes were evaluated. The results showed that dietary FA supplementation dramatically improved semen quality of aged roosters, manifested by increasing semen volume, sperm concentration, sperm motility, and sperm membrane functional integrity. Furthermore, seminiferous tubule epithelial height (SEH) and testis scores were increased by dietary supplementation with FA. Dietary FA also remarkably augmented the transcription level of spermatogenesis-related gene (CREM, PCK2, DDX4, and GDNF). No significant differences were observed in serum concentrations of testosterone between FAS and CON groups. We noted significant upregulation Beclin-1 and ATG5 protein expressions, and the ratio of LC3-Ⅱ/Ⅰ, as well as significant downregulation of p-mTOR protein expressions in testicular tissue of aged roosters with FA supplementation. In addition, dietary FA supplementation significantly increased the protein expression of H3K9me2 and reduced the protein expression of H3K27me2. In summary, dietary FA supplementation improved the testicular autophagy through the mTOR-signaling pathway, and altered histone methylation in the testis. Dietary supplementation with FA can ameliorate semen quality and spermatogenesis of aged roosters.
Collapse
|
11
|
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.
Collapse
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;
| |
Collapse
|
12
|
Castellano-Castillo D, Ramos-Molina B, Cardona F, Queipo-Ortuño MI. Epigenetic regulation of white adipose tissue in the onset of obesity and metabolic diseases. Obes Rev 2020; 21:e13054. [PMID: 32542987 DOI: 10.1111/obr.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/16/2022]
Abstract
Obesity and metabolic syndrome are among the most prevalent health problems in developed countries. The impairment of adipose tissue (AT) function is partially responsible for the aetiology of these conditions. Epigenetics refers to several processes that add modifications to either the DNA or chromatin architectural proteins (histones). These processes can regulate gene expression, chromatin compaction and DNA repair. Epigenetics includes mechanisms by which the cell can adapt the cellular response to the environmental conditions. Here, we review the role of epigenetics in the onset of obesity and related metabolic disorders, with special focus on AT. We highlight the importance of nutrients and lifestyle in the regulation of the epigenetic mechanisms and how they can impact on AT plasticity and function in obesity and metabolic diseases. Thus, the epigenetic landscape emerges as a fine-tune regulator of the cellular responses according to the energetic, metabolic and physiological conditions of the cell. Alterations in metabolic pathways deregulated during obesity and metabolic syndrome could in part explain the disturbances in the epigenetic marks of the AT in these disorders. The understanding of how this epigenetic deregulation may affect AT biology and function could lead to new therapeutic approaches based on epigenetic strategies.
Collapse
Affiliation(s)
- Daniel Castellano-Castillo
- Hospital Clínico Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
| | - Bruno Ramos-Molina
- Hospital Universitario Virgen de la Arrixaca, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Fernando Cardona
- Hospital Clínico Universitario Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga, Málaga, Spain
| | - María Isabel Queipo-Ortuño
- Unidad de Gestión Clínica Intercentros de Oncología Medica, Hospitales Universitarios Regional y Virgen de la Victoria, Instituto de Investigación Biomédica de Málaga (IBIMA)-CIMES-UMA, Universidad de Málaga, Málaga, Spain
| |
Collapse
|
13
|
Gong X, Yu Q, Duan K, Tong Y, Zhang X, Mei Q, Lu L, Yu X, Li S. Histone acetyltransferase Gcn5 regulates gene expression by promoting the transcription of histone methyltransferase SET1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194603. [PMID: 32663628 DOI: 10.1016/j.bbagrm.2020.194603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/20/2020] [Accepted: 07/08/2020] [Indexed: 01/26/2023]
Abstract
Many chromatin modifying factors regulate gene expression in an as-yet-unknown indirect manner. Revealing the molecular basis for this indirect gene regulation will help understand their precise roles in gene regulation and associated biological processes. Here, we studied histone modifying enzymes that indirectly regulate gene expression by modulating the expression of histone methyltransferase, Set1. Through unbiased screening of the histone H3/H4 mutant library, we identified 13 histone substitution mutations with reduced levels of Set1 and H3K4 trimethylation (H3K4me3) and 2 mutations with increased levels of Set1 and H3K4me3, which concentrate at 3 structure clusters. Among these substitutions, the H3K14A mutant substantially reduces SET1 transcription and H3K4me3. H3K14 is acetylated by histone acetyltransferase Gcn5 at SET1 promoter, which then promotes SET1 transcription to maintain normal H3K4me3 levels. In contrast, the histone deacetylase Rpd3 deacetylates H3K14 to repress SET1 transcription and hence reduce H3K4me3 levels, establishing a dynamic crosstalk between H3K14ac and H3K4me3. By promoting the transcription of SET1 and maintaining H3K4me3 levels, Gcn5 regulates the transcription of a subset gene in an indirect manner. Collectively, we propose a model wherein Gcn5 promotes the expression of chromatin modifiers to regulate histone crosstalk and gene transcription.
Collapse
Affiliation(s)
- Xuanyunjing Gong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Kai Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Yue Tong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xinyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qianyun Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Li Lu
- Institute of TCM and Natural Products, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| |
Collapse
|
14
|
Wu Y, Zhang S, Gong X, Yu Q, Zhang Y, Luo M, Zhang X, Workman JL, Yu X, Li S. Glycolysis regulates gene expression by promoting the crosstalk between H3K4 trimethylation and H3K14 acetylation in Saccharomyces cerevisiae. J Genet Genomics 2019; 46:561-574. [PMID: 32014433 DOI: 10.1016/j.jgg.2019.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/18/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022]
Abstract
Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains largely unknown. Here, we report that glucose specifically induces histone H3K4 trimethylation (H3K4me3), an evolutionarily conserved histone covalent modification associated with active gene transcription, and that glycolytic enzymes and metabolites are required for this induction. Although glycolysis supplies S-adenosylmethionine for histone methyltransferase Set1 to catalyze H3K4me3, glucose induces H3K4me3 primarily by inhibiting histone demethylase Jhd2-catalyzed H3K4 demethylation. Glycolysis provides acetyl-CoA to stimulate histone acetyltransferase Gcn5 to acetylate H3K14, which then inhibits the binding of Jhd2 to chromatin to increase H3K4me3. By repressing Jhd2-mediated H3K4 demethylation, glycolytic enzymes regulate gene expression and cell survival during chronological aging. Thus, our results elucidate how cells reprogram their gene expression programs in response to glucose availability via histone modifications.
Collapse
Affiliation(s)
- Yinsheng Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Shihao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xuanyunjing Gong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Mingdan Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xianhua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| |
Collapse
|
15
|
Liu CF, Tang WW. Epigenetics in Cardiac Hypertrophy and Heart Failure. JACC Basic Transl Sci 2019; 4:976-993. [PMID: 31909304 PMCID: PMC6938823 DOI: 10.1016/j.jacbts.2019.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
Heart failure (HF) is a complex syndrome affecting millions of people around the world. Over the past decade, the therapeutic potential of targeting epigenetic regulators in HF has been discussed extensively. Recent advances in next-generation sequencing techniques have contributed substantial progress in our understanding of the role of DNA methylation, post-translational modifications of histones, adenosine triphosphate (ATP)-dependent chromatin conformation and remodeling, and non-coding RNAs in HF pathophysiology. In this review, we summarize epigenomic studies on human and animal models in HF.
Collapse
Key Words
- BET, bromodomain
- EZH2, Enhancer of zeste homolog 2
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- HDM, histone demethylase
- HF, heart failure
- HMT, histone methyltransferase
- PRC2, polycomb repressor complex 2
- PTMs, post-translational modifications
- TAD, topologically associating domains
- TMAO, trimethylamine N-oxide
- cardiac hypertrophy
- epigenetics
- heart failure
- lnc-RNAs, long ncRNAs
Collapse
Affiliation(s)
- Chia-Feng Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - W.H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio
| |
Collapse
|
16
|
Asai A, Konno M, Koseki J, Taniguchi M, Vecchione A, Ishii H. One-carbon metabolism for cancer diagnostic and therapeutic approaches. Cancer Lett 2019; 470:141-148. [PMID: 31759958 DOI: 10.1016/j.canlet.2019.11.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 12/31/2022]
Abstract
Altered metabolism is critical for the rapid and unregulated proliferation of cancer cells; hence the requirement for an abundant source of nucleotides. One characteristic of this metabolic reprogramming is in one-carbon (1C) metabolism, which is particularly noteworthy for its role in DNA synthesis. Various forms of methylation are also noteworthy as they relate to cancer cell survival and proliferation. In recent years, 1C metabolism has received substantial attention for its role in cancer malignancy via these functions. Therefore, therapeutic inhibitors targeting 1C metabolism have been utilized as anticancer drugs. This review outlines the importance of 1C metabolism and its clinical application in cancer. Understanding 1C metabolism could aid the development of novel cancer diagnostic and therapeutic methods.
Collapse
Affiliation(s)
- Ayumu Asai
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan; Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan; Artificial Intelligence Research Center, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Jun Koseki
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Masateru Taniguchi
- Artificial Intelligence Research Center, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Rome "Sapienza", Santo Andrea Hospital, Via di Grottarossa, Rome, 1035-00189, Italy
| | - Hideshi Ishii
- Department of Medical Data Science, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan.
| |
Collapse
|
17
|
Serefidou M, Venkatasubramani AV, Imhof A. The Impact of One Carbon Metabolism on Histone Methylation. Front Genet 2019; 10:764. [PMID: 31555321 PMCID: PMC6722216 DOI: 10.3389/fgene.2019.00764] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
The effect of one carbon metabolism on DNA methylation has been well described, bridging nutrition, metabolism, and epigenetics. This modification is mediated by the metabolite S-adenosyl methionine (SAM), which is also the methyl-donating substrate of histone methyltransferases. Therefore, SAM levels that are influenced by several nutrients, enzymes, and metabolic cofactors also have a potential impact on histone methylation. Although this modification plays a major role in chromatin accessibility and subsequently in gene expression in healthy or diseased states, its role in translating nutritional changes in chromatin structure has not been extensively studied. Here, we aim to review the literature of known mechanistic links between histone methylation and the central one carbon metabolism.
Collapse
Affiliation(s)
- Magdalini Serefidou
- Biomedical Center Munich, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| | | | - Axel Imhof
- Biomedical Center Munich, Department of Molecular Biology, Ludwig-Maximilians-University Munich, Munich, Germany
| |
Collapse
|
18
|
Canonical Wnt is inhibited by targeting one-carbon metabolism through methotrexate or methionine deprivation. Proc Natl Acad Sci U S A 2019; 116:2987-2995. [PMID: 30679275 PMCID: PMC6386671 DOI: 10.1073/pnas.1820161116] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Metabolism, one of the most conserved features across all domains of life, is interwoven with cellular signaling networks and the posttranslational modification state of proteins. Methionine is an essential amino acid in one-carbon metabolism that serves as the substrate for S-adenosylmethionine, the universal methyl donor for cellular methylation. Here we report that the use of methionine-depleted medium inhibits Wnt-induced endolysosomal formation and canonical Wnt/β-catenin signaling. Use of methotrexate, a folate cycle inhibitor used in cancer chemotherapy, prevented PRMT1 and GSK3 vesicular sequestration, decreased Wnt-driven endolysosomal activity, and reduced canonical Wnt β-catenin luciferase signaling. In sum, these results imply a role for one-carbon metabolism in the regulation of Wnt signaling and endolysosomal biology. The nutrient-sensing metabolite S-adenosylmethionine (SAM) controls one-carbon metabolism by donating methyl groups to biochemical building blocks, DNA, RNA, and protein. Our recent work uncovered a requirement for cytoplasmic arginine methylation during Wnt signaling through the activity of protein arginine methyltransferase 1 (PRMT1), which transfers one-carbon groups from SAM to many protein substrates. Here, we report that treatments that decrease levels of the universal methyl donor SAM were potent inhibitors of Wnt signaling and of Wnt-induced digestion of extracellular proteins in endolysosomes. Thus, arginine methylation provides the canonical Wnt pathway with metabolic sensing properties through SAM. The rapid accumulation of Wnt-induced endolysosomes within 30 minutes was inhibited by the depletion of methionine, an essential amino acid that serves as the direct substrate for SAM production. We also found that methionine is required for GSK3 sequestration into multivesicular bodies through microautophagy, an essential step in Wnt signaling activity. Methionine starvation greatly reduced Wnt-induced endolysosomal degradation of extracellular serum proteins. Similar results were observed by addition of nicotinamide (vitamin B3), which serves as a methyl group sink. Methotrexate, a pillar in the treatment of cancer since 1948, decreases SAM levels. We show here that methotrexate blocked Wnt-induced endocytic lysosomal activity and reduced canonical Wnt signaling. Importantly, the addition of SAM during methionine depletion or methotrexate treatment was sufficient to rescue endolysosomal function and Wnt signaling. Inhibiting the Wnt signaling pathway by decreasing one-carbon metabolism provides a platform for designing interventions in Wnt-driven disease.
Collapse
|
19
|
Yu X, Ma R, Wu Y, Zhai Y, Li S. Reciprocal Regulation of Metabolic Reprogramming and Epigenetic Modifications in Cancer. Front Genet 2018; 9:394. [PMID: 30283496 PMCID: PMC6156463 DOI: 10.3389/fgene.2018.00394] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/29/2018] [Indexed: 11/13/2022] Open
Abstract
Cancer cells reprogram their metabolism to meet their demands for survival and proliferation. The metabolic plasticity of tumor cells help them adjust to changes in the availability and utilization of nutrients in the microenvironment. Recent studies revealed that many metabolites and metabolic enzymes have non-metabolic functions contributing to tumorigenesis. One major function is regulating epigenetic modifications to facilitate appropriate responses to environmental cues. Accumulating evidence showed that epigenetic modifications could in turn alter metabolism in tumors. Although a comprehensive understanding of the reciprocal connection between metabolic and epigenetic rewiring in cancer is lacking, some conceptual advances have been made. Understanding the link between metabolism and epigenetic modifications in cancer cells will shed lights on the development of more effective cancer therapies.
Collapse
Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Rui Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Yinsheng Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Yansheng Zhai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, China
| |
Collapse
|
20
|
Ye C, Tu BP. Sink into the Epigenome: Histones as Repositories That Influence Cellular Metabolism. Trends Endocrinol Metab 2018; 29:626-637. [PMID: 30001904 PMCID: PMC6109460 DOI: 10.1016/j.tem.2018.06.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 01/28/2023]
Abstract
Epigenetic modifications on chromatin are most commonly thought to be involved in the transcriptional regulation of gene expression. Due to their dependency on small-molecule metabolites, these modifications can relay information about cellular metabolic state to the genome for the activation or repression of particular sets of genes. In this review we discuss emerging evidence that these modifications might also have a metabolic purpose. Due to their abundance, the histones have the capacity to store substantial amounts of useful metabolites or to enable important metabolic transformations. Such metabolic functions for histones could help to explain the widespread occurrence of particular modifications that may not always be strongly correlated with transcriptional activity.
Collapse
Affiliation(s)
- Cunqi Ye
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA
| | - Benjamin P Tu
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.
| |
Collapse
|
21
|
Schvartzman JM, Thompson CB, Finley LWS. Metabolic regulation of chromatin modifications and gene expression. J Cell Biol 2018; 217:2247-2259. [PMID: 29760106 PMCID: PMC6028552 DOI: 10.1083/jcb.201803061] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Schvartzman et al. review how alterations in the levels of specific metabolites in mammalian cells result in chromatin modifications that influence gene expression. Dynamic regulation of gene expression in response to changing local conditions is critical for the survival of all organisms. In metazoans, coherent regulation of gene expression programs underlies the development of functionally distinct cell lineages. The cooperation between transcription factors and the chromatin landscape enables precise control of gene expression in response to cell-intrinsic and cell-extrinsic signals. Many of the chemical modifications that decorate DNA and histones are adducts derived from intermediates of cellular metabolic pathways. In addition, several of the enzymes that can remove these marks use metabolites as part of their enzymatic reaction. These observations have led to the hypothesis that fluctuations in metabolite levels influence the deposition and removal of chromatin modifications. In this review, we consider the emerging evidence that cellular metabolic activity contributes to gene expression and cell fate decisions through metabolite-dependent effects on chromatin organization.
Collapse
Affiliation(s)
- Juan Manuel Schvartzman
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY .,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
22
|
Misale MS, Witek Janusek L, Tell D, Mathews HL. Chromatin organization as an indicator of glucocorticoid induced natural killer cell dysfunction. Brain Behav Immun 2018; 67:279-289. [PMID: 28911980 PMCID: PMC5696065 DOI: 10.1016/j.bbi.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 09/01/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022] Open
Abstract
It is well-established that psychological distress reduces natural killer cell immune function and that this reduction can be due to the stress-induced release of glucocorticoids. Glucocorticoids are known to alter epigenetic marks associated with immune effector loci, and are also known to influence chromatin organization. The purpose of this investigation was to assess the effect of glucocorticoids on natural killer cell chromatin organization and to determine the relationship of chromatin organization to natural killer cell effector function, e.g. interferon gamma production. Interferon gamma production is the prototypic cytokine produced by natural killer cells and is known to modulate both innate and adaptive immunity. Glucocorticoid treatment of human peripheral blood mononuclear cells resulted in a significant reduction in interferon gamma production. Glucocorticoid treatment also resulted in a demonstrable natural killer cell nuclear phenotype. This phenotype was localization of the histone, post-translational epigenetic mark, H3K27me3, to the nuclear periphery. Peripheral nuclear localization of H3K27me3 was directly related to cellular levels of interferon gamma. This nuclear phenotype was determined by direct visual inspection and by use of an automated, high through-put technology, the Amnis ImageStream. This technology combines the per-cell information content provided by standard microscopy with the statistical significance afforded by large sample sizes common to standard flow cytometry. Most importantly, this technology provides for a direct assessment of the localization of signal intensity within individual cells. The results demonstrate glucocorticoids to dysregulate natural killer cell function at least in part through altered H3K27me3 nuclear organization and demonstrate H3K27me3 chromatin organization to be a predictive indicator of glucocorticoid induced immune dysregulation of natural killer cells.
Collapse
Affiliation(s)
- Michael S Misale
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Linda Witek Janusek
- Marcella Niehoff School of Nursing, Department of Health Promotion, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Dina Tell
- Marcella Niehoff School of Nursing, Department of Health Promotion, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States
| | - Herbert L Mathews
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Health Science Division, 2160 South First Ave., Maywood, IL 60153, United States.
| |
Collapse
|
23
|
Gao J, Cahill CM, Huang X, Roffman JL, Lamon-Fava S, Fava M, Mischoulon D, Rogers JT. S-Adenosyl Methionine and Transmethylation Pathways in Neuropsychiatric Diseases Throughout Life. Neurotherapeutics 2018; 15:156-175. [PMID: 29340929 PMCID: PMC5794704 DOI: 10.1007/s13311-017-0593-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
S-Adenosyl methionine (SAMe), as a major methyl donor, exerts its influence on central nervous system function through cellular transmethylation pathways, including the methylation of DNA, histones, protein phosphatase 2A, and several catecholamine moieties. Based on available evidence, this review focuses on the lifelong range of severe neuropsychiatric and neurodegenerative diseases and their associated neuropathologies, which have been linked to the deficiency/load of SAMe production or/and the disturbance in transmethylation pathways. Also included in this review are the present-day applications of SAMe in the treatment in these diseases in each age group.
Collapse
Affiliation(s)
- Jin Gao
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Clinical Psychology, Qilu Hospital of Shandong University, Qingdao, Shandong Province, China
| | - Catherine M Cahill
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xudong Huang
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua L Roffman
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefania Lamon-Fava
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Maurizio Fava
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Mischoulon
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jack T Rogers
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
24
|
Krautkramer KA, Dhillon RS, Denu JM, Carey HV. Metabolic programming of the epigenome: host and gut microbial metabolite interactions with host chromatin. Transl Res 2017; 189:30-50. [PMID: 28919341 PMCID: PMC5659875 DOI: 10.1016/j.trsl.2017.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/14/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023]
Abstract
The mammalian gut microbiota has been linked to host developmental, immunologic, and metabolic outcomes. This collection of trillions of microbes inhabits the gut and produces a myriad of metabolites, which are measurable in host circulation and contribute to the pathogenesis of human diseases. The link between endogenous metabolite availability and chromatin regulation is a well-established and active area of investigation; however, whether microbial metabolites can elicit similar effects is less understood. In this review, we focus on seminal and recent research that establishes chromatin regulatory roles for both endogenous and microbial metabolites. We also highlight key physiologic and disease settings where microbial metabolite-host chromatin interactions have been established and/or may be pertinent.
Collapse
Affiliation(s)
- Kimberly A Krautkramer
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis.
| | - Rashpal S Dhillon
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, Wis; Wisconsin Institute for Discovery, Madison, Wis; Morgridge Institute for Research, Madison, Wis
| | - Hannah V Carey
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, Wis
| |
Collapse
|
25
|
Weinhouse C. Mitochondrial-epigenetic crosstalk in environmental toxicology. Toxicology 2017; 391:5-17. [PMID: 28855114 DOI: 10.1016/j.tox.2017.08.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022]
Abstract
Crosstalk between the nuclear epigenome and mitochondria, both in normal physiological function and in responses to environmental toxicant exposures, is a developing sub-field of interest in environmental and molecular toxicology. The majority (∼99%) of mitochondrial proteins are encoded in the nuclear genome, so programmed communication among nuclear, cytoplasmic, and mitochondrial compartments is essential for maintaining cellular health. In this review, we will focus on correlative and mechanistic evidence for direct impacts of each system on the other, discuss demonstrated or potential crosstalk in the context of chemical insult, and highlight biological research questions for future study. We will first review the two main signaling systems: nuclear signaling to the mitochondria [anterograde signaling], best described in regulation of oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis in response to environmental signals received by the nucleus, and mitochondrial signals to the nucleus [retrograde signaling]. Both signaling systems can communicate intracellular energy needs or a need to compensate for dysfunction to maintain homeostasis, but both can also relay inappropriate signals in the presence of dysfunction in either system and contribute to adverse health outcomes. We will first review these two signaling systems and highlight known or biologically feasible epigenetic contributions to both, then briefly discuss the emerging field of epigenetic regulation of the mitochondrial genome, and finally discuss putative "crosstalk phenotypes", including biological phenomena, such as caloric restriction, maintenance of stemness, and circadian rhythm, and states of disease or loss of function, such as cancer and aging, in which both the nuclear epigenome and mitochondria are strongly implicated.
Collapse
Affiliation(s)
- Caren Weinhouse
- Duke Global Health Institute, Duke University, Durham, NC 27708, United States.
| |
Collapse
|
26
|
Abstract
In this review, van der Knapp and Verrijzer discuss the current understanding of the molecular mechanisms connecting metabolism to gene expression and their implications for development and disease. To make the appropriate developmental decisions or maintain homeostasis, cells and organisms must coordinate the expression of their genome and metabolic state. However, the molecular mechanisms that relay environmental cues such as nutrient availability to the appropriate gene expression response remain poorly understood. There is a growing awareness that central components of intermediary metabolism are cofactors or cosubstrates of chromatin-modifying enzymes. As such, their concentrations constitute a potential regulatory interface between the metabolic and chromatin states. In addition, there is increasing evidence for a direct involvement of classic metabolic enzymes in gene expression control. These dual-function proteins may provide a direct link between metabolic programing and the control of gene expression. Here, we discuss our current understanding of the molecular mechanisms connecting metabolism to gene expression and their implications for development and disease.
Collapse
Affiliation(s)
- Jan A van der Knaap
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
| |
Collapse
|
27
|
Yu Q, Tong C, Luo M, Xue X, Mei Q, Ma L, Yu X, Mao W, Kong L, Yu X, Li S. Regulation of SESAME-mediated H3T11 phosphorylation by glycolytic enzymes and metabolites. PLoS One 2017; 12:e0175576. [PMID: 28426732 PMCID: PMC5398556 DOI: 10.1371/journal.pone.0175576] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Cancer cells prefer aerobic glycolysis, but little is known about the underlying mechanism. Recent studies showed that the rate-limiting glycolytic enzymes, pyruvate kinase M2 (PKM2) directly phosphorylates H3 at threonine 11 (H3T11) to regulate gene expression and cell proliferation, revealing its non-metabolic functions in connecting glycolysis and histone modifications. We have reported that the yeast homolog of PKM2, Pyk1 phosphorylates H3T11 to regulate gene expression and oxidative stress resistance. But how glycolysis regulates H3T11 phosphorylation remains unclear. Here, using a series of glycolytic enzyme mutants and commercial available metabolites, we investigated the role of glycolytic enzymes and metabolites on H3T11 phosphorylation. Mutation of glycolytic genes including phosphoglucose isomerase (PGI1), enolase (ENO2), triosephosphate isomerase (TPI1), or folate biosynthesis enzyme (FOL3) significantly reduced H3T11 phosphorylation. Further study demonstrated that glycolysis regulates H3T11 phosphorylation by fueling the substrate, phosphoenonylpyruvate and the coactivator, FBP to Pyk1. Thus, our results provide a comprehensive view of how glycolysis modulates H3T11 phosphorylation.
Collapse
Affiliation(s)
- Qi Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Chong Tong
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Mingdan Luo
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Xiangyan Xue
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Qianyun Mei
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Xiaolan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Wuxiang Mao
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Lingbao Kong
- Department of HumanPopulation Genetics, Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China
| | - Xilan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
- * E-mail: (XY); (SL)
| | - Shanshan Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
- * E-mail: (XY); (SL)
| |
Collapse
|
28
|
Tran TQ, Lowman XH, Kong M. Molecular Pathways: Metabolic Control of Histone Methylation and Gene Expression in Cancer. Clin Cancer Res 2017; 23:4004-4009. [PMID: 28404599 DOI: 10.1158/1078-0432.ccr-16-2506] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/05/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic alterations contribute to tumor development, progression, and therapeutic response. Many epigenetic enzymes use metabolic intermediates as cofactors to modify chromatin structure. Emerging evidence suggests that fluctuation in metabolite levels may regulate activities of these chromatin-modifying enzymes. Here, we summarize recent progress in understanding the cross-talk between metabolism and epigenetic control of gene expression in cancer. We focus on how metabolic changes, due to diet, genetic mutations, or tumor microenvironment, regulate histone methylation status and, consequently, affect gene expression profiles to promote tumorigenesis. Importantly, we also suggest some potential therapeutic approaches to target the oncogenic role of metabolic alterations and epigenetic modifications in cancer. Clin Cancer Res; 23(15); 4004-9. ©2017 AACR.
Collapse
Affiliation(s)
- Thai Q Tran
- Department of Cancer Biology, Beckman Research Institute of City of Hope Cancer Center, Duarte, California
| | - Xazmin H Lowman
- Department of Cancer Biology, Beckman Research Institute of City of Hope Cancer Center, Duarte, California
| | - Mei Kong
- Department of Cancer Biology, Beckman Research Institute of City of Hope Cancer Center, Duarte, California.
| |
Collapse
|
29
|
Krautkramer KA, Rey FE, Denu JM. Chemical signaling between gut microbiota and host chromatin: What is your gut really saying? J Biol Chem 2017; 292:8582-8593. [PMID: 28389558 DOI: 10.1074/jbc.r116.761577] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammals and their gut microbial communities share extensive and tightly coordinated co-metabolism of dietary substrates. A large number of microbial metabolites have been detected in host circulation and tissues and, in many cases, are linked to host metabolic, developmental, and immunological states. The presence of these metabolites in host tissues intersects with regulation of the host's epigenetic machinery. Although it is established that the host's epigenetic machinery is sensitive to levels of endogenous metabolites, the roles for microbial metabolites in epigenetic regulation are just beginning to be elucidated. This review focuses on eukaryotic chromatin regulation by endogenous and gut microbial metabolites and how these regulatory events may impact host developmental and metabolic phenotypes.
Collapse
Affiliation(s)
- Kimberly A Krautkramer
- From the Wisconsin Institute for Discovery, Morgridge Institute for Research, and the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53715 and
| | - Federico E Rey
- the Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706
| | - John M Denu
- From the Wisconsin Institute for Discovery, Morgridge Institute for Research, and the Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53715 and
| |
Collapse
|
30
|
Liu M, Pile LA. The Transcriptional Corepressor SIN3 Directly Regulates Genes Involved in Methionine Catabolism and Affects Histone Methylation, Linking Epigenetics and Metabolism. J Biol Chem 2016; 292:1970-1976. [PMID: 28028175 DOI: 10.1074/jbc.m116.749754] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/23/2016] [Indexed: 11/06/2022] Open
Abstract
Chromatin modification and cellular metabolism are tightly connected. Chromatin modifiers regulate the expression of genes involved in metabolism and, in turn, the levels of metabolites. The generated metabolites are utilized by chromatin modifiers to affect epigenetic modification. The mechanism for this cross-talk, however, remains incompletely understood. The corepressor SIN3 controls histone acetylation through association with the histone deacetylase RPD3. The SIN3 complex is known to regulate genes involved in a number of metabolic processes. Here, we find that Drosophila SIN3 binds to the promoter region of genes involved in methionine catabolism and that this binding affects histone modification, which in turn influences gene expression. Specifically, we observe that reduced expression of SIN3 leads to an increase in S-adenosylmethionine (SAM), which is the major cellular donor of methyl groups for protein modification. Additionally, Sin3A knockdown results in an increase in global histone H3K4me3 levels. Furthermore, decreased H3K4me3 caused by knockdown of either SAM synthetase (Sam-S) or the histone methyltransferase Set1 is restored to near normal levels when SIN3 is also reduced. Taken together, these results indicate that knockdown of Sin3A directly alters the expression of methionine metabolic genes to increase SAM, which in turn leads to an increase in global H3K4me3. Our study reveals that SIN3 is an important epigenetic regulator directly connecting methionine metabolism and histone modification.
Collapse
Affiliation(s)
- Mengying Liu
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Lori A Pile
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
| |
Collapse
|
31
|
Vlaming H, Molenaar TM, van Welsem T, Poramba-Liyanage DW, Smith DE, Velds A, Hoekman L, Korthout T, Hendriks S, Altelaar AFM, van Leeuwen F. Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1. eLife 2016; 5. [PMID: 27922451 PMCID: PMC5179194 DOI: 10.7554/elife.18919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 12/02/2016] [Indexed: 12/22/2022] Open
Abstract
Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel. Screening of a barcoded yeast knock-out collection for regulators of histone H3K79 methylation by Dot1 identified all known regulators as well as novel players and processes. These include histone deposition, homologous recombination, and adenosine kinase, which influences the methionine cycle. Gcn5, the acetyltransferase within the SAGA complex, was found to regulate histone methylation and H2B ubiquitination. The concept of Epi-ID is widely applicable and can be readily applied to other chromatin features. DOI:http://dx.doi.org/10.7554/eLife.18919.001 To fit into the nucleus of eukaryotic cells (which include plant, animal and yeast cells), DNA wraps around histone proteins to form a structure called chromatin. Histones can be modified by a variety of chemical tags, which affect how easily nearby DNA can be accessed by other molecules in the cell. These modifications therefore help to control the activity of the genes encoded in the DNA and other key processes such as DNA repair. If histone modifications are not regulated correctly, diseases such as cancer may result. Enzymes generally perform the actual modification, but there is another layer of regulation that controls the activity of these enzymes that not much is known about. The activity of an enzyme that performs a histone modification known as H3K79 methylation (which involves a methyl chemical group being added to a particular region of a particular histone protein) has been linked to some forms of leukemia. Collections of mutant yeast cells can be used to identify the factors that regulate histone modifications in both yeast and human cells. However, current methods that screen for these regulators are time consuming. To make the search for histone modification regulators more efficient, Vlaming et al. developed a new screening procedure called Epi-ID that can measure the amount of a specific histone modification in thousands of budding yeast mutants at the same time. In Epi-ID, each mutant yeast cell has a unique DNA sequence, or “barcode”. The mutant cells are mixed together and the barcodes that are modified by a particular histone modification – such as H3K79 methylation – are isolated and then counted using a DNA sequencing technique. A high barcode count of a certain mutant indicates that more of the histone modification occurs in that mutant. Using Epi-ID to survey H3K79 methylation enabled Vlaming et al. to successfully identify all previously known H3K79 methylation regulators, as well several new ones. These new regulators included enzymes that deposit histones on DNA, that carry out DNA repair, and that modify or de-modify histone proteins. To move forward with the newly identified regulators, it will be important to analyze how they control H3K79 methylation in yeast cells and to determine whether the regulators also control H3K79 methylation in human cells. Finally, Epi-ID can be used to identify regulators of other types of histone modifications. A better understanding of chromatin regulation – and H3K79 methylation regulation in particular – can increase our understanding of diseases in which chromatin is deregulated, and may yield new strategies for the treatment of such diseases. DOI:http://dx.doi.org/10.7554/eLife.18919.002
Collapse
Affiliation(s)
- Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Thom M Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Desiree E Smith
- Department of Clinical Chemistry, Metabolic Laboratory, VU University Medical Center, Amsterdam, Netherlands
| | - Arno Velds
- Central Genomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Liesbeth Hoekman
- Mass Spectrometry/Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tessy Korthout
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sjoerd Hendriks
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - A F Maarten Altelaar
- Mass Spectrometry/Proteomics Facility, Netherlands Cancer Institute, Amsterdam, Netherlands.,Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| |
Collapse
|
32
|
Friso S, Udali S, De Santis D, Choi SW. One-carbon metabolism and epigenetics. Mol Aspects Med 2016; 54:28-36. [PMID: 27876555 DOI: 10.1016/j.mam.2016.11.007] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
The function of one-carbon metabolism is that of regulating the provision of methyl groups for biological methylation reactions including that of DNA and histone proteins. Methylation at specific sites into the DNA sequence and at histone tails are among the major epigenetic feature of mammalian genome for the regulation of gene expression. The enzymes within one-carbon metabolism are dependent from a number of vitamins or nutrients that serve either as co-factors or methyl acceptors or donors among which folate, vitamin B12, vitamin B6, betaine, choline and methionine have a major role. Several evidences show that there is a strict inter-relationship between one-carbon metabolism nutrients and epigenetic phenomena. Epigenetics is closely involved in gene transcriptional regulation through modifications super-imposed to the nucleotide sequence of DNA, such as DNA methylation, through chromatin remodeling systems that involves post-translational modifications of histones or through non-coding RNAs-based mechanisms. The epigenetic features of the genome are potentially modifiable by the action of several environmental factors among which nutrients cover a special place and interest considering their potential of influencing regulatory pathways at a molecular level by specific nutritional intervention and eventually influence disease prevention and outcomes. The present review will focus on the link between one-carbon nutrients and epigenetic phenomena based on the current knowledge from findings in cell culture, animal models and human studies.
Collapse
Affiliation(s)
- Simonetta Friso
- Department of Medicine, University of Verona School of Medicine, Verona, Italy.
| | - Silvia Udali
- Department of Medicine, University of Verona School of Medicine, Verona, Italy
| | - Domenica De Santis
- Department of Medicine, University of Verona School of Medicine, Verona, Italy
| | - Sang-Woon Choi
- Tufts University School of Nutrition Science and Policy, Boston, MA, USA; Chaum Life Center, CHA University, Seoul, South Korea
| |
Collapse
|
33
|
Howe CG, Liu X, Hall MN, Ilievski V, Caudill MA, Malysheva O, Lomax-Luu AM, Parvez F, Siddique AB, Shahriar H, Uddin MN, Islam T, Graziano JH, Costa M, Gamble MV. Sex-Specific Associations between One-Carbon Metabolism Indices and Posttranslational Histone Modifications in Arsenic-Exposed Bangladeshi Adults. Cancer Epidemiol Biomarkers Prev 2016; 26:261-269. [PMID: 27765800 DOI: 10.1158/1055-9965.epi-16-0202] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 09/09/2016] [Accepted: 10/10/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Posttranslational histone modifications (PTHMs) are altered by arsenic, an environmental carcinogen. PTHMs are also influenced by nutritional methyl donors involved in one-carbon metabolism (OCM), which may protect against epigenetic dysregulation. METHODS We measured global levels of three PTHMs, which are dysregulated in cancers (H3K36me2, H3K36me3, H3K79me2), in peripheral blood mononuclear cells (PBMC) from 324 participants enrolled in the Folic Acid and Creatine Trial, a randomized trial in arsenic-exposed Bangladeshi adults. Sex-specific associations between several blood OCM indices (folate, vitamin B12, choline, betaine, homocysteine) and PTHMs were examined at baseline using regression models, adjusted for multiple tests by controlling for the false discovery rate (PFDR). We also evaluated the effects of folic acid supplementation (400 μg/d for 12 weeks), compared with placebo, on PTHMs. RESULTS Associations between choline and H3K36me2 and between vitamin B12 and H3K79me2 differed significantly by sex (Pdiff < 0.01 and <0.05, respectively). Among men, plasma choline was positively associated with H3K36me2 (PFDR < 0.05), and among women, plasma vitamin B12 was positively associated with H3K79me2 (PFDR < 0.01). Folic acid supplementation did not alter any of the PTHMs examined (PFDR = 0.80). CONCLUSIONS OCM indices may influence PTHMs in a sex-dependent manner, and folic acid supplementation, at this dose and duration, does not alter PTHMs in PBMCs. IMPACT This is the first study to examine the influences of OCM indices on PTHMs in a population that may have increased susceptibility to cancer development due to widespread exposure to arsenic-contaminated drinking water and a high prevalence of hyperhomocysteinemia. Cancer Epidemiol Biomarkers Prev; 26(2); 261-9. ©2016 AACR.
Collapse
Affiliation(s)
- Caitlin G Howe
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Xinhua Liu
- Department of Biostatistics, Mailman School of Public Health, New York
| | - Megan N Hall
- Department of Epidemiology, Mailman School of Public Health, New York
| | - Vesna Ilievski
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Olga Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Angela M Lomax-Luu
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Abu B Siddique
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Hasan Shahriar
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Mohammad N Uddin
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Tariqul Islam
- Columbia University Arsenic Project in Bangladesh, Dhaka, Bangladesh
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| | - Max Costa
- Department of Environmental Medicine, NYU Langone Medical Center, New York University, New York
| | - Mary V Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, New York
| |
Collapse
|
34
|
Metabolic interactions with cancer epigenetics. Mol Aspects Med 2016; 54:50-57. [PMID: 27620316 DOI: 10.1016/j.mam.2016.09.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/30/2016] [Accepted: 09/03/2016] [Indexed: 01/31/2023]
Abstract
Cancer cells have epigenetic alterations that are known to drive cancer progression. The reversibility of the epigenetic posttranslational modifications on chromatin and DNA renders targeting these modifications an attractive means for cancer therapy. Cellular epigenetic status interacts with cell metabolism, and we are now beginning to understand the nature of how this interaction occurs and the biological contexts that mediate its function. Given the tremendous interest in understanding and targeting metabolic reprogramming in cancer, this nexus also provides opportunities for exploring the liabilities of cancers. This review summarizes recent developments in our understanding of the interaction of cancer metabolism and epigenetics.
Collapse
|
35
|
Howe CG, Gamble MV. Influence of Arsenic on Global Levels of Histone Posttranslational Modifications: a Review of the Literature and Challenges in the Field. Curr Environ Health Rep 2016; 3:225-37. [PMID: 27352015 PMCID: PMC4967376 DOI: 10.1007/s40572-016-0104-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Arsenic is a human carcinogen and also increases the risk for non-cancer outcomes. Arsenic-induced epigenetic dysregulation may contribute to arsenic toxicity. Although there are several reviews on arsenic and epigenetics, these have largely focused on DNA methylation. Here, we review investigations of the effects of arsenic on global levels of histone posttranslational modifications (PTMs). Multiple studies have observed that arsenic induces higher levels of H3 lysine 9 dimethylation (H3K9me2) and also higher levels of H3 serine 10 phosphorylation (H3S10ph), which regulate chromosome segregation. In contrast, arsenic causes a global loss of H4K16ac, a histone PTM that is a hallmark of human cancers. Although the findings for other histone PTMs have not been entirely consistent across studies, we discuss biological factors which may contribute to these inconsistencies, including differences in the dose, duration, and type of arsenic species examined; the tissue or cell line evaluated; differences by sex; and exposure timing. We also discuss two important considerations for the measurement of histone PTMs: proteolytic cleavage of histones and arsenic-induced alterations in histone expression.
Collapse
Affiliation(s)
- Caitlin G. Howe
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University. Address: 11 Floor, 722 W. 168 Street, New York, New York, 10032. . Phone: 212-305-1205. Fax: 212-305-3857
| | - Mary V. Gamble
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University. Address: 11 Floor, 722 W. 168 Street, New York, New York, 10032. . Phone: 212-305-7949. Fax: 212-305-3857
| |
Collapse
|
36
|
Su X, Wellen KE, Rabinowitz JD. Metabolic control of methylation and acetylation. Curr Opin Chem Biol 2015; 30:52-60. [PMID: 26629854 DOI: 10.1016/j.cbpa.2015.10.030] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Methylation and acetylation of DNA and histone proteins are the chemical basis for epigenetics. From bacteria to humans, methylation and acetylation are sensitive to cellular metabolic status. Modification rates depend on the availability of one-carbon and two-carbon substrates (S-adenosylmethionine, acetyl-CoA, and in bacteria also acetyl-phosphate). In addition, they are sensitive to demodification enzyme cofactors (α-ketoglutarate, NAD(+)) and structural analog metabolites that function as epigenetic enzyme inhibitors (e.g., S-adenosylhomocysteine, 2-hydroxyglutarate). Methylation and acetylation likely initially evolved to tailor protein activities in microbes to their metabolic milieu. While the extracellular environment of mammals is more tightly controlled, the combined impact of nutrient abundance and metabolic enzyme expression impacts epigenetics in mammals sufficiently to drive important biological outcomes such as stem cell fate and cancer.
Collapse
Affiliation(s)
- Xiaoyang Su
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
37
|
Lempradl A, Pospisilik JA, Penninger JM. Exploring the emerging complexity in transcriptional regulation of energy homeostasis. Nat Rev Genet 2015; 16:665-81. [PMID: 26460345 DOI: 10.1038/nrg3941] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Obesity and its associated diseases are expected to affect more than 1 billion people by the year 2030. These figures have sparked intensive research into the molecular control of food intake, nutrient distribution, storage and metabolism--processes that are collectively termed energy homeostasis. Recent decades have also seen dramatic developments in our understanding of gene regulation at the signalling, chromatin and post-transcriptional levels. The seemingly exponential growth in this complexity now poses a major challenge for translational researchers in need of simplified but accurate paradigms for clinical use. In this Review, we consider the current understanding of transcriptional control of energy homeostasis, including both transcriptional and epigenetic regulators, and crosstalk between pathways. We also provide insights into emerging developments and challenges in this field.
Collapse
Affiliation(s)
- Adelheid Lempradl
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - J Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr Bohr-Gasse 3, 1030 Vienna, Austria
| |
Collapse
|
38
|
Liu Y, Liu N, Yin Y, Chen Y, Jiang J, Ma Z. Histone H3K4 methylation regulates hyphal growth, secondary metabolism and multiple stress responses inFusarium graminearum. Environ Microbiol 2015; 17:4615-30. [DOI: 10.1111/1462-2920.12993] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 07/17/2015] [Accepted: 07/18/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Ye Liu
- Institute of Biotechnology; Zhejiang University; Hangzhou 310058 China
| | - Na Liu
- Institute of Biotechnology; Zhejiang University; Hangzhou 310058 China
| | - Yanni Yin
- Institute of Biotechnology; Zhejiang University; Hangzhou 310058 China
| | - Yun Chen
- Institute of Biotechnology; Zhejiang University; Hangzhou 310058 China
| | - Jinhua Jiang
- Institute of Quality and Standard for Agro-products; Zhejiang Academy of Agricultural Sciences; Hangzhou 310021 Zhejiang China
| | - Zhonghua Ma
- Institute of Biotechnology; Zhejiang University; Hangzhou 310058 China
| |
Collapse
|
39
|
Abstract
Epigenetic mechanisms by which cells inherit information are, to a large extent, enabled by DNA methylation and posttranslational modifications of histone proteins. These modifications operate both to influence the structure of chromatin per se and to serve as recognition elements for proteins with motifs dedicated to binding particular modifications. Each of these modifications results from an enzyme that consumes one of several important metabolites during catalysis. Likewise, the removal of these marks often results in the consumption of a different metabolite. Therefore, these so-called epigenetic marks have the capacity to integrate the expression state of chromatin with the metabolic state of the cell. This review focuses on the central roles played by acetyl-CoA, S-adenosyl methionine, NAD(+), and a growing list of other acyl-CoA derivatives in epigenetic processes. We also review how metabolites that accumulate as a result of oncogenic mutations are thought to subvert the epigenetic program.
Collapse
Affiliation(s)
- Ryan Janke
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Anne E Dodson
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Jasper Rine
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| |
Collapse
|
40
|
|
41
|
Kellenberger CA, Sales-Lee J, Pan Y, Gassaway MM, Herr AE, Hammond MC. A minimalist biosensor: Quantitation of cyclic di-GMP using the conformational change of a riboswitch aptamer. RNA Biol 2015; 12:1189-97. [PMID: 26114964 DOI: 10.1080/15476286.2015.1062970] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cyclic di-GMP (c-di-GMP) is a second messenger that is important in regulating bacterial physiology and behavior, including motility and virulence. Many questions remain about the role and regulation of this signaling molecule, but current methods of detection are limited by either modest sensitivity or requirements for extensive sample purification. We have taken advantage of a natural, high affinity receptor of c-di-GMP, the Vc2 riboswitch aptamer, to develop a sensitive and rapid electrophoretic mobility shift assay (EMSA) for c-di-GMP quantitation that required minimal engineering of the RNA.
Collapse
Affiliation(s)
| | - Jade Sales-Lee
- a Department of Chemistry ; University of California, Berkeley ; Berkeley , CA USA
| | - Yuchen Pan
- b Graduate Program in Bioengineering; University of California, Berkeley ; Berkeley , CA USA
| | - Madalee M Gassaway
- a Department of Chemistry ; University of California, Berkeley ; Berkeley , CA USA
| | - Amy E Herr
- b Graduate Program in Bioengineering; University of California, Berkeley ; Berkeley , CA USA
| | - Ming C Hammond
- a Department of Chemistry ; University of California, Berkeley ; Berkeley , CA USA.,c Department of Molecular & Cell Biology ; University of California, Berkeley ; Berkeley , CA USA
| |
Collapse
|
42
|
Huang Z, Cai L, Tu BP. Dietary control of chromatin. Curr Opin Cell Biol 2015; 34:69-74. [PMID: 26094239 DOI: 10.1016/j.ceb.2015.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 12/28/2022]
Abstract
Organisms must be able to rapidly alter gene expression in response to changes in their nutrient environment. This review summarizes evidence that epigenetic modifications of chromatin depend on particular metabolites of intermediary metabolism, enabling the facile regulation of gene expression in tune with metabolic state. Nutritional or dietary control of chromatin is an often-overlooked, yet fundamental regulatory mechanism directly linked to human physiology. Nutrient-sensitive epigenetic marks are dynamic, suggesting rapid turnover, and may have functions beyond the regulation of gene transcription, including pH regulation and as carbon sources in cancer cells.
Collapse
Affiliation(s)
- Zhiguang Huang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Ling Cai
- Children's Medical Center Research Institute, UT Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| |
Collapse
|
43
|
Yu L, Yang G, Weng X, Liang P, Li L, Li J, Fan Z, Tian W, Wu X, Xu H, Fang M, Ji Y, Li Y, Chen Q, Xu Y. Histone Methyltransferase SET1 Mediates Angiotensin II-Induced Endothelin-1 Transcription and Cardiac Hypertrophy in Mice. Arterioscler Thromb Vasc Biol 2015; 35:1207-17. [PMID: 25814673 DOI: 10.1161/atvbaha.115.305230] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 03/16/2015] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Endothelin-1 is a potent vasoconstrictor derived from vascular endothelium. Elevated endothelin-1 levels are observed in a host of cardiovascular pathologies including cardiomyopathy. The epigenetic mechanism responsible for endothelin-1 induction in these pathological processes remains elusive. APPROACH AND RESULTS We report here that induction of endothelin-1 expression in endothelial cells by angiotensin II (Ang II) was accompanied by the accumulation of histone H3K4 trimethylation, a preeminent histone modification for transcriptional activation, on the endothelin-1 promoter. In the meantime, Ang II stimulated the expression and the occupancy of Suv, Ez, and Trithorax domain 1 (SET1), a mammalian histone H3K4 trimethyltransferase, on the endothelin-1 promoter, both in vitro and in vivo. SET1 was recruited to the endothelin-1 promoter by activating protein 1 (c-Jun/c-Fos) and synergized with activating protein 1 to activate endothelin-1 transcription in response to Ang II treatment. Knockdown of SET1 in endothelial cells blocked Ang II-induced endothelin-1 synthesis and abrogated hypertrophy of cultured cardiomyocyte. Finally, endothelial-specific depletion of SET1 in mice attenuated Ang II-induced pathological hypertrophy and cardiac fibrosis. CONCLUSIONS Our data suggest that SET1 epigenetically activates endothelin-1 transcription in endothelial cells, thereby contributing to Ang II-induced cardiac hypertrophy. As such, screening of small-molecule compound that inhibits SET1 activity will likely offer a new therapeutic solution to the treatment of cardiomyopathy.
Collapse
Affiliation(s)
- Liming Yu
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Guang Yang
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Xinyu Weng
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Peng Liang
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Luyang Li
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Jianfei Li
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Zhiwen Fan
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Wenfang Tian
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Xiaoyan Wu
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Huihui Xu
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Minming Fang
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Yong Ji
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Yuehua Li
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Qi Chen
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.)
| | - Yong Xu
- From the Key Laboratory of Cardiovascular Disease and Department of Pathophysiology (L.Y., G.Y., X.W., P.L., L.L., J.L., Z.F., W.T., X.W., H.X., M.F., Y.J., Y.L., Q.C., Y.X.) and Laboratory Center for Basic Medical Sciences (X.W.), Nanjing Medical University, Nanjing, China; and Department of Surgery, Jiangsu Jiankang Vocational University, Nanjing, China (M.F.).
| |
Collapse
|
44
|
Fan J, Krautkramer KA, Feldman JL, Denu JM. Metabolic regulation of histone post-translational modifications. ACS Chem Biol 2015; 10:95-108. [PMID: 25562692 DOI: 10.1021/cb500846u] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone post-translational modifications regulate transcription and other DNA-templated functions. This process is dynamically regulated by specific modifying enzymes whose activities require metabolites that either serve as cosubstrates or act as activators/inhibitors. Therefore, metabolism can influence histone modification by changing local concentrations of key metabolites. Physiologically, the epigenetic response to metabolism is important for nutrient sensing and environment adaption. In pathologic states, the connection between metabolism and histone modification mediates epigenetic abnormality in complex disease. In this review, we summarize recent studies of the molecular mechanisms involved in metabolic regulation of histone modifications and discuss their biological significance.
Collapse
Affiliation(s)
- Jing Fan
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Kimberly A. Krautkramer
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Jessica L. Feldman
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| |
Collapse
|
45
|
Kolybaba A, Classen AK. Sensing cellular states--signaling to chromatin pathways targeting Polycomb and Trithorax group function. Cell Tissue Res 2014; 356:477-93. [PMID: 24728925 DOI: 10.1007/s00441-014-1824-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/22/2014] [Indexed: 02/06/2023]
Abstract
Cells respond to extra- and intra-cellular signals by dynamically changing their gene expression patterns. After termination of the original signal, new expression patterns are maintained by epigenetic DNA and histone modifications. This represents a powerful mechanism that enables long-term phenotypic adaptation to transient signals. Adaptation of epigenetic landscapes is important for mediating cellular differentiation during development and allows adjustment to altered environmental conditions throughout life. Work over the last decade has begun to elucidate the way that extra- and intra-cellular signals lead to changes in gene expression patterns by directly modulating the function of chromatin-associated proteins. Here, we review key signaling-to-chromatin pathways that are specifically thought to target Polycomb and Trithorax group complexes, a classic example of epigenetically acting gene silencers and activators important in development, stem cell differentiation and cancer. We discuss the influence that signals triggered by kinase cascades, metabolic fluctuations and cell-cycle dynamics have on the function of these protein complexes. Further investigation into these pathways will be important for understanding the mechanisms that maintain epigenetic stability and those that promote epigenetic plasticity.
Collapse
Affiliation(s)
- Addie Kolybaba
- Ludwig Maximilians University Munich, Faculty of Biology, Grosshaderner Strasse 2-4, 82152, Planegg-Martinsried, Germany
| | | |
Collapse
|
46
|
Abstract
PURPOSE OF REVIEW Nutrition exerts a pervasive impact on normal and pathological conditions of the nervous system. One critical pathway is the methionine cycle, in which folate and B12 convert homocysteine to methionine, which is in turn converted to S-adenosyl methionine (SAM; the major methyl donor). As a consequence of methylation, however, SAM is converted to the neurotoxin homocysteine and must be excreted or drawn back into the methionine cycle, which requires additional folate and B12. Dietary or genetic folate deficiency impairs this cycle, leading to developmental disorders, including those of the nervous system. RECENT FINDINGS Folate and SAM exert profound epigenetic effects via DNA and histone methylation. Maternal supplementation during pregnancy has fostered an increase in individuals harboring genetic polymorphisms that compromise folate usage. Such individuals harbor a lifetime requirement for additional dietary folate, often not met beyond peri/postnatal periods. Herein, we consider the potential link of failure to meet this additional requirement to early and age-related cognitive compromise. SUMMARY Compromises in the methionine cycle can manifest as a spectrum of disorders throughout life. These considerations underscore how prenatal nutritional supplementation can alleviate developmental disorders by inadvertently establishing latent conditions that, in the absence of continued supplementation, may lead to age-related cognitive decline.
Collapse
|