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Zhang Y, Wang Q, Xue H, Guo Y, Wei S, Li F, Gong L, Pan W, Jiang P. Epigenetic Regulation of Autophagy in Bone Metabolism. FUNCTION 2024; 5:zqae004. [PMID: 38486976 PMCID: PMC10935486 DOI: 10.1093/function/zqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 03/17/2024] Open
Abstract
The skeletal system is crucial for supporting bodily functions, protecting vital organs, facilitating hematopoiesis, and storing essential minerals. Skeletal homeostasis, which includes aspects such as bone density, structural integrity, and regenerative processes, is essential for normal skeletal function. Autophagy, an intricate intracellular mechanism for degrading and recycling cellular components, plays a multifaceted role in bone metabolism. It involves sequestering cellular waste, damaged proteins, and organelles within autophagosomes, which are then degraded and recycled. Autophagy's impact on bone health varies depending on factors such as regulation, cell type, environmental cues, and physiological context. Despite being traditionally considered a cytoplasmic process, autophagy is subject to transcriptional and epigenetic regulation within the nucleus. However, the precise influence of epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNA expression, on cellular fate remains incompletely understood. The interplay between autophagy and epigenetic modifications adds complexity to bone cell regulation. This article provides an in-depth exploration of the intricate interplay between these two regulatory paradigms, with a focus on the epigenetic control of autophagy in bone metabolism. Such an understanding enhances our knowledge of bone metabolism-related disorders and offers insights for the development of targeted therapeutic strategies.
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Affiliation(s)
- Yazhou Zhang
- Department of Foot and Ankle Surgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Qianqian Wang
- Department of Pediatric Intensive Care Unit, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Hongjia Xue
- Department of Computer Science, University College London, London, WC1E 6BT, UK
| | - Yujin Guo
- Institute of Clinical Pharmacy & Pharmacology, Jining First People’s Hospital, Jining 272000, China
| | - Shanshan Wei
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, China
- Department of Graduate, Shandong Academy of Medical Sciences, Shandong First Medical University, Jinan 250000, China
| | - Fengfeng Li
- Department of Neurosurgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Linqiang Gong
- Department of Gastroenterology, Tengzhou Central People's Hospital, Tengzhou 277500, China
| | - Weiliang Pan
- Department of Foot and Ankle Surgery, Tengzhou Central People’s Hospital, Tengzhou 277500, China
| | - Pei Jiang
- Translational Pharmaceutical Laboratory, Jining First People’s Hospital, Shandong First Medical University, Jining 272000, China
- Institute of Translational Pharmacy, Jining Medical Research Academy, Jining 272000, China
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2
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Ji G, Xiao X, Huang M, Wu Q. Jmjd6 regulates ES cell homeostasis and enhances reprogramming efficiency. Heliyon 2022; 8:e09105. [PMID: 35846449 PMCID: PMC9280369 DOI: 10.1016/j.heliyon.2022.e09105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/10/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Jmjd6 is a conserved nuclear protein which possesses histone arginine demethylation and lysyl hydroxylase activity. Previous studies have revealed that Jmjd6 is essential for cell differentiation and embryo development. However, the role of Jmjd6 in mammalian ES cell identity and reprogramming has been unclear. Here we report that depletion of Jmjd6 not only results in downregulation of pluripotency genes but also is implicated in apoptosis, glycolysis, cell cycle and protein hydroxylation. We also revealed the reduction of BrdU incorporation in Jmjd6 depleted cells. Reprogramming efficiency of MEFs can be enhanced with Jmjd6 overexpression while the efficiency was reduced upon Jmjd6 depletion. Together, these results suggest that Jmjd6 can regulate ES cell homeostasis and enhance somatic cell reprogramming.
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3
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Lopez L, Perrella G, Calderini O, Porceddu A, Panara F. Genome-Wide Identification of Histone Modification Gene Families in the Model Legume Medicago truncatula and Their Expression Analysis in Nodules. PLANTS 2022; 11:plants11030322. [PMID: 35161303 PMCID: PMC8838541 DOI: 10.3390/plants11030322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 01/22/2023]
Abstract
Histone methylation and acetylation are key processes in the epigenetic regulation of plant growth, development, and responses to environmental stimuli. The genes encoding for the enzymes that are responsible for these chromatin post-translational modifications, referred to as histone modification genes (HMGs), have been poorly investigated in Leguminosae species, despite their importance for establishment and activity of nitrogen-fixing nodules. In silico analysis of Medicago truncatula HMGs identified 81 histone methyltransferases, 46 histone demethylases, 64 histone acetyltransferases, and 15 histone deacetylases. MtHMGs were analyzed for their structure and domain composition, and some combinations that were not yet reported in other plant species were identified. Genes have been retrieved from M. truncatula A17 and R108 genotypes as well as M. sativa CADL and Zhongmu No.1; the gene number and distribution were compared with Arabidopsis thaliana. Furthermore, by analyzing the expression data that were obtained at various developmental stages and in different zones of nitrogen-fixing nodules, we identified MtHMG loci that could be involved in nodule development and function. This work sets a reference for HMG genomic organization in legumes which will be useful for functional investigation that is aimed at elucidating HMGs involvement in nodule development and symbiotic nitrogen fixation.
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Affiliation(s)
- Loredana Lopez
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
| | - Giorgio Perrella
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
| | - Ornella Calderini
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 06128 Perugia, Italy
- Correspondence: (O.C.); (F.P.); Tel.: +39-075-501-4858 (O.C.); +39-0835-974-523 (F.P.)
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Viale Italia, 39a, 07100 Sassari, Italy;
| | - Francesco Panara
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
- Correspondence: (O.C.); (F.P.); Tel.: +39-075-501-4858 (O.C.); +39-0835-974-523 (F.P.)
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Parbin S, Damodharan S, Rajyaguru PI. Arginine methylation and cytoplasmic mRNA fate: An exciting new partnership. Yeast 2021; 38:441-452. [PMID: 34048611 DOI: 10.1002/yea.3653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 12/22/2022] Open
Abstract
Posttranslational modifications play a crucial role in regulating gene expression. Among these modifications, arginine methylation has recently attracted tremendous attention due to its role in multiple cellular functions. This review discusses the recent advances that have established arginine methylation as a major player in determining cytoplasmic messenger RNA (mRNA) fate. We specifically focus on research that implicates arginine methylation in regulating mRNA translation, decay, and RNA granule dynamics. Based on this research, we highlight a few emerging future avenues that will lead to exciting discoveries in this field.
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Affiliation(s)
- Sabnam Parbin
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Integrative Genomics Core Unit, University Medical Centre, Göttingen, Göttingen, Germany
| | - Subha Damodharan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Sex-Specific Alterations in Cardiac DNA Methylation in Adult Mice by Perinatal Lead Exposure. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18020577. [PMID: 33445541 PMCID: PMC7826866 DOI: 10.3390/ijerph18020577] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/27/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022]
Abstract
Environmental factors play an important role in the etiology of cardiovascular diseases. Cardiovascular diseases exhibit marked sexual dimorphism; however, the sex-specific effects of environmental exposures on cardiac health are incompletely understood. Perinatal and adult exposures to the metal lead (Pb) are linked to several adverse cardiovascular outcomes, but the sex-specific effects of this toxicant on the heart have received little attention. Perinatal environmental exposures can lead to disease through disruption of the normal epigenetic programming that occurs during early development. Using a mouse model of human-relevant perinatal environmental exposure, we investigated the effects of exposure to Pb during gestation and lactation on DNA methylation in the hearts of adult offspring mice (n = 6 per sex). Two weeks prior to mating, dams were assigned to control or Pb acetate (32 ppm) water, and exposure continued until offspring were weaned at three weeks of age. Enhanced reduced-representation bisulfite sequencing was used to measure DNA methylation in the hearts of offspring at five months of age. Although Pb exposure stopped at three weeks of age, we discovered hundreds of differentially methylated cytosines (DMCs) and regions (DMRs) in males and females at five months of age. DMCs/DMRs and their associated genes were sex-specific, with a small, but statistically significant subset overlapping between sexes. Pathway analysis revealed altered methylation of genes important for cardiac and other tissue development in males, and histone demethylation in females. Together, these data demonstrate that perinatal exposure to Pb induces sex-specific changes in cardiac DNA methylation that are present long after cessation of exposure, and highlight the importance of considering sex in environmental epigenetics and mechanistic toxicology studies.
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6
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Hargarten JC, Williamson PR. Epigenetic Regulation of Autophagy: A Path to the Control of Autoimmunity. Front Immunol 2018; 9:1864. [PMID: 30154791 PMCID: PMC6102341 DOI: 10.3389/fimmu.2018.01864] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
Autoimmune diseases are a significant cause of debilitation and mortality globally and are in need of cost-effective therapeutics. Autophagy is a cellular pathway that facilitates immune modulation involved in both pathogen control and autoimmunity. Regulation is multifactorial and includes a number of epigenetic pathways which can involve modification of DNA-binding histones to induce autophagy-related mRNA synthesis or microRNA and decapping-associated mRNA degradation which results in autophagy suppression. Appreciation of epigenetic-based pathways involved in autophagy and autoimmunity may facilitate application of a burgeoning group of epigenetic pharmaceuticals to these important diseases.
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Affiliation(s)
- Jessica C Hargarten
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Peter R Williamson
- Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
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7
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Mbenza NM, Vadakkedath PG, McGillivray DJ, Leung IKH. NMR studies of the non-haem Fe(II) and 2-oxoglutarate-dependent oxygenases. J Inorg Biochem 2017; 177:384-394. [PMID: 28893416 DOI: 10.1016/j.jinorgbio.2017.08.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/21/2017] [Accepted: 08/30/2017] [Indexed: 01/13/2023]
Abstract
The non-haem Fe(II) and 2-oxoglutarate (2OG)-dependent oxygenases belong to a superfamily of structurally-related enzymes that play important biological roles in plants, microorganisms and animals. Structural, mechanistic and functional studies of 2OG oxygenases require efficient and effective biophysical tools. Nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study this enzyme superfamily. It has been applied to obtain information about enzyme kinetics, identify and characterise 2OG oxygenase-catalysed oxidation products, elucidate the catalytic mechanism, monitor ligand binding and study protein dynamics. This review summarises the types of information that NMR spectroscopy can provide in the studies of 2OG oxygenases, highlights the advantages of the technique and describes its drawbacks.
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Affiliation(s)
- Naasson M Mbenza
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Praveen G Vadakkedath
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand.; MacDiarmid Institute for Advanced Materials and Nanotechnology, PO Box 600, Wellington 6140, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand..
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8
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Rana AK, Ankri S. Reviving the RNA World: An Insight into the Appearance of RNA Methyltransferases. Front Genet 2016; 7:99. [PMID: 27375676 PMCID: PMC4893491 DOI: 10.3389/fgene.2016.00099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 12/13/2022] Open
Abstract
RNA, the earliest genetic and catalytic molecule, has a relatively delicate and labile chemical structure, when compared to DNA. It is prone to be damaged by alkali, heat, nucleases, or stress conditions. One mechanism to protect RNA or DNA from damage is through site-specific methylation. Here, we propose that RNA methylation began prior to DNA methylation in the early forms of life evolving on Earth. In this article, the biochemical properties of some RNA methyltransferases (MTases), such as 2′-O-MTases (Rlml/RlmN), spOUT MTases and the NSun2 MTases are dissected for the insight they provide on the transition from an RNA world to our present RNA/DNA/protein world.
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Affiliation(s)
- Ajay K Rana
- Division of Biology, State Forensic Science Laboratory, Ministry of Home Affairs, Government of Jharkhand Ranchi, India
| | - Serge Ankri
- Department of Molecular Microbiology, The Ruth and Bruce Rappaport Faculty of Medicine, Technion Israel Institute of Technology Haifa, Israel
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9
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Tsukada YI, Akiyama T, Nakayama KI. Maternal TET3 is dispensable for embryonic development but is required for neonatal growth. Sci Rep 2015; 5:15876. [PMID: 26507142 PMCID: PMC4623673 DOI: 10.1038/srep15876] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 10/05/2015] [Indexed: 01/01/2023] Open
Abstract
The development of multicellular organisms is accompanied by reprogramming of the epigenome in specific cells, with the epigenome of most cell types becoming fixed after differentiation. Genome-wide reprogramming of DNA methylation occurs in primordial germ cells and in fertilized eggs during mammalian embryogenesis. The 5-methylcytosine (5mC) content of DNA thus undergoes a marked decrease in the paternal pronucleus of mammalian zygotes. This loss of DNA methylation has been thought to be mediated by an active demethylation mechanism independent of replication and to be required for development. TET3-mediated sequential oxidation of 5mC has recently been shown to contribute to the genome-wide loss of 5mC in the paternal pronucleus of mouse zygotes. We now show that TET3 localizes not only to the paternal pronucleus but also to the maternal pronucleus and oxidizes both paternal and maternal DNA in mouse zygotes, although these phenomena are less pronounced in the female pronucleus. Genetic ablation of TET3 in oocytes had no significant effect on oocyte development, maturation, or fertilization or on pregnancy, but it resulted in neonatal sublethality. Our results thus indicate that zygotic 5mC oxidation mediated by maternal TET3 is required for neonatal growth but is not essential for development.
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Affiliation(s)
- Yu-Ichi Tsukada
- Division of Molecular Immunology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.,Advanced Biological Information Research Division, INAMORI Frontier Research Center, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tomohiko Akiyama
- Department of Systems Medicine, Sakaguchi Laboratory, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160-8562, Japan
| | - Keiichi I Nakayama
- Division of Cell Regulation Systems, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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10
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Dong C, Zhang H, Xu C, Arrowsmith CH, Min J. Structure and function of dioxygenases in histone demethylation and DNA/RNA demethylation. IUCRJ 2014; 1:540-9. [PMID: 25485134 PMCID: PMC4224472 DOI: 10.1107/s2052252514020922] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/18/2014] [Indexed: 05/18/2023]
Abstract
Iron(II) and 2-oxoglutarate (2OG)-dependent dioxygenases involved in histone and DNA/RNA demethylation convert the cosubstrate 2OG and oxygen to succinate and carbon dioxide, resulting in hydroxylation of the methyl group of the substrates and subsequent demethylation. Recent evidence has shown that these 2OG dioxygenases play vital roles in a variety of biological processes, including transcriptional regulation and gene expression. In this review, the structure and function of these dioxygenases in histone and nucleic acid demethylation will be discussed. Given the important roles of these 2OG dioxygenases, detailed analysis and comparison of the 2OG dioxygenases will guide the design of target-specific small-molecule chemical probes and inhibitors.
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Affiliation(s)
- Cheng Dong
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Heng Zhang
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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11
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Yilmaz-Ozcan S, Sade A, Kucukkaraduman B, Kaygusuz Y, Senses KM, Banerjee S, Gure AO. Epigenetic mechanisms underlying the dynamic expression of cancer-testis genes, PAGE2, -2B and SPANX-B, during mesenchymal-to-epithelial transition. PLoS One 2014; 9:e107905. [PMID: 25229454 PMCID: PMC4168264 DOI: 10.1371/journal.pone.0107905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 08/22/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer-testis (CT) genes are expressed in various cancers but not in normal tissues other than in cells of the germline. Although DNA demethylation of promoter-proximal CpGs of CT genes is linked to their expression in cancer, the mechanisms leading to demethylation are unknown. To elucidate such mechanisms we chose to study the Caco-2 colorectal cancer cell line during the course of its spontaneous differentiation in vitro, as we found CT genes, in particular PAGE2, -2B and SPANX-B, to be up-regulated during this process. Differentiation of these cells resulted in a mesenchymal-to-epithelial transition (MET) as evidenced by the gain of epithelial markers CDX2, Claudin-4 and E-cadherin, and a concomitant loss of mesenchymal markers Vimentin, Fibronectin-1 and Transgelin. PAGE2 and SPAN-X up-regulation was accompanied by an increase in Ten-eleven translocation-2 (TET2) expression and cytosine 5-hydroxymethylation as well as the disassociation of heterochromatin protein 1 and the polycomb repressive complex 2 protein EZH2 from promoter-proximal regions of these genes. Reversal of differentiation resulted in down-regulation of PAGE2, -2B and SPANX-B, and induction of epithelial-to-mesenchymal transition (EMT) markers, demonstrating the dynamic nature of CT gene regulation in this model.
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Affiliation(s)
- Sinem Yilmaz-Ozcan
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Asli Sade
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Baris Kucukkaraduman
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Yasemin Kaygusuz
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Kerem Mert Senses
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Sreeparna Banerjee
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Osmay Gure
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
- * E-mail:
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12
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Fernandez J, Marroquin-Guzman M, Nandakumar R, Shijo S, Cornwell KM, Li G, Wilson RA. Plant defence suppression is mediated by a fungal sirtuin during rice infection byMagnaporthe oryzae. Mol Microbiol 2014; 94:70-88. [DOI: 10.1111/mmi.12743] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Jessie Fernandez
- Department of Plant Pathology; University of Nebraska-Lincoln; Lincoln NE 68583 USA
| | | | - Renu Nandakumar
- Proteomic and Metabolomic Core Facility; Redox Biology Center; Department of Biochemistry; University of Nebraska-Lincoln; Lincoln NE 68588 USA
| | - Sara Shijo
- Department of Plant Pathology; University of Nebraska-Lincoln; Lincoln NE 68583 USA
| | - Kathryn M. Cornwell
- Department of Plant Pathology; University of Nebraska-Lincoln; Lincoln NE 68583 USA
| | - Gang Li
- Department of Plant Pathology; University of Nebraska-Lincoln; Lincoln NE 68583 USA
| | - Richard A. Wilson
- Department of Plant Pathology; University of Nebraska-Lincoln; Lincoln NE 68583 USA
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13
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Salminen A, Kaarniranta K, Hiltunen M, Kauppinen A. Krebs cycle dysfunction shapes epigenetic landscape of chromatin: Novel insights into mitochondrial regulation of aging process. Cell Signal 2014; 26:1598-603. [DOI: 10.1016/j.cellsig.2014.03.030] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/30/2014] [Indexed: 02/09/2023]
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14
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Cell cycle progression in response to oxygen levels. Cell Mol Life Sci 2014; 71:3569-82. [PMID: 24858415 PMCID: PMC4143607 DOI: 10.1007/s00018-014-1645-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 05/01/2014] [Accepted: 05/05/2014] [Indexed: 02/06/2023]
Abstract
Hypoxia' or decreases in oxygen availability' results in the activation of a number of different responses at both the whole organism and the cellular level. These responses include drastic changes in gene expression, which allow the organism (or cell) to cope efficiently with the stresses associated with the hypoxic insult. A major breakthrough in the understanding of the cellular response to hypoxia was the discovery of a hypoxia sensitive family of transcription factors known as the hypoxia inducible factors (HIFs). The hypoxia response mounted by the HIFs promotes cell survival and energy conservation. As such, this response has to deal with important cellular process such as cell division. In this review, the integration of oxygen sensing with the cell cycle will be discussed. HIFs, as well as other components of the hypoxia pathway, can influence cell cycle progression. The role of HIF and the cell molecular oxygen sensors in the control of the cell cycle will be reviewed.
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15
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Sudestada1, a Drosophila ribosomal prolyl-hydroxylase required for mRNA translation, cell homeostasis, and organ growth. Proc Natl Acad Sci U S A 2014; 111:4025-30. [PMID: 24550463 DOI: 10.1073/pnas.1314485111] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome sequences predict the presence of many 2-oxoglutarate (2OG)-dependent oxygenases of unknown biochemical and biological functions in Drosophila. Ribosomal protein hydroxylation is emerging as an important 2OG oxygenase catalyzed pathway, but its biological functions are unclear. We report investigations on the function of Sudestada1 (Sud1), a Drosophila ribosomal oxygenase. As with its human and yeast homologs, OGFOD1 and Tpa1p, respectively, we identified Sud1 to catalyze prolyl-hydroxylation of the small ribosomal subunit protein RPS23. Like OGFOD1, Sud1 catalyzes a single prolyl-hydroxylation of RPS23 in contrast to yeast Tpa1p, where Pro-64 dihydroxylation is observed. RNAi-mediated Sud1 knockdown hinders normal growth in different Drosophila tissues. Growth impairment originates from both reduction of cell size and diminution of the number of cells and correlates with impaired translation efficiency and activation of the unfolded protein response in the endoplasmic reticulum. This is accompanied by phosphorylation of eIF2α and concomitant formation of stress granules, as well as promotion of autophagy and apoptosis. These observations, together with those on enzyme homologs described in the companion articles, reveal conserved biochemical and biological roles for a widely distributed ribosomal oxygenase.
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16
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Glutamate-induced epigenetic and morphological changes allow rat Müller cell dedifferentiation but not further acquisition of a photoreceptor phenotype. Neuroscience 2013; 254:347-60. [DOI: 10.1016/j.neuroscience.2013.09.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/23/2013] [Accepted: 09/25/2013] [Indexed: 11/22/2022]
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17
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Cadet J, Wagner JR. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 764-765:18-35. [PMID: 24045206 DOI: 10.1016/j.mrgentox.2013.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 09/04/2013] [Indexed: 12/14/2022]
Abstract
5-Methylcytosine and methylated histones have been considered for a long time as stable epigenetic marks of chromatin involved in gene regulation. This concept has been recently revisited with the detection of large amounts of 5-hydroxymethylcytosine, now considered as the sixth DNA base, in mouse embryonic stem cells, Purkinje neurons and brain tissues. The dioxygenases that belong to the ten eleven translocation (TET) oxygenase family have been shown to initiate the formation of this methyl oxidation product of 5-methylcytosine that is also generated although far less efficiently by radical reactions involving hydroxyl radical and one-electron oxidants. It was found as additional striking data that iterative TET-mediated oxidation of 5-hydroxymethylcytosine gives rise to 5-formylcytosine and 5-carboxylcytosine. This survey focuses on chemical and biochemical aspects of the enzymatic oxidation reactions of 5-methylcytosine that are likely to be involved in active demethylation pathways through the implication of enzymatic deamination of 5-methylcytosine oxidation products and/or several base excision repair enzymes. The high biological relevance of the latter modified bases explains why major efforts have been devoted to the design of a broad range of assays aimed at measuring globally or at the single base resolution, 5-hydroxymethylcytosine and the two other oxidation products in the DNA of cells and tissues. Another critical issue that is addressed in this review article deals with the assessment of the possible role of 5-methylcytosine oxidation products, when present in elevated amounts in cellular DNA, in terms of mutagenesis and interference with key cellular enzymes including DNA and RNA polymerases.
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Affiliation(s)
- Jean Cadet
- Direction des Sciences de la Matière, Institut Nanosciences et Cryogénie, CEA/Grenoble, 38054 Grenoble, France; Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
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Li J, Braganza A, Sobol RW. Base excision repair facilitates a functional relationship between Guanine oxidation and histone demethylation. Antioxid Redox Signal 2013; 18:2429-43. [PMID: 23311711 PMCID: PMC3671628 DOI: 10.1089/ars.2012.5107] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SIGNIFICANCE Appropriately controlled epigenetic regulation is critical for the normal development and health of an organism. Misregulation of epigenetic control via deoxyribonucleic acid (DNA) methylation or histone methylation has been associated with cancer and chromosomal instability syndromes. RECENT ADVANCES The main function of the proteins in the base excision repair (BER) pathway is to repair DNA single-strand breaks and deamination, oxidation, and alkylation-induced DNA base damage that may result from chemotherapy, environmental exposure, or byproducts of cellular metabolism. Recent studies have suggested that one or more BER proteins may also participate in epigenetic regulation to facilitate gene expression modulation via alteration of the state of DNA methylation or via a reaction coupled to histone modification. BER proteins have also been reported to play an essential role in pluripotent stem cell reprogramming. CRITICAL ISSUES One emerging function for BER in epigenetic regulation is the repair of base lesions induced by hydrogen peroxide as a byproduct of lysine-specific demethylase 1 (LSD1) enzymatic activity (LSD1/LSD2-coupled BER) for transcriptional regulation. FUTURE DIRECTIONS To shed light on this novel role of BER, this review focuses on the repair of oxidative lesions in nuclear DNA that are induced during LSD1-mediated histone demethylation. Further, we highlight current studies suggesting a role for BER proteins in transcriptional regulation of gene expression via BER-coupled active DNA demethylation in mammalian cells. Such efforts to address the role of BER proteins in epigenetic regulation could broaden cancer therapeutic strategies to include epigenetic modifiers combined with BER inhibitors.
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Affiliation(s)
- Jianfeng Li
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Abstract
Epigenetic genome marking and chromatin regulation are central to establishing tissue-specific gene expression programs, and hence to several biological processes. Until recently, the only known epigenetic mark on DNA in mammals was 5-methylcytosine, established and propagated by DNA methyltransferases and generally associated with gene repression. All of a sudden, a host of new actors—novel cytosine modifications and the ten eleven translocation (TET) enzymes—has appeared on the scene, sparking great interest. The challenge is now to uncover the roles they play and how they relate to DNA demethylation. Knowledge is accumulating at a frantic pace, linking these new players to essential biological processes (e.g. cell pluripotency and development) and also to cancerogenesis. Here, we review the recent progress in this exciting field, highlighting the TET enzymes as epigenetic DNA modifiers, their physiological roles, and their functions in health and disease. We also discuss the need to find relevant TET interactants and the newly discovered TET–O-linked N-acetylglucosamine transferase (OGT) pathway.
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Kim SH, Lee HY, Yi H, Ahn YM, Kim YS. Haloperidol induces demethylation and expression of the dual specificity phosphatase 6 gene in MIA PaCa-2 human pancreatic cancer cells. Life Sci 2012; 91:1317-22. [DOI: 10.1016/j.lfs.2012.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 09/18/2012] [Accepted: 10/01/2012] [Indexed: 12/30/2022]
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