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Ramakrishnan M, Papolu PK, Satish L, Vinod KK, Wei Q, Sharma A, Emamverdian A, Zou LH, Zhou M. Redox status of the plant cell determines epigenetic modifications under abiotic stress conditions and during developmental processes. J Adv Res 2022; 42:99-116. [PMID: 35690579 PMCID: PMC9788946 DOI: 10.1016/j.jare.2022.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The oxidation-reduction (redox) status of the cell influences or regulates transcription factors and enzymes involved in epigenetic changes, such as DNA methylation, histone protein modifications, and chromatin structure and remodeling. These changes are crucial regulators of chromatin architecture, leading to differential gene expression in eukaryotes. But the cell's redox homeostasis is difficult to sustain since the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS) is not equal in plants at different developmental stages and under abiotic stress conditions. Exceeding optimum ROS and RNS levels leads to oxidative stress and thus alters the redox status of the cell. Consequently, this alteration modulates intracellular epigenetic modifications that either mitigate or mediate the plant growth and stress response. AIM OF REVIEW Recent studies suggest that the altered redox status of the cell reform the cellular functions and epigenetic changes. Recent high-throughput techniques have also greatly advanced redox-mediated gene expression discovery, but the integrated view of the redox status, and its associations with epigenetic changes and subsequent gene expression in plants are still scarce. In this review, we accordingly focus on how the redox status of the cell affects epigenetic modifications in plants under abiotic stress conditions and during developmental processes. This is a first comprehensive review on the redox status of the cell covering the redox components and signaling, redox status alters the post-translational modification of proteins, intracellular epigenetic modifications, redox interplay during DNA methylation, redox regulation of histone acetylation and methylation, redox regulation of miRNA biogenesis, redox regulation of chromatin structure and remodeling and conclusion, future perspectives and biotechnological opportunities for the future development of the plants. KEY SCIENTIFIC CONCEPTS OF REVIEW The interaction of redox mediators such as ROS, RNS and antioxidants regulates redox homeostasis and redox-mediated epigenetic changes. We discuss how redox mediators modulate epigenetic changes and show the opportunities for smart use of the redox status of the cell in plant development and abiotic stress adaptation. However, how a redox mediator triggers epigenetic modification without activating other redox mediators remains yet unknown.
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Affiliation(s)
- Muthusamy Ramakrishnan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China.
| | - Pradeep K Papolu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Lakkakula Satish
- Department of Biotechnology Engineering, & The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva - 84105, Israel; Applied Phycology and Biotechnology Division, Marine Algal Research Station, CSIR - Central Salt and Marine Chemicals Research Institute, Mandapam 623519, Tamil Nadu, India
| | | | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Abolghassem Emamverdian
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, Jiangsu, China; Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, Jiangsu, China
| | - Long-Hai Zou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; Zhejiang Provincial Collaborative Innovation Centre for Bamboo Resources and High-efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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Histone Modifications in Neurological Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:95-107. [DOI: 10.1007/978-3-031-05460-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Li W, Wu H, Sui S, Wang Q, Xu S, Pang D. Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way. Front Cell Dev Biol 2021; 9:736935. [PMID: 34595180 PMCID: PMC8476812 DOI: 10.3389/fcell.2021.736935] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
Histone modifications (HMs) contribute to maintaining genomic stability, transcription, DNA repair, and modulating chromatin in cancer cells. Furthermore, HMs are dynamic and reversible processes that involve interactions between numerous enzymes and molecular components. Aberrant HMs are strongly associated with tumorigenesis and progression of breast cancer (BC), although the specific mechanisms are not completely understood. Moreover, there is no comprehensive overview of abnormal HMs in BC, and BC therapies that target HMs are still in their infancy. Therefore, this review summarizes the existing evidence regarding HMs that are involved in BC and the potential mechanisms that are related to aberrant HMs. Moreover, this review examines the currently available agents and approved drugs that have been tested in pre-clinical and clinical studies to evaluate their effects on HMs. Finally, this review covers the barriers to the clinical application of therapies that target HMs, and possible strategies that could help overcome these barriers and accelerate the use of these therapies to cure patients.
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Affiliation(s)
- Wei Li
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Hao Wu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shiyao Sui
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Qin Wang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shouping Xu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Da Pang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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Pasyukova EG, Symonenko AV, Rybina OY, Vaiserman AM. Epigenetic enzymes: A role in aging and prospects for pharmacological targeting. Ageing Res Rev 2021; 67:101312. [PMID: 33657446 DOI: 10.1016/j.arr.2021.101312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
The development of interventions aimed at improving healthspan is one of the priority tasks for the academic and public health authorities. It is also the main objective of a novel branch in biogerontological research, geroscience. According to the geroscience concept, targeting aging is an effective way to combat age-related disorders. Since aging is an exceptionally complex process, system-oriented integrated approaches seem most appropriate for such an interventional strategy. Given the high plasticity and adaptability of the epigenome, epigenome-targeted interventions appear highly promising in geroscience research. Pharmaceuticals targeted at mechanisms involved in epigenetic control of gene activity are actively developed and implemented to prevent and treat various aging-related conditions such as cardiometabolic, neurodegenerative, inflammatory disorders, and cancer. In this review, we describe the roles of epigenetic mechanisms in aging; characterize enzymes contributing to the regulation of epigenetic processes; particularly focus on epigenetic drugs, such as inhibitors of DNA methyltransferases and histone deacetylases that may potentially affect aging-associated diseases and longevity; and discuss possible caveats associated with the use of epigenetic drugs.
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Affiliation(s)
- Elena G Pasyukova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Alexander V Symonenko
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Olga Y Rybina
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia; Federal State Budgetary Educational Institution of Higher Education «Moscow Pedagogical State University», M. Pirogovskaya Str. 1/1, Moscow, 119991, Russia
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Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci 2020. [DOI: 10.1007/s12038-020-00099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Yang YR, Li CW, Wang JH, Huang XS, Yuan YF, Hu J, Liu K, Liang BC, Liu Z, Shi XL. Ubiquitylomes Analysis of the Whole blood in Postmenopausal Osteoporosis Patients and healthy Postmenopausal Women. Orthop Surg 2019; 11:1187-1200. [PMID: 31762184 PMCID: PMC6904657 DOI: 10.1111/os.12556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives To determine the mechanisms of ubiquitination in postmenopausal osteoporosis and investigate the ubiquitinated spectrum of novel targets between healthy postmenopausal women and postmenopausal osteoporosis patients, we performed ubiquitylome analysis of the whole blood of postmenopausal women and postmenopausal osteoporosis patients. Methods To obtain a more comprehensive understanding of the postmenopausal osteoporosis mechanism, we performed a quantitative assessment of the ubiquitylome in whole blood from seven healthy postmenopausal women and seven postmenopausal osteoporosis patients using high‐performance liquid chromatography fractionation, affinity enrichment, and liquid chromatography coupled to tandem mass spectrometry (LC‐MS/MS). To examine the ubiquitylome data, we performed enrichment analysis using an ubiquitylated amino acid motif, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Results Altogether, 133 ubiquitinated sites and 102 proteins were quantified. A difference of more than 1.2 times is considered significant upregulation and less than 0.83 significant downregulation; 32 ubiquitinated sites on 25 proteins were upregulated and 101 ubiquitinated sites on 77 proteins were downregulated. These quantified proteins, both with differently ubiquitinated sites, participated in various cellular processes, such as cellular processes, biological regulation processes, response to stimulus processes, single‐organism and metabolic processes. Ubiquitin conjugating enzyme activity and ubiquitin‐like protein conjugating enzyme activity were the most highly enriched in molecular function of upregulated sites with corresponding proteins, but they were not enriched in downregulated in sites with corresponding proteins. The KEGG pathways analysis of quantified proteins with differentiated ubiquitinated sites found 13 kinds of molecular interactions and functional pathways, such as glyoxylate and decarboxylate metabolism, dopaminergic synapse, ubiquitin‐mediated proteolysis, salivary secretion, coagulation and complement cascades, Parkinson's disease, and hippo signaling pathway. In addition, hsa04120 ubiquitin‐mediated proteolysis was the most highly enriched in proteins with upregulated sites, hsa04610 complement and coagulation cascades was the most highly enriched in proteins with downregulated ubiquitinated sites, and hsa04114 Oocyte meiosis was the most highly enriched among all differential proteins. Conclusion Our study expands the understanding of the spectrum of novel targets that are differentially ubiquitinated in whole blood from healthy postmenopausal women and postmenopausal osteoporosis patients. The findings will contribute toward our understanding of the underlying proteostasis pathways in postmenopausal osteoporosis and the potential identification of diagnostic biomarkers in whole blood.
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Affiliation(s)
- Yi-Ran Yang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chun-Wen Li
- Department of Diagnostics of Traditional Chinese Medicine, College of Basic Medical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun-Hua Wang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiao-Sheng Huang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi-Feng Yuan
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiong Hu
- The Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kang Liu
- The Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Bo-Cheng Liang
- The Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhong Liu
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiao-Lin Shi
- The Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
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Wu X, Xu Q, Chen P, Yu C, Ye L, Huang C, Li T. Effect of SMYD3 on biological behavior and H3K4 methylation in bladder cancer. Cancer Manag Res 2019; 11:8125-8133. [PMID: 31564972 PMCID: PMC6730607 DOI: 10.2147/cmar.s213885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/24/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose Our goal was to investigate the effect of SMYD3 on the biological behavior and histone 3 lysine-4 (H3K4) methylation of bladder cancer (BLAC). Patients and methods qRT-PCR identified that SMYD3 expression level in BLAC cell lines (T24, 5637, BUI-87 and J-82) and human normal uroepithelial cell line SV-HUC1. We also constructed green fluorescence protein lentiviral vector using the gene short hairpin RNA (shRNA) system. We used Western blot to analyze the SMYD3, H3K4me1, H3K4me2 and H3K4me3 expression levels in shRNA transfection lines. We also performed a colony-forming assay to determine colony-forming ability, cell counting kit-8 for cell proliferation detection, Transwell assay to determine cell migration and invasion and Annexin V-FITC/PI double staining to analyze cell apoptosis. Results The SMYD3 expression level was significantly higher in BLAC cell lines (T24, 5637, BUI-87 and J-82) than in human normal uroepithelial cell line SV-HUC1, and exhibited the highest expression level in T24 cells, among the cell lines tested. qRT-PCR and Western blot analysis results showed that SMYD3 was successfully suppressed in shRNA transfection lines, and identified that SMYD3 suppression resulted inhibited H3K4me2 and H3K4me3 but not H3K4me1. SMYD3 knockdown cells accelerated cell apoptosis and exhibited low cell colony-forming ability, proliferation ability, inhibition of cell migration and invasion compared with normal cells. Conclusion SMYD3 may be activated in BLAC cells to increase H3K4 activity to modulate cell proliferation, migration and invasion ability. The data will be a useful source for future therapy.
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Affiliation(s)
- Xiang Wu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Urology, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
| | - Qingjiang Xu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Urology, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
| | - Pingzhou Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Urology, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
| | - Chenbo Yu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Urology, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
| | - Liefu Ye
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Urology, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
| | - Chen Huang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Thoracic Surgery, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
| | - Tao Li
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, People's Republic of China.,Department of Urology, Fujian Provincial Hospital, Fuzhou 350001, People's Republic of China
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Cijsouw T, Ramsey AM, Lam TT, Carbone BE, Blanpied TA, Biederer T. Mapping the Proteome of the Synaptic Cleft through Proximity Labeling Reveals New Cleft Proteins. Proteomes 2018; 6:proteomes6040048. [PMID: 30487426 PMCID: PMC6313906 DOI: 10.3390/proteomes6040048] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 12/21/2022] Open
Abstract
Synapses are specialized neuronal cell-cell contacts that underlie network communication in the mammalian brain. Across neuronal populations and circuits, a diverse set of synapses is utilized, and they differ in their molecular composition to enable heterogenous connectivity patterns and functions. In addition to pre- and post-synaptic specializations, the synaptic cleft is now understood to be an integral compartment of synapses that contributes to their structural and functional organization. Aiming to map the cleft proteome, this study applied a peroxidase-mediated proximity labeling approach and used the excitatory synaptic cell adhesion protein SynCAM 1 fused to horseradish peroxidase (HRP) as a reporter in cultured cortical neurons. This reporter marked excitatory synapses as measured by confocal microcopy and was targeted to the edge zone of the synaptic cleft as determined using 3D dSTORM super-resolution imaging. Proximity labeling with a membrane-impermeant biotin-phenol compound restricted labeling to the cell surface, and Label-Free Quantitation (LFQ) mass spectrometry combined with ratiometric HRP tagging of membrane vs. synaptic surface proteins was used to identify the proteomic content of excitatory clefts. Novel cleft candidates were identified, and Receptor-type tyrosine-protein phosphatase zeta was selected and successfully validated. This study supports the robust applicability of peroxidase-mediated proximity labeling for synaptic cleft proteomics and its potential for understanding synapse heterogeneity in health and changes in diseases such as psychiatric disorders and addiction.
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Affiliation(s)
- Tony Cijsouw
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Austin M Ramsey
- Department of Physiology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M. Keck Biotechnology Resource Laboratory, Yale University School of Medicine, 300 George Street, New Haven, CT 06511, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Beatrice E Carbone
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
| | - Thomas A Blanpied
- Department of Physiology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Thomas Biederer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA 02111, USA.
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Abstract
Epigenetics is the study of heritable mechanisms that can modify gene activity and phenotype without modifying the genetic code. The basis for the concept of epigenetics originated more than 2,000 yr ago as a theory to explain organismal development. However, the definition of epigenetics continues to evolve as we identify more of the components that make up the epigenome and dissect the complex manner by which they regulate and are regulated by cellular functions. A substantial and growing body of research shows that nutrition plays a significant role in regulating the epigenome. Here, we critically assess this diverse body of evidence elucidating the role of nutrition in modulating the epigenome and summarize the impact such changes have on molecular and physiological outcomes with regards to human health.
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Affiliation(s)
- Folami Y Ideraabdullah
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Steven H Zeisel
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
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Epigenetic modifications of gene expression by lifestyle and environment. Arch Pharm Res 2017; 40:1219-1237. [PMID: 29043603 DOI: 10.1007/s12272-017-0973-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
Epigenetics oftenly described as the heritable changes in gene expression independent of changes in DNA sequence. Various environmental factors such as nutrition-dietary components, lifestyle, exercise, physical activity, toxins, and other contributing factors remodel the genome either in a constructive or detrimental way. Since epigenetic changes are reversible and nutrition is one of the many epigenetic regulators that modify gene expression without changing the DNA sequence, dietary nutrients and bioactive food components contribute to epigenetic phenomena either by directly suppressing DNA methylation or histone catalyzing enzymes or by changing the availability of substrates required for enzymatic reactions. Diets that contain catechol-dominant polyphenols are reported to suppress enzyme activity and activate epigenetically silenced genes. Furthermore, several dietary nutrients play a crucial role in one-carbon metabolism including folate, cobalamin, riboflavin, pyridoxine, and methionine by directly affecting S-adenosyl-L-methionine. Soy polyphenols block DNA methyltransferases and histone deacetylases to reverse aberrant CpG island methylation. Organosulfur rich compounds such as the sulforaphane found in broccoli appear to normalize DNA methylation and activate miR-140 expression, which represses SOX9 and ALDH1 and decreases tumor growth. The purpose of this short communication is to overview the epigenetic regulatory mechanisms of diet and other environmental factors. We discuss the epigenetic contributions of dietary components with a particular focus on nutritional polyphenols and flavonoids as epigenetic mediators that modify epigenetic tags and control gene expression. These mechanisms provide new insights to better understand the influence of dietary nutrients on epigenetic modifications and gene expression.
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Characterization of histone-related chemical modifications in formalin-fixed paraffin-embedded and fresh-frozen human pancreatic cancer xenografts using LC-MS/MS. J Transl Med 2017; 97:279-288. [PMID: 27941757 DOI: 10.1038/labinvest.2016.134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 10/22/2016] [Accepted: 11/03/2016] [Indexed: 01/22/2023] Open
Abstract
Post-translational modifications (PTMs) of histones including acetylation, methylation, and ubiquitination are known to be involved in the epigenetic regulation of gene expression and thus can have an important role in tumorigenesis. A number of PTMs have been linked to pancreatic cancer and are frequently studied as potential targets for cancer therapy or diagnosis. The availability of biobank-stored, formalin-fixed, paraffin-embedded (FFPE) materials and advanced proteomic analytical tools make it possible to detect histone-related PTMs using predicted mass shifts caused by specific modification. It is, however, important to take into account the fact that formaldehyde (FA) present in the FFPE material is chemically reactive and may undergo condensation reactions, for example, with terminal amino groups and active CH functionalities of the studied proteins. As supported by the results of this study, the possibility to misinterpret such protein condensation product as endogenous PTMs should be taken into consideration in all proteomic analytical work involving FFPE materials. In this study, we used liquid chromatography-tandem mass spectrometry to assess preassumed modification of the lysine residues of histone proteins in FFPE or fresh-frozen (FF) tumor xenografts, derived from the human pancreatic cancer cell line, Capan-1. Here we report modifications with a defined mass shift of +14.016, +28.031, +42.011, or +114.043 Da, corresponding to apparent methylation, dimethylation, acetylation, or ubiquitination that were differentially distributed between the groups. The identified modifications were significantly more frequent in FFPE samples as compared with FF samples. Our results indicate that FFPE tissue processing may result in persistent chemical modifications of histones, which correspond in mass shift of important PTMs. Herein, we highlight the importance to investigate and report FA-formed modifications in FFPE-treated tissues, as well as the necessity of careful manual examination of observed modifications to eliminate false-positive PTMs.
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Uram Ł, Szuster M, Filipowicz A, Zaręba M, Wałajtys-Rode E, Wołowiec S. Cellular uptake of glucoheptoamidated poly(amidoamine) PAMAM G3 dendrimer with amide-conjugated biotin, a potential carrier of anticancer drugs. Bioorg Med Chem 2016; 25:706-713. [PMID: 27919613 DOI: 10.1016/j.bmc.2016.11.047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 11/19/2022]
Abstract
In search for soluble derivatives of PAMAM dendrimers as potential carriers for hydrophobic drugs, the conjugates of PAMAM G3 with biotin, further converted into glycodendrimer with d-glucoheptono-1,4-lactone, were prepared. Polyamidoamine dendrimer (PAMAM) of third generation, G3 was functionalized with four biotin equivalents covalently attached to terminal amine nitrogens via amide bond G34B. The remaining 28 amine groups were blocked by glucoheptoamide substituents (gh) to give G34B28gh or with one fluorescein equivalent (attached by reaction of G34B with fluorescein isothiocyanate, FITC) via thiourea bond as FITC followed by exhaustive glucoheptoamidation to get G34B27gh1F. As a control the G3 substituted totally with 32 glucoheptoamide residues, G3gh and its fluorescein labeled analogue G331gh1F were synthesized. The glucoheptoamidation of PAMAM G0 dendrimer with glucoheptono-1,4-lactone was performed in order to fully characterize the 1H NMR spectra of glucoheptoamidated PAMAM dendrimers and to control the derivatization of G3 with glucoheptono-1,4-lactone. Another two derivatives of G3, namely G34B28gh1F' and G332ghF', with ester bonded fluorescein were also obtained. Biological properties of obtained dendrimer conjugates were estimated in vitro with human cell lines: normal fibroblast (BJ) and two cancer glioblastoma (U-118 MG) and squamous carcinoma (SCC-15), including cytotoxicity by reduction of XTT and neutral red (NR) assays. Cellular uptake of dendrimer conjugates was evaluated with confocal microscopy. Obtained results confirmed, that biotinylated bioconjugates have always lower cytotoxicity and 3-4 times higher cellular uptake than non-biotinylated dendrimer conjugates in all cell lines. Comparison of various cell lines revealed different dose-dependent cell responses and the lower cytotoxicity of examined dendrimer conjugates for normal fibroblasts and squamous carcinoma, as compared with much higher cytotoxic effects seen in glioblastoma cell line. Synthetized multi-functional conjugate (G34B27gh1F) is a promising candidate as biocompatible vehicle for hydrophobic molecules used in anticancer therapy.
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Affiliation(s)
- Łukasz Uram
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland.
| | - Magdalena Szuster
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland
| | - Aleksandra Filipowicz
- Faculty of Medical Sciences, Rzeszów University of Information Technology and Management, 2 Sucharskiego Str, 35-225 Rzeszów, Poland
| | - Magdalena Zaręba
- Faculty of Chemistry, Rzeszów University of Technology, 6 Powstańców Warszawy Ave, 35-959 Rzeszów, Poland
| | - Elżbieta Wałajtys-Rode
- Department of Drug Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 75 Koszykowa Str, 00-664 Warsaw, Poland
| | - Stanisław Wołowiec
- Centre for Innovative Research in Medical and Natural Sciences, Faculty of Medicine, University of Rzeszów, Warzywna 1a, 35-310 Rzeszów, Poland
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The Gut Microbiota and their Metabolites: Potential Implications for the Host Epigenome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 902:33-44. [PMID: 27161349 DOI: 10.1007/978-3-319-31248-4_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The gut microbiota represents a metabolically active biomass of up to 2 kg in adult humans. Microbiota-derived molecules significantly contribute to the host metabolism. Large amounts of bacterial metabolites are taken up by the host and are subsequently utilized by the human body. For instance, short chain fatty acids produced by the gut microbiota are a major energy source of humans.It is widely accepted that microbiota-derived metabolites are used as fuel for beta-oxidation (short chain fatty acids) and participate in many metabolic processes (vitamins, such as folic acid). Apart from these direct metabolic effects, it also becomes more and more evident that these metabolites can interact with the mammalian epigenetic machinery. By interacting with histones and DNA they may be able to manipulate the host's chromatin state and functionality and hence its physiology and health.In this chapter, we summarize the current knowledge on possible interactions of different bacterial metabolites with the mammalian epigenetic machinery, mostly based on in vitro data. We discuss the putative impact on chromatin marks, for example histone modifications and DNA methylation. Subsequently, we speculate about possible beneficial and adverse consequences for the epigenome, the physiology and health of the host, as well as plausible future applications of this knowledge for in vivo translation to support personal health.
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The Impact of External Factors on the Epigenome: In Utero and over Lifetime. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2568635. [PMID: 27294112 PMCID: PMC4887632 DOI: 10.1155/2016/2568635] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/12/2016] [Accepted: 04/26/2016] [Indexed: 01/07/2023]
Abstract
Epigenetic marks change during fetal development, adult life, and aging. Some changes play an important role in the establishment and regulation of gene programs, but others seem to occur without any apparent physiological role. An important future challenge in the field of epigenetics will be to describe how the environment affects both of these types of epigenetic change and to learn if interaction between them can determine healthy and disease phenotypes during lifetime. Here we discuss how chemical and physical environmental stressors, diet, life habits, and pharmacological treatments can affect the epigenome during lifetime and the possible impact of these epigenetic changes on pathophysiological processes.
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Biotin-mediated epigenetic modifications: Potential defense against the carcinogenicity of benzo[a]pyrene. Toxicol Lett 2016; 241:216-24. [DOI: 10.1016/j.toxlet.2015.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/03/2015] [Accepted: 11/08/2015] [Indexed: 12/16/2022]
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Kim B, Hong J. An overview of naturally occurring histone deacetylase inhibitors. Curr Top Med Chem 2015; 14:2759-82. [PMID: 25487010 DOI: 10.2174/1568026615666141208105614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 11/26/2014] [Accepted: 11/29/2014] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) have recently emerged as key elements in epigenetic control of gene expression. Due to the implication of HDACs in a variety of diseases ranging from cancer to neurodegenerative disorder, HDAC inhibitors have received increased attention in recent years. Over the last few decades, a myriad of HDAC inhibitors containing a wide variety of structural features have been identified from natural sources. Here, we review the discovery, synthesis, biological properties, and modes of action of these naturally occurring HDAC inhibitors and consider their implications for future research.
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Affiliation(s)
| | - Jiyong Hong
- Duke University, Department of Chemistry, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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Sadakierska-Chudy A, Filip M. A comprehensive view of the epigenetic landscape. Part II: Histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox Res 2014; 27:172-97. [PMID: 25516120 PMCID: PMC4300421 DOI: 10.1007/s12640-014-9508-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/31/2022]
Abstract
The complexity of the genome is regulated by epigenetic mechanisms, which act on the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal. In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing. In addition to well-known phenomena, including DNA methylation and histone modification, new, important elements, including nucleosome mobility, histone tail clipping, and regulatory ncRNA molecules, are being discovered. The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin. We also emphasize the significance of cross-talk among chromatin marks and ncRNAs in epigenetic control.
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Affiliation(s)
- Anna Sadakierska-Chudy
- Laboratory of Drug Addiction Pharmacology, Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 31-343, Kraków, Poland,
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Xu YM, Du JY, Lau ATY. Posttranslational modifications of human histone H3: an update. Proteomics 2014; 14:2047-60. [PMID: 25044606 DOI: 10.1002/pmic.201300435] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 05/30/2014] [Accepted: 07/04/2014] [Indexed: 02/05/2023]
Abstract
Histone proteins, the fundamental components of chromatin, are highly conserved proteins that present in eukaryotic nuclei. They organize genomic DNA to form nucleosomes, the basic units of chromatin. PTMs of histones play essential roles in many biological processes, such as chromatin condensation, gene expression, cell differentiation, and apoptosis. With the advancement of proteomic technology, a growing number of histone PTMs have been identified, including ADP-ribosylation, biotinylation, citrullination, crotonylation, O-GlcNAcylation, glutathionylation, succinylation, and so on. Because of the fast growing list of these PTMs in just a few years, the functions of these marks are being studied intensively. As histone H3 has the most number of PTMs among the histone members, in this review, we would like to present the overall concepts of the more familiar PTMs as well as discussing all the recently identified yet less well-known PTMs on human histone H3.
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Affiliation(s)
- Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, P. R. China
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Arnaudo AM, Garcia BA. Proteomic characterization of novel histone post-translational modifications. Epigenetics Chromatin 2013; 6:24. [PMID: 23916056 PMCID: PMC3737111 DOI: 10.1186/1756-8935-6-24] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/01/2013] [Indexed: 11/10/2022] Open
Abstract
Histone post-translational modifications (PTMs) have been linked to a variety of biological processes and disease states, thus making their characterization a critical field of study. In the last 5 years, a number of novel sites and types of modifications have been discovered, greatly expanding the histone code. Mass spectrometric methods are essential for finding and validating histone PTMs. Additionally, novel proteomic, genomic and chemical biology tools have been developed to probe PTM function. In this snapshot review, proteomic tools for PTM identification and characterization will be discussed and an overview of PTMs found in the last 5 years will be provided.
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Affiliation(s)
- Anna M Arnaudo
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine University of Pennsylvania, 1009C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA.
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Zhou J, Wang D, Schlegel V, Zempleni J. Development of an internet based system for modeling biotin metabolism using Bayesian networks. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2011; 104:254-9. [PMID: 21356565 PMCID: PMC3132571 DOI: 10.1016/j.cmpb.2011.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 02/04/2011] [Indexed: 05/30/2023]
Abstract
Biotin is an essential water-soluble vitamin crucial for maintaining normal body functions. The importance of biotin for human health has been under-appreciated but there is plenty of opportunity for future research with great importance for human health. Currently, carrying out predictions of biotin metabolism involves tedious manual manipulations. In this paper, we report the development of BiotinNet, an internet based program that uses Bayesian networks to integrate published data on various aspects of biotin metabolism. Users can provide a combination of values on the levels of biotin related metabolites to obtain the predictions on other metabolites that are not specified. As an inherent feature of Bayesian networks, the uncertainty of the prediction is also quantified and reported to the user. This program enables convenient in silico experiments regarding biotin metabolism, which can help researchers design future experiments while new data can be continuously incorporated.
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Affiliation(s)
- Jinglei Zhou
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Dong Wang
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE 68583, USA, Tel: +1 4024724921 fax: +1 4024720736
| | - Vicki Schlegel
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Reyes-Carmona S, Valadéz-Graham V, Aguilar-Fuentes J, Zurita M, León-Del-Río A. Trafficking and chromatin dynamics of holocarboxylase synthetase during development of Drosophila melanogaster. Mol Genet Metab 2011; 103:240-8. [PMID: 21463962 DOI: 10.1016/j.ymgme.2011.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/05/2011] [Accepted: 03/05/2011] [Indexed: 11/26/2022]
Abstract
This work examines the cellular localization of holocarboxylase synthetase (HCS) and its association to chromatin during different stages of development of Drosophila melanogaster. While HCS is well known for its role in the attachment of biotin to biotin-dependent carboxylase, it also regulates the transcription of HCS and carboxylases genes by triggering a cGMP-dependent signal transduction cascade. Further, its presence in the nucleus of cells suggests additional regulatory roles, but the mechanism involved has remained elusive. In this study, we show in D. melanogaster that HCS migrates to the nucleus at the gastrulation stage. In polytene chromosomes, it is associated to heterochromatin bands where it co-localizes with histone 3 trimethylated at lysine 9 (H3K9met3) but not with the euchromatin mark histone 3 acetylated at lysine 9 (H3K9ac). Further, we demonstrate the association of HCS with the hsp70 promoter by immunofluorescence and chromatin immuno-precipitation (ChIP) of associated DNA sequences. We demonstrate the occupancy of HCS to the core promoter region of the transcriptionally inactive hsp70 gene. On heat-shock activation of the hsp70 promoter, HCS is displaced and the promoter region becomes enriched with the TFIIH subunits XPD and XPB and elongating RNA pol II, the latter also demonstrated using ChIP assays. We suggest that HCS may have a role in the repression of gene expression through a mechanism involving its trafficking to the nucleus and interaction with heterochromatic sites coincident with H3K9met3.
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Affiliation(s)
- Sandra Reyes-Carmona
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México DF 04510, Mexico.
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Bioactive food components, cancer cell growth limitation and reversal of glycolytic metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:697-706. [DOI: 10.1016/j.bbabio.2010.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 08/10/2010] [Accepted: 08/15/2010] [Indexed: 02/07/2023]
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Fernandez-Mejia C, Lazo-de-la-Vega-Monroy ML. Biological Effects of Pharmacological Concentrations of Biotin. J Evid Based Complementary Altern Med 2011. [DOI: 10.1177/1533210110392947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Understanding the molecular mechanisms of vitamins has opened new perspectives regarding the relationship between nutritional signals and biological functions, which, in turn, has led to the development of new therapeutic agents. Although little is known about water-soluble vitamins as genetic modulators, evidence about their effects on gene expression has grown. In the case of biotin, besides its role as a carboxylase prosthetic group, it also affects gene expression and has a wide repertoire of effects on biological functions. Only recently, the role of pharmacological concentrations of biotin on systemic functions has attracted attention, and it is now being reconsidered with the help of new technologies. This novel approach could lead to new perspectives in its use as a therapeutic agent. The present review is focused on the effects of pharmacological concentrations of biotin on several biological functions and on the biotin signaling pathways that participate in gene expression.
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Bountra C, Oppermann U, Heightman TD. Animal models of epigenetic regulation in neuropsychiatric disorders. Curr Top Behav Neurosci 2011; 7:281-322. [PMID: 21225415 DOI: 10.1007/7854_2010_104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Epigenetics describes the phenomenon of heritable changes in gene regulation that are governed by non-Mendelian processes, primarily through biochemical modifications to chromatin structure that occur during cell development and differentiation. Numerous lines of evidence link abnormal levels of chromatin modifications (either to DNA, histones, or both) in patients with a wide variety of diseases including cancer, psychiatry, neurodegeneration, metabolic and inflammatory disorders. Drugs that target the proteins controlling chromatin modifications can modulate the expression of clusters of genes, potentially offering higher therapeutic efficacy than classical agents with single target pharmacologies that are susceptible to biochemical pathway degeneracy. Here, we summarize recent research linking epigenetic dysregulation with diseases in neurosciences, the application of relevant animal models, and the potential for small molecule modulator development to facilitate target discovery, validation and translation into clinical treatments.
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Affiliation(s)
- Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK,
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25
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Abstract
Nutrients can reverse or change epigenetic phenomena such as DNA methylation and histone modifications, thereby modifying the expression of critical genes associated with physiologic and pathologic processes, including embryonic development, aging, and carcinogenesis. It appears that nutrients and bioactive food components can influence epigenetic phenomena either by directly inhibiting enzymes that catalyze DNA methylation or histone modifications, or by altering the availability of substrates necessary for those enzymatic reactions. In this regard, nutritional epigenetics has been viewed as an attractive tool to prevent pediatric developmental diseases and cancer as well as to delay aging-associated processes. In recent years, epigenetics has become an emerging issue in a broad range of diseases such as type 2 diabetes mellitus, obesity, inflammation, and neurocognitive disorders. Although the possibility of developing a treatment or discovering preventative measures of these diseases is exciting, current knowledge in nutritional epigenetics is limited, and further studies are needed to expand the available resources and better understand the use of nutrients or bioactive food components for maintaining our health and preventing diseases through modifiable epigenetic mechanisms.
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Affiliation(s)
- Sang-Woon Choi
- Vitamins and Carcinogenesis Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111,To whom correspondence should be addressed. E-mail:
| | - Simonetta Friso
- Department of Medicine, University of Verona School of Medicine, Verona 37134, Italy
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Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc Natl Acad Sci U S A 2010; 107:19915-20. [PMID: 21045127 DOI: 10.1073/pnas.1009023107] [Citation(s) in RCA: 278] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dynamic posttranslational modification of serine and threonine residues of nucleocytoplasmic proteins by β-N-acetylglucosamine (O-GlcNAc) is a regulator of cellular processes such as transcription, signaling, and protein-protein interactions. Like phosphorylation, O-GlcNAc cycles in response to a wide variety of stimuli. Although cycling of O-GlcNAc is catalyzed by only two highly conserved enzymes, O-GlcNAc transferase (OGT), which adds the sugar, and β-N-acetylglucosaminidase (O-GlcNAcase), which hydrolyzes it, the targeting of these enzymes is highly specific and is controlled by myriad interacting subunits. Here, we demonstrate by multiple specific immunological and enzymatic approaches that histones, the proteins that package DNA within the nucleus, are O-GlcNAcylated in vivo. Histones also are substrates for OGT in vitro. We identify O-GlcNAc sites on histones H2A, H2B, and H4 using mass spectrometry. Finally, we show that histone O-GlcNAcylation changes during mitosis and with heat shock. Taken together, these data show that O-GlcNAc cycles dynamically on histones and can be considered part of the histone code.
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Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes. J Nutr Biochem 2010; 22:328-33. [PMID: 20691578 DOI: 10.1016/j.jnutbio.2010.02.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 02/14/2010] [Accepted: 02/23/2010] [Indexed: 11/24/2022]
Abstract
Covalent histone modifications play crucial roles in chromatin structure and genome stability. We previously reported biotinylation of lysine (K) residues in histones H2A, H3 and H4 by holocarboxylase synthetase and demonstrated that K12-biotinylated histone H4 (H4K12bio) is enriched in repeat regions and participates in gene repression. The biological functions of biotinylation marks other than H4K12bio are poorly understood. Here, novel biotinylation site-specific antibodies against H3K9bio, H3K18bio and H4K8bio were used in chromatin immunoprecipitation studies to obtain first insights into possible biological functions of these marks. Chromatin immunoprecipitation assays were conducted in human primary fibroblasts and Jurkat lymphoblastoma cells, and revealed that H3K9bio, H3K18bio and H4K8bio are enriched in repeat regions such as pericentromeric alpha satellite repeats and long-terminal repeats while being depleted in transcriptionally active promoters in euchromatin. Transcriptional stimulation of the repressed interleukin-2 promoter triggered a rapid depletion of histone biotinylation marks at this locus in Jurkat cells, which was paralleled by an increase in interleukin-2 mRNA. Importantly, the enrichment of H3K9bio, H3K18bio and H4K8bio at genomic loci depended on the concentration of biotin in culture media at nutritionally relevant levels, suggesting a novel mechanism of gene regulation by biotin.
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Bailey LM, Wallace JC, Polyak SW. Holocarboxylase synthetase: correlation of protein localisation with biological function. Arch Biochem Biophys 2010; 496:45-52. [PMID: 20153287 DOI: 10.1016/j.abb.2010.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 10/19/2022]
Abstract
Holocarboxylase synthetase (HCS) governs the cellular fate of the essential micronutrient biotin (Vitamin H or B7). HCS is responsible for attaching biotin onto the biotin-dependent enzymes that reside in the cytoplasm and mitochondria. Evidence for an alternative role, viz the regulation of gene expression, has also been reported. Recent immunohistochemical studies reported HCS is primarily nuclear, inconsistent with the location of HCS activity. Improved understanding of biotin biology demands greater knowledge about HCS. Here, we investigated the localisation of HCS and its isoforms. Three variants were observed that differ at the N-terminus. All HCS isoforms were predominantly non-nuclear, consistent with the distribution of biotin protein ligase activity. Unlike the longer constructs, the Met(58) isoform was also detected in the nucleus--a novel observation suggesting shuttling activity between nucleus and cytoplasm. We resolved that the previous controversies in the literature are due to specificity and detection limitations that arise when using partially purified antibodies.
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Affiliation(s)
- L M Bailey
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
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Healy S, Perez-Cadahia B, Jia D, McDonald MK, Davie JR, Gravel RA. Biotin is not a natural histone modification. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:719-33. [PMID: 19770080 DOI: 10.1016/j.bbagrm.2009.09.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 08/21/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
Abstract
In addition to its role as the cofactor of biotin-dependent carboxylases, biotin has been demonstrated to have a role in cellular processes including transcription and gene silencing. Histones have been proposed to be modified by biotin in a site-specific manner, providing a pathway by which biotin acts as a regulatory molecule for gene expression. However, there is uncertainty whether biotin attachment to histones in vitro can be extrapolated to biotin as a native histone modification. We critically examined a number of methods used to detect biotin attachment on histones, including [(3)H]-biotin uptake, Western blot analysis of histones, and mass spectrometry of affinity purified histone fragments with the objective of determining if the in vivo occurrence of histone biotinylation could be conclusively established. We found for each of these methods that, while biotin could be readily detected on native carboxylases or histones biotinylated in vitro, biotin attachment on native histones could not be detected in cell cultures from various sources. We conclude that biotin is absent in native histones to a sensitivity of at least one part per 100,000, suggesting that the regulatory impact of biotin on gene expression must be through alternate mechanisms.
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Affiliation(s)
- Shannon Healy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 4N1.
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