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Li M, Zhang CL, Zhou DS, Chan SH, Liu XQ, Chen SN, Yang ZY, Ju FE, Sang XY, Liu ZX, Zhang QX, Pan YM, Deng SS, Wang XM, Zhong L, Zhang XD, Du X. Identification of COQ2 as a regulator of proliferation and lipid peroxidation through genome-scale CRISPR-Cas9 screening in myeloma cells. Br J Haematol 2024; 204:1307-1324. [PMID: 38462771 DOI: 10.1111/bjh.19375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024]
Abstract
Multiple myeloma (MM) is the second most common malignant haematological disease with a poor prognosis. The limit therapeutic progress has been made in MM patients with cancer relapse, necessitating deeper research into the molecular mechanisms underlying its occurrence and development. A genome-wide CRISPR-Cas9 loss-of-function screening was utilized to identify potential therapeutic targets in our research. We revealed that COQ2 plays a crucial role in regulating MM cell proliferation and lipid peroxidation (LPO). Knockout of COQ2 inhibited cell proliferation, induced cell cycle arrest and reduced tumour growth in vivo. Mechanistically, COQ2 promoted the activation of the MEK/ERK cascade, which in turn stabilized and activated MYC protein. Moreover, we found that COQ2-deficient MM cells increased sensitivity to the LPO activator, RSL3. Using an inhibitor targeting COQ2 by 4-CBA enhanced the sensitivity to RSL3 in primary CD138+ myeloma cells and in a xenograft mouse model. Nevertheless, co-treatment of 4-CBA and RSL3 induced cell death in bortezomib-resistant MM cells. Together, our findings suggest that COQ2 promotes cell proliferation and tumour growth through the activation of the MEK/ERK/MYC axis and targeting COQ2 could enhance the sensitivity to ferroptosis in MM cells, which may be a promising therapeutic strategy for the treatment of MM patients.
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Affiliation(s)
- Miao Li
- Department of Dermatovenereology, Pelvic Floor Disorders Center, Scientific Research Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gynecology, Pelvic Floor Disorders Center, Scientific Research Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Chang-Lin Zhang
- Department of Dermatovenereology, Pelvic Floor Disorders Center, Scientific Research Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gynecology, Pelvic Floor Disorders Center, Scientific Research Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Di-Sheng Zhou
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Sze-Hoi Chan
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xue-Qi Liu
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shu-Na Chen
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zi-Yi Yang
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Fei-Er Ju
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xiao-Yan Sang
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zi-Xuan Liu
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Qiao-Xia Zhang
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Yu-Ming Pan
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Si-Si Deng
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xiao-Mei Wang
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Li Zhong
- Department of Dermatovenereology, Pelvic Floor Disorders Center, Scientific Research Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Department of Gynecology, Pelvic Floor Disorders Center, Scientific Research Center, Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xing-Ding Zhang
- Key Laboratory for Efficacy and Safety Evaluation of Hematological Malignancy Targeted Medicine of Guangdong Provincial Drug Administration, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xin Du
- Department of Hematology and Shenzhen Bone Marrow Transplantation Public Service Platform, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
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2
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Sendera A, Adamczyk-Grochala J, Pikuła B, Cholewa M, Banaś-Ząbczyk A. Electromagnetic field (50 Hz) enhance metabolic potential and induce adaptive/reprogramming response mediated by the increase of N6-methyladenosine RNA methylation in adipose-derived mesenchymal stem cells in vitro. Toxicol In Vitro 2024; 95:105743. [PMID: 38040129 DOI: 10.1016/j.tiv.2023.105743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/08/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Electromagnetic fields (EMF) have an impact on numerous cellular processes. It can positively and negatively affect adipose-derived stem cells (ASCs) thus their fate through the influence of specific factors and protein secretion. EMF can be a great factor for preconditioning ASCs for regenerative medicine purposes, however, understanding the cell's biological response to its effects in vitro is essential. METHODS ASCs were exposed to the EMF (50 Hz; 1.5 mT) for 24 and 48 h, and then cell biological response was analyzed. RESULTS 24 h exposure of ASCs to EMF, significantly increased N6-methyladenosine (m6A) RNA methylation, indicating epitranscriptomic changes as an important factor in ASCs preconditioning. Furthermore, the expression of stem cell markers such as Nanog, Oct-4, Sox-2, CD44, and CD105 increased after 24 h of EMF exposure. Besides, western blot analysis showed upregulation of p21 and DNMT2/TRDMT1 protein levels compared to control cells with no differences in the p53 profile. Moreover, after 24 h of exposure to EMF, cell membrane flexibility, the metabolic potential of cells as well as the distribution, morphology, and metabolism of mitochondria were altered. CONCLUSION ASCs undergo a process of mobilization and adaptation under the EMF influence through the increased m6A RNA modifications. These conditions may "force" ASCs to redefine their stem cell fate mediated by RNA-modifying enzymes and alter their reprogramming decision of as differentiation begins.
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Affiliation(s)
- Anna Sendera
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszow, Poland
| | - Jagoda Adamczyk-Grochala
- Department of Biotechnology, Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Barbara Pikuła
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszow, Poland
| | - Marian Cholewa
- Institute of Physics, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Agnieszka Banaś-Ząbczyk
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszow, Poland.
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3
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Park MJ, Sohn WM, Bae YA. Genome-wide identification of histone lysine methyltransferases and their implications in the epigenetic regulation of eggshell formation-related genes in a trematode parasite Clonorchis sinensis. PARASITES, HOSTS AND DISEASES 2024; 62:98-116. [PMID: 38443774 PMCID: PMC10915263 DOI: 10.3347/phd.23116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/20/2023] [Indexed: 03/07/2024]
Abstract
Epigenetic writers including DNA and histone lysine methyltransferases (DNMT and HKMT, respectively) play an initiative role in the differentiation and development of eukaryotic organisms through the spatiotemporal regulation of functional gene expressions. However, the epigenetic mechanisms have long been suspected in helminth parasites lacking the major DNA methyltransferases DNMT1 and DNMT3a/3b. Very little information on the evolutionary status of the epigenetic tools and their role in regulating chromosomal genes is currently available in the parasitic trematodes. We previously suggested the probable role of a DNMT2-like protein (CsDNMT2) as a genuine epigenetic writer in a trematode parasite Clonorchis sinensis. Here, we analyzed the phylogeny of HKMT subfamily members in the liver fluke and other platyhelminth species. The platyhelminth genomes examined conserved genes for the most of SET domain-containing HKMT and Disruptor of Telomeric Silencing 1 subfamilies, while some genes were expanded specifically in certain platyhelminth genomes. Related to the high gene dosages for HKMT activities covering differential but somewhat overlapping substrate specificities, variously methylated histones were recognized throughout the tissues/organs of C. sinensis adults. The temporal expressions of genes involved in eggshell formation were gradually decreased to their lowest levels proportionally to aging, whereas those of some epigenetic tool genes were re-boosted in the later adult stages of the parasite. Furthermore, these expression levels were significantly affected by treatment with DNMT and HKMT inhibitors. Our data strongly suggest that methylated histones are potent epigenetic markers that modulate the spatiotemporal expressions of C. sinensis genes, especially those involved in sexual reproduction.
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Affiliation(s)
- Min-Ji Park
- Department of Microbiology, College of Medicine and Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999,
Korea
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999,
Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Young-An Bae
- Department of Microbiology, College of Medicine and Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999,
Korea
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4
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Wadhwa N, Kapoor S, Kapoor M. Arabidopsis T-DNA mutants affected in TRDMT1/DNMT2 show differential protein synthesis and compromised stress tolerance. FEBS J 2024; 291:92-113. [PMID: 37584564 DOI: 10.1111/febs.16935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 08/17/2023]
Abstract
TRDMT1/DNMT2 belongs to the conserved family of nucleic acid methyltransferases. Unlike the animal systems, studies on TRDMT1/DNMT2 in land plants have been limited. We show that TRDMT1/DNMT2 is strongly conserved in the green lineage. Studies in mosses have previously shown that TRDMT1/DNMT2 plays a crucial role in modulating molecular networks involved in stress perception and signalling and in transcription/stability of specific tRNAs under stress. To gain deeper insight into its biological roles in a flowering plant, we examined more closely the previously reported Arabidopsis SALK_136635C line deficient in TRDMT1/DNMT2 function [Goll MG et al. (2006) Science 311, 395-398]. RNAs derived from Arabidopsis Dnmt2-deficient plants lacked m5 C38 in tRNAAsp . In this study, by transient expression assays we show that Arabidopsis TRDMT1/DNMT2 is distributed in the nucleus, cytoplasm and RNA-processing bodies, suggesting a role for TRDMT1/DNMT2 in RNA metabolic processes possibly by shuttling between cellular compartments. Bright-field and high-resolution SEM and qPCR analysis reveal roles of TRDMT1/DNMT2 in proper growth and developmental progression. Quantitative proteome analysis by LC-MS/MS coupled with qPCR shows AtTRDMT1/AtDNMT2 function to be crucial for protein synthesis and cellular homeostasis via housekeeping roles and proteins with poly-Asp stretches and RNA pol II activity on selected genes are affected in attrdmt1/atdnmt2. This shift in metabolic pathways primes the mutant plants to become increasingly sensitive to oxidative and osmotic stress. Taken together, our study sheds light on the mechanistic role of TRDMT1/DNMT2 in a flowering plant.
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Affiliation(s)
- Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Sanjay Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
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5
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Lewinska A, Adamczyk-Grochala J, Wnuk M. TRDMT1-mediated RNA C-5 methylation as a novel target in anticancer therapy. Biochim Biophys Acta Rev Cancer 2023; 1878:188964. [PMID: 37625528 DOI: 10.1016/j.bbcan.2023.188964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023]
Abstract
Affected landscape of RNA modifications is frequently observed in different cancer cells that can be associated with the development of cancer cell phenotypic traits such as sustained proliferation, migration and invasion, apoptosis resistance and metabolic reprograming. DNMT2/TRDMT1 5-methylcytosine methyltransferase, initially classified as DNA methyltransferase, can methylate both tRNA and mRNA promoting tRNA stability and proper protein synthesis, and orchestrating DNA damage response (DDR) and DNA stability, respectively. TRDMT1 is associated with cancer progression as its levels can be elevated and its mutations can be observed in a number of cancer types. TRDMT1 gene knockout (KO) can sensitize cancer cells of different origin to radiotherapy and chemotherapy. In the present review paper, based on literature data, the physiological and pathophysiological roles of TRDMT1 in different biological systems are described with the emphasis on human normal and cancer cells. Potential TRDMT1 substrates, inhibitors and regulatory mechanisms of catalytic activity and cellular localization are also presented and evaluated. TRDMT1 as a novel promising target in anticancer therapy is proposed and discussed.
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Affiliation(s)
- Anna Lewinska
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | - Jagoda Adamczyk-Grochala
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Maciej Wnuk
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
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6
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Wadhwa N, Singh D, Yadav R, Kapoor S, Kapoor M. Role of TRDMT1/DNMT2 in stress adaptation and its influence on transcriptome and proteome dynamics under osmotic stress in Physcomitrium patens. PHYSIOLOGIA PLANTARUM 2023; 175:e14014. [PMID: 37882266 DOI: 10.1111/ppl.14014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 10/27/2023]
Abstract
Early land plants such as the moss Physcomitrium patens lack several morphological traits that offer protection to tracheophytes from environmental stresses. These plants instead have evolved several physiological and biochemical mechanisms that facilitate them to adapt to terrestrial stresses such as drought. We have previously shown that loss-of-function mutants of tRNA (cytosine(38)-C(5))-methyltransferase TRDMT1/DNMT2 in P. patens are highly sensitive to oxidative and osmotic stress. To gain insight into the role of PpTRDMT1/PpDNMT2 in modulating genetic networks under osmotic stress, genome-wide transcriptome and proteome studies were undertaken in wild-type and ppdnmt2 plants. Transcriptome analysis revealed 375 genes to be differentially expressed in the ppdnmt2 under stress compared to the WT. Most of these genes are affiliated with carbohydrate metabolic pathways, photosynthesis, cell wall biogenesis, pathways related to isotropic and polarised cell growth and transcription factors among others. Histochemical staining showed elevated levels of reactive oxygen species in ppdnmt2 while transmission electron microscopy revealed no distinct defects in the ultrastructure of chloroplasts. Immunoprecipitation using PpDNMT2-specific antibody coupled with mass spectrometry revealed core proteins of the glycolytic pathway, antioxidant enzymes, proteins of amino acid biosynthetic pathways and photosynthesis-related proteins among others to co-purify with PpTRDMT1/PpDNMT2 under osmotic stress. Yeast two-hybrid assays, protein deletion and α-galactosidase assays showed the cytosol glycolytic protein glyceraldehyde 3-phosphate dehydrogenase to bind to the catalytic motifs in PpTRDMT1/PpDNMT2. Results presented in this study allow us to better understand genetic networks linking enzymes of energy metabolism, epigenetic processes and RNA pol II-mediated transcription during osmotic stress tolerance in P. patens.
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Affiliation(s)
- Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Darshika Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Radha Yadav
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, Delhi, India
| | - Meenu Kapoor
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, Delhi, India
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7
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Drewell RA, Cormier TC, Steenwyk JL, Denis JS, Tabima J, Dresch J, Larochelle D. The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing. NAR Genom Bioinform 2023; 5:lqad035. [PMID: 37081864 PMCID: PMC10111430 DOI: 10.1093/nargab/lqad035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/13/2023] [Accepted: 03/30/2023] [Indexed: 04/22/2023] Open
Abstract
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing.
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Affiliation(s)
- Robert A Drewell
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Tayla C Cormier
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacob L Steenwyk
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James St Denis
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Javier F Tabima
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Jacqueline M Dresch
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Denis A Larochelle
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, USA
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8
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Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
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Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
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9
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Zimmermann RA, Fischer TR, Schwickert M, Nidoieva Z, Schirmeister T, Kersten C. Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6. Int J Mol Sci 2023; 24:ijms24076109. [PMID: 37047081 PMCID: PMC10094593 DOI: 10.3390/ijms24076109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Targeting RNA methyltransferases with small molecules as inhibitors or tool compounds is an emerging field of interest in epitranscriptomics and medicinal chemistry. For two challenging RNA methyltransferases that introduce the 5-methylcytosine (m5C) modification in different tRNAs, namely DNMT2 and NSUN6, an ultra-large commercially available chemical space was virtually screened by physicochemical property filtering, molecular docking, and clustering to identify new ligands for those enzymes. Novel chemotypes binding to DNMT2 and NSUN6 with affinities down to KD,app = 37 µM and KD,app = 12 µM, respectively, were identified using a microscale thermophoresis (MST) binding assay. These compounds represent the first molecules with a distinct structure from the cofactor SAM and have the potential to be developed into activity-based probes for these enzymes. Additionally, the challenges and strategies of chemical space docking screens with special emphasis on library focusing and diversification are discussed.
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Affiliation(s)
- Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Zarina Nidoieva
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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10
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Schulz NKE, Mohamed FF, Lo LK, Peuß R, de Buhr MF, Kurtz J. Paternal knockdown of tRNA(cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in red flour beetles. INSECT MOLECULAR BIOLOGY 2022; 31:711-721. [PMID: 35790040 DOI: 10.1111/imb.12798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Intergenerational effects from fathers to offspring are increasingly reported from diverse organisms, but the underlying mechanisms remain speculative. Paternal trans-generational immune priming (TGIP) was demonstrated in the red flour beetle Tribolium castaneum: non-infectious bacterial exposure of fathers protects their offspring against an infectious challenge for at least two generations. Epigenetic processes, such as cytosine methylation of nucleic acids, have been proposed to enable transfer of information from fathers to offspring. Here we studied a potential role in TGIP of the Dnmt2 gene (renamed as Trdmt1 in humans), which encodes a highly conserved enzyme that methylates different RNAs, including specific cytosines of a set of tRNAs. Dnmt2 has previously been reported to be involved in intergenerational epigenetic inheritance in mice and protection against viruses in fruit flies. We first studied gene expression and found that Dnmt2 is expressed in various life history stages and tissues of T. castaneum, with high expression in the reproductive organs. RNAi-mediated knockdown of Dnmt2 in fathers was systemic, slowed down offspring larval development and increased mortality of the adult offspring upon bacterial infection. However, these effects were independent of bacterial exposure of the fathers. In conclusion, our results point towards a role of Dnmt2 for paternal effects, while elucidation of the mechanisms behind paternal TGIP needs further studies.
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Affiliation(s)
- Nora K E Schulz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Fakry F Mohamed
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Institute of Virology Muenster, Center for Molecular Biology of Inflammation (ZMBE), University Hospital Muenster, Muenster, Germany
| | - Lai Ka Lo
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Robert Peuß
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Maike F de Buhr
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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11
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DNA Methyltransferases: From Evolution to Clinical Applications. Int J Mol Sci 2022; 23:ijms23168994. [PMID: 36012258 PMCID: PMC9409253 DOI: 10.3390/ijms23168994] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.
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12
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Filip K, Lewińska A, Adamczyk-Grochala J, Marino Gammazza A, Cappello F, Lauricella M, Wnuk M. 5-Azacytidine Inhibits the Activation of Senescence Program and Promotes Cytotoxic Autophagy during Trdmt1-Mediated Oxidative Stress Response in Insulinoma β-TC-6 Cells. Cells 2022; 11:cells11071213. [PMID: 35406777 PMCID: PMC8997412 DOI: 10.3390/cells11071213] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023] Open
Abstract
5-Azacytidine (5-azaC), a methyltransferase inhibitor and anticancer drug, can promote several cellular stress responses such as apoptosis, autophagy, and senescence. The action of 5-azaC is complex and can be modulated by dose, time of treatment, and co-administration with oxidants. Insulinoma is a rare pancreatic neuroendocrine tumor with limited chemotherapeutic options. In the present study, two cellular models of insulinoma were considered, namely NIT-1 and β-TC-6 mouse cells, to evaluate the effects of 5-azaC post-treatment during hydrogen peroxide-induced oxidative stress. 5-azaC attenuated the development of oxidant-induced senescent phenotype in both cell lines. No pro-apoptotic action of 5-azaC was observed in cells treated with the oxidant. On the contrary, 5-azaC stimulated an autophagic response, as demonstrated by the increase in phosphorylated eIF2α and elevated pools of autophagic marker LC3B in oxidant-treated β-TC-6 cells. Notably, autophagy resulted in increased necrotic cell death in β-TC-6 cells with higher levels of nitric oxide compared to less affected NIT-1 cells. In addition, 5-azaC increased levels of RNA methyltransferase Trdmt1, but lowered 5-mC and m6A levels, suggesting Trdmt1 inhibition. We postulate that the 5-azaC anticancer action may be potentiated during oxidative stress conditions that can be used to sensitize cancer cells, at least insulinoma cells, with limited drug responsiveness.
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Affiliation(s)
- Kamila Filip
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy; (K.F.); (A.M.G.); (F.C.)
| | - Anna Lewińska
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Nature Sciences, University of Rzeszow, 35959 Rzeszow, Poland; (J.A.-G.); (M.W.)
- Correspondence: (A.L.); (M.L.)
| | - Jagoda Adamczyk-Grochala
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Nature Sciences, University of Rzeszow, 35959 Rzeszow, Poland; (J.A.-G.); (M.W.)
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy; (K.F.); (A.M.G.); (F.C.)
| | - Francesco Cappello
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Human Anatomy and Histology, University of Palermo, 90127 Palermo, Italy; (K.F.); (A.M.G.); (F.C.)
- Euro-Mediterranean Institutes of Science and Technology, 90139 Palermo, Italy
| | - Marianna Lauricella
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
- Correspondence: (A.L.); (M.L.)
| | - Maciej Wnuk
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Nature Sciences, University of Rzeszow, 35959 Rzeszow, Poland; (J.A.-G.); (M.W.)
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13
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Abstract
Malaria parasites need to cope with changing environmental conditions that require strong countermeasures to ensure pathogen survival in the human and mosquito hosts. The molecular mechanisms that protect Plasmodium falciparum homeostasis during the complex life cycle remain unknown. Here, we identify cytosine methylation of tRNAAsp (GTC) as being critical to maintain stable protein synthesis. Using conditional knockout (KO) of a member of the DNA methyltransferase family, called Pf-DNMT2, RNA bisulfite sequencing demonstrated the selective cytosine methylation of this enzyme of tRNAAsp (GTC) at position C38. Although no growth defect on parasite proliferation was observed, Pf-DNMT2KO parasites showed a selective downregulation of proteins with a GAC codon bias. This resulted in a significant shift in parasite metabolism, priming KO parasites for being more sensitive to various types of stress. Importantly, nutritional stress made tRNAAsp (GTC) sensitive to cleavage by an unknown nuclease and increased gametocyte production (>6-fold). Our study uncovers an epitranscriptomic mechanism that safeguards protein translation and homeostasis of sexual commitment in malaria parasites. IMPORTANCE P. falciparum is the most virulent malaria parasite species, accounting for the majority of the disease mortality and morbidity. Understanding how this pathogen is able to adapt to different cellular and environmental stressors during its complex life cycle is crucial in order to develop new strategies to tackle the disease. In this study, we identified the writer of a specific tRNA cytosine methylation site as a new layer of epitranscriptomic regulation in malaria parasites that regulates the translation of a subset of parasite proteins (>400) involved in different metabolic pathways. Our findings give insight into a novel molecular mechanism that regulates P. falciparum response to drug treatment and sexual commitment.
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14
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The expression and clinical significance of the tRNA aspartic acid methyltransferase 1 protein in gastric cancer. Int J Clin Oncol 2021; 26:2229-2236. [PMID: 34689291 DOI: 10.1007/s10147-021-02019-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study aimed to investigate the role of the tRNA aspartic acid methyltransferase 1 (TRDMT1) protein in the development and progression of gastric cancer (GC). METHODS The 90 GC tissues and 35 paracancerous tissues (gastric mucosa) were collected from patients (31 males and 59 females; average age 66), who were pathologically diagnosed as GC. The expression of TRDMT1 in three GC cell lines (MKN28, BGC823, and MGC803) and tissues from GC patients were detected by western blotting and immunological staining, respectively. The relationship between TRDMT1 expression and clinicopathological parameters in GC patients was explored. TRDMT1 was knocked down by RNAi lentivirus in GC cells. GC cell migration and invasion were analyzed using scratch and transwell assays. RESULTS TRDMT1 expression in the GC cell lines was higher than that in the normal gastric mucosal epithelial cell line (P < 0.05). Positive TRDMT1 protein expression in the GC tissue was higher than that in the adjacent tissue. The expression of TRDMT1 was positively associated with tumor size, histological grade, invasion depth, lymph node metastasis, and tumor node metastasis (TNM) stage (P < 0.05). High TRDMT1 expression predicted poor OS of GC patients. Tumor size, differentiation degree, invasion depth, lymph node metastasis, TNM stage, and TRDMT1 expression were independent predictors of the OS of GC patients. Knockdown of TRDMT1 inhibited the migration and invasion of MKN28 cells. CONCLUSION TRDMT1 was highly expressed in GC cell lines and tissues. TRDMT1 expression was independent predictor of the OS of GC patients. TRDMT1 knockdown reduced GC cell migration and invasion. All these results suggested that TRDMT1 has the potential to be used as a target for the diagnosis and treatment of GC.
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15
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Bloniarz D, Adamczyk-Grochala J, Lewinska A, Wnuk M. The lack of functional DNMT2/TRDMT1 gene modulates cancer cell responses during drug-induced senescence. Aging (Albany NY) 2021; 13:15833-15874. [PMID: 34139673 PMCID: PMC8266355 DOI: 10.18632/aging.203203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/28/2021] [Indexed: 01/20/2023]
Abstract
Cellular senescence may be a side effect of chemotherapy and other anti-cancer treatments that may promote inflammation and paracrine secondary senescence in healthy tissues. DNMT2/TRDMT1 methyltransferase is implicated in the regulation of cellular lifespan and DNA damage response (DDR). In the present study, the responses to senescence inducing concentrations of doxorubicin and etoposide in different cancer cells with DNMT2/TRDMT1 gene knockout were evaluated, namely changes in the cell cycle, apoptosis, autophagy, interleukin levels, genetic stability and DDR, and 5-mC and NSUN1-6 levels. Moreover, the effect of azacytidine post-treatment was considered. Diverse responses were revealed that was based on type of cancer cells (breast and cervical cancer, osteosarcoma and glioblastoma cells) and anti-cancer drugs. DNMT2/TRDMT1 gene knockout in drug-treated glioblastoma cells resulted in decreased number of apoptotic and senescent cells, IL-8 levels and autophagy, and increased number of necrotic cells, DNA damage and affected DDR compared to drug-treated glioblastoma cells with unmodified levels of DNMT2/TRDMT1. We suggest that DNMT2/TRDMT1 gene knockout in selected experimental settings may potentiate some adverse effects associated with chemotherapy-induced senescence.
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Affiliation(s)
- Dominika Bloniarz
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Rzeszow 35-310, Poland
| | - Jagoda Adamczyk-Grochala
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Rzeszow 35-310, Poland
| | - Anna Lewinska
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Rzeszow 35-310, Poland
| | - Maciej Wnuk
- Department of Biotechnology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, Rzeszow 35-310, Poland
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16
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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17
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Ashrafizadeh M, Zarabi A, Hushmandi K, Moghadam ER, Hashemi F, Daneshi S, Hashemi F, Tavakol S, Mohammadinejad R, Najafi M, Dudha N, Garg M. C-Myc Signaling Pathway in Treatment and Prevention of Brain Tumors. Curr Cancer Drug Targets 2021; 21:2-20. [PMID: 33069197 DOI: 10.2174/1568009620666201016121005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/26/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022]
Abstract
Brain tumors are responsible for high morbidity and mortality worldwide. Several factors such as the presence of blood-brain barrier (BBB), sensitive location in the brain, and unique biological features challenge the treatment of brain tumors. The conventional drugs are no longer effective in the treatment of brain tumors, and scientists are trying to find novel therapeutics for brain tumors. In this way, identification of molecular pathways can facilitate finding an effective treatment. c-Myc is an oncogene signaling pathway capable of regulation of biological processes such as apoptotic cell death, proliferation, survival, differentiation, and so on. These pleiotropic effects of c-Myc have resulted in much fascination with its role in different cancers, particularly brain tumors. In the present review, we aim to demonstrate the upstream and down-stream mediators of c-Myc in brain tumors such as glioma, glioblastoma, astrocytoma, and medulloblastoma. The capacity of c-Myc as a prognostic factor in brain tumors will be investigated. Our goal is to define an axis in which the c-Myc signaling pathway plays a crucial role and to provide direction for therapeutic targeting in these signaling networks in brain tumors.
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Affiliation(s)
- Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Universite Caddesi No. 27, Orhanli, Tuzla, 34956 Istanbul, Turkey
| | - Ali Zarabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956, Istanbul, Turkey
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farid Hashemi
- DVM. Graduated, Young Researcher and Elite Club, Kazerun Branch, Islamic Azad University, Kazeroon, Iran
| | - Salman Daneshi
- Department of Public Health, School of Health, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Fardin Hashemi
- Student Research Committee, Department of physiotherapy, Faculty of rehabilitation, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Reza Mohammadinejad
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman 7619813159, Iran
| | - Masoud Najafi
- Medical Technology Research Center, Institute of Health Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Namrata Dudha
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, Uttar Pradesh, India
| | - Manoj Garg
- Amity of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida-201313, India
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18
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Chen YS, Yang WL, Zhao YL, Yang YG. Dynamic transcriptomic m 5 C and its regulatory role in RNA processing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1639. [PMID: 33438329 DOI: 10.1002/wrna.1639] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
RNA 5-methylcytosine (m5 C) is a prevalent RNA modification in multiple RNA species, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), and noncoding RNAs (ncRNAs), and broadly distributed from archaea, prokaryotes to eukaryotes. The multiple detecting techniques of m5 C have been developed, such as m5 C-RIP-seq, miCLIP-seq, AZA-IP-seq, RNA-BisSeq, TAWO-seq, and Nanopore sequencing. These high-throughput techniques, combined with corresponding analysis pipeline, provide a precise m5 C landscape contributing to the deciphering of its biological functions. The m5 C modification is distributed along with mRNA and enriched around 5'UTR and 3'UTR, and conserved in tRNAs and rRNAs. It is dynamically regulated by its related enzymes, including methyltransferases (NSUN, DNMT, and TRDMT family members), demethylases (TET families and ALKBH1), and binding proteins (ALYREF and YBX1). So far, accumulative studies have revealed that m5 C participates in a variety of RNA metabolism, including mRNA export, RNA stability, and translation. Depletion of m5 C modification in the organism could cause dysfunction of mitochondria, drawback of stress response, frustration of gametogenesis and embryogenesis, abnormality of neuro and brain development, and has been implicated in cell migration and tumorigenesis. In this review, we provide a comprehensive summary of dynamic regulatory elements of RNA m5 C, including methyltransferases (writers), demethylases (erasers), and binding proteins (readers). We also summarized the related detecting technologies and biological functions of the RNA 5-methylcytosine, and provided future perspectives in m5 C research. This article is categorized under: RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Yu-Sheng Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Lan Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center For Bioinformation, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
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19
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Xiang S, Ma Y, Shen J, Zhao Y, Wu X, Li M, Yang X, Kaboli PJ, Du F, Ji H, Zheng Y, Li X, Li J, Wen Q, Xiao Z. m 5C RNA Methylation Primarily Affects the ErbB and PI3K-Akt Signaling Pathways in Gastrointestinal Cancer. Front Mol Biosci 2020; 7:599340. [PMID: 33365328 PMCID: PMC7750483 DOI: 10.3389/fmolb.2020.599340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022] Open
Abstract
5-Methylcytosine (m5C) is a kind of methylation modification that occurs in both DNA and RNA and is present in the highly abundant tRNA and rRNA. It has an important impact on various human diseases including cancer. The function of m5C is modulated by regulatory proteins, including methyltransferases (writers) and special binding proteins (readers). This study aims at comprehensive study of the m5C RNA methylation-related genes and the main pathways under m5C RNA methylation in gastrointestinal (GI) cancer. Our result showed that the expression of m5C writers and reader was mostly up-regulated in GI cancer. The NSUN2 gene has the highest proportion of mutations found in GI cancer. Importantly, in liver cancer, higher expression of almost all m5C regulators was significantly associated with lower patient survival rate. In addition, the expression level of m5C-related genes is significantly different at various pathological stages. Finally, we have found through bioinformatics analysis that m5C regulatory proteins are closely related to the ErbB/PI3K–Akt signaling pathway and GSK3B was an important target for m5C regulators. Besides, the compound termed streptozotocin may be a key candidate drug targeting on GSK3B for molecular targeted therapy in GI cancer.
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Affiliation(s)
- Shixin Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yongshun Ma
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xiao Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yuan Zheng
- Neijiang Health and Health Vocational College, Neijiang, China
| | - Xiang Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M.) Affiliated to Southwest Medical University, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
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20
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Abstract
Wild mammalian species, including bats, constitute the natural reservoir of betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides in these low-CpG viral genomes in the presence of ZAP consistently leads to decreased viral replication and virulence. Because ZAP exhibits tissue-specific expression, viruses infecting different tissues are expected to have different CpG signatures, suggesting a means to identify viral tissue-switching events. The author shows that SARS-CoV-2 has the most extreme CpG deficiency in all known betacoronavirus genomes. This suggests that SARS-CoV-2 may have evolved in a new host (or new host tissue) with high ZAP expression. A survey of CpG deficiency in viral genomes identified a virulent canine coronavirus (alphacoronavirus) as possessing the most extreme CpG deficiency, comparable with that observed in SARS-CoV-2. This suggests that the canine tissue infected by the canine coronavirus may provide a cellular environment strongly selecting against CpG. Thus, viral surveys focused on decreasing CpG in viral RNA genomes may provide important clues about the selective environments and viral defenses in the original hosts.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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21
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Hudon Thibeault AA, Laprise C. Cell-Specific DNA Methylation Signatures in Asthma. Genes (Basel) 2019; 10:E932. [PMID: 31731604 PMCID: PMC6896152 DOI: 10.3390/genes10110932] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering the role of environmental exposure on asthma development, an increasing amount of literature has been published on epigenetic modifications associated with this pathology and especially on DNA methylation, in an attempt to better understand its missing heritability. These studies have been conducted in different tissues, but mainly in blood or its peripheral mononuclear cells. However, there is growing evidence that epigenetic changes that occur in one cell type cannot be directly translated into another one. In this review, we compare alterations in DNA methylation from different cells of the immune system and of the respiratory tract. The cell types in which data are obtained influences the global status of alteration of DNA methylation in asthmatic individuals compared to control (an increased or a decreased DNA methylation). Given that several genes were cell-type-specific, there is a great need for comparative studies on DNA methylation from different cells, but from the same individuals in order to better understand the role of epigenetics in asthma pathophysiology.
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Affiliation(s)
- Andrée-Anne Hudon Thibeault
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
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22
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Kumari N, Karmakar A, Ganesan SK. Targeting epigenetic modifications as a potential therapeutic option for diabetic retinopathy. J Cell Physiol 2019; 235:1933-1947. [PMID: 31531859 DOI: 10.1002/jcp.29180] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022]
Abstract
Diabetic retinopathy (DR) is the leading cause of visual impairment in adults of working age (20-65 years) in developed countries. The metabolic memory phenomena (persistent effect of a glycemic insult even after retrieved) associated with it has increased the risk of developing the complication even after the termination of the glycemic insult. Hence, the need for finding early diagnosis and treatment options has been of great concern. Epigenetic modifications which generally occur during the beginning stages of the disease are responsible for the metabolic memory effect. Therefore, the therapy based on the reversal of the associated epigenetic mechanism can bring new insight in the area of early diagnosis and treatment mechanism. This review discusses the diabetic retinopathy, its pathogenesis, current treatment options, need of finding novel treatment options, and different epigenetic alterations associated with DR. However, the main focus is emphasized on various epigenetic modifications particularly DNA methylation which are responsible for the initiation and progression of diabetic retinopathy and the use of different epigenetic inhibitors as a novel therapeutic option for DR.
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Affiliation(s)
- Nidhi Kumari
- Laboratory of Translational Genetics, Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditi Karmakar
- Laboratory of Translational Genetics, Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Senthil Kumar Ganesan
- Laboratory of Translational Genetics, Structural Biology & Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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23
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Guo X, Xie Q, Li B, Su H. Molecular characterization and transcription analysis of DNA methyltransferase genes in tomato (Solanum lycopersicum). Genet Mol Biol 2019; 43:e20180295. [PMID: 31429858 PMCID: PMC7197986 DOI: 10.1590/1678-4685-gmb-2018-0295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/08/2019] [Indexed: 11/22/2022] Open
Abstract
DNA methylation plays an important role in plant growth and development, gene expression regulation, and maintenance of genome stability. However, only little information regarding stress-related DNA methyltransferases (MTases) genes is available in tomato. Here, we report the analysis of nine tomato MTases, which were categorized into four known subfamilies. Structural analysis suggested their DNA methylase domains are highly conserved, whereas the N-terminals are divergent. Tissue-specific analysis of these MTase genes revealed that SlCMT2, SlCMT3, and SlDRM5 were expressed higher in young leaves, while SlMET1, SlCMT4, SlDRM7, and SlDRM8 were highly expressed in immature green fruit, and their expression declined continuously with further fruit development. In contrast, SlMETL was highly expressed in ripening fruit and displayed an up-regulated tendency during fruit development. In addition, the expression of SlMET1 in the ripening of mutant rin and Nr tomatoes is significantly higher compared to wild-type tomato, suggesting that SlMET1 was negatively regulated by the ethylene signal and ripening regulator MADS-RIN. Furthermore, expression analysis under abiotic stresses revealed that these MTase genes were stress-responsive and may function diversely in different stress conditions. Overall, our results provide valuable information for exploring the regulation of tomato fruit ripening and response to abiotic stress through DNA methylation.
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Affiliation(s)
- Xuhu Guo
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Qian Xie
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Baoyuan Li
- Shanxi Datong University, School of Life Sciences, Datong, China.,Shanxi Datong University, Applied Biotechnology Institute, Datong, China
| | - Huanzhen Su
- Shanxi Datong University, School of Life Sciences, Datong, China
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24
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Di Serio F, Torchetti EM, Daròs JA, Navarro B. Reassessment of Viroid RNA Cytosine Methylation Status at the Single Nucleotide Level. Viruses 2019; 11:E357. [PMID: 31003406 PMCID: PMC6521008 DOI: 10.3390/v11040357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 11/17/2022] Open
Abstract
Composed of a few hundreds of nucleotides, viroids are infectious, circular, non-protein coding RNAs able to usurp plant cellular enzymes and molecular machineries to replicate and move in their hosts. Several secondary and tertiary RNA structural motifs have been implicated in the viroid infectious cycle, but whether modified nucleotides, such as 5C-methylcytosine (m5C), also play a role has not been deeply investigated so far. Here, the possible existence of m5C in both RNA polarity strands of potato spindle tuber viroid and avocado sunblotch viroid -which are representative members of the nucleus- and chloroplast-replicating viroids, respectively- has been assessed at single nucleotide level. We show that a standard bisulfite protocol efficiently used for identifying m5C in cellular RNAs may generate false positive results in the case of the highly structured viroid RNAs. Applying a bisulfite conversion protocol specifically adapted to RNAs with high secondary structure, no m5C was identified in both polarity strands of both viroids, indicating that this specific nucleotide modification does not likely play a role in viroid biology.
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Affiliation(s)
- Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante (CNR), 70126 Bari, Italy.
| | | | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022 Valencia, Spain.
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante (CNR), 70126 Bari, Italy.
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25
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Halby L, Marechal N, Pechalrieu D, Cura V, Franchini DM, Faux C, Alby F, Troffer-Charlier N, Kudithipudi S, Jeltsch A, Aouadi W, Decroly E, Guillemot JC, Page P, Ferroud C, Bonnefond L, Guianvarc'h D, Cavarelli J, Arimondo PB. Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0072. [PMID: 29685976 DOI: 10.1098/rstb.2017.0072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA, RNA and histone methylation is implicated in various human diseases such as cancer or viral infections, playing a major role in cell process regulation, especially in modulation of gene expression. Here we developed a convergent synthetic pathway starting from a protected bromomethylcytosine derivative to synthesize transition state analogues of the DNA methyltransferases. This approach led to seven 5-methylcytosine-adenosine compounds that were, surprisingly, inactive against hDNMT1, hDNMT3Acat, TRDMT1 and other RNA human and viral methyltransferases. Interestingly, compound 4 and its derivative 2 showed an inhibitory activity against PRMT4 in the micromolar range. Crystal structures showed that compound 4 binds to the PRMT4 active site, displacing strongly the S-adenosyl-l-methionine cofactor, occupying its binding site, and interacting with the arginine substrate site through the cytosine moiety that probes the space filled by a substrate peptide methylation intermediate. Furthermore, the binding of the compounds induces important structural switches. These findings open new routes for the conception of new potent PRMT4 inhibitors based on the 5-methylcytosine-adenosine scaffold.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Ludovic Halby
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France.,Maison Française d'Oxford, CNRS, MEAE, 2-10 Norham Road, Oxford, UK
| | - Nils Marechal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Céline Faux
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France
| | - Fréderic Alby
- Laboratoire Pierre Fabre, 3 avenue H. Curien, 31100 Toulouse, France
| | - Nathalie Troffer-Charlier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Wahiba Aouadi
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Etienne Decroly
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Jean-Claude Guillemot
- Laboratoire Architecture Fonction des Macromolécules Biologiques (AFMB-UMR 7257), Aix-Marseille Université & CNRS, 163 avenue de Luminy, 13288 Marseille cedex 09, France
| | - Patrick Page
- Epiremed SAS, 1 Rue des Pénitents Blancs, 31000 Toulouse, France
| | - Clotilde Ferroud
- Laboratoire de chimie moléculaire, CMGPCE, EA7341, Conservatoire National des Arts et Métiers, 2 rue Conté, 75003 Paris, France
| | - Luc Bonnefond
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Dominique Guianvarc'h
- Sorbonne Universités, UPMC Université Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), 4 place Jussieu, 75005 Paris, France.,Département de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Paola B Arimondo
- CNRS FRE3600 ETaC, bât. IBCG, 31062 Toulouse, France .,Churchill College, CB3 0DS Cambridge, UK
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26
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c-Myc activation promotes cofilin-mediated F-actin cytoskeleton remodeling and telomere homeostasis as a response to oxidant-based DNA damage in medulloblastoma cells. Redox Biol 2019; 24:101163. [PMID: 30901604 PMCID: PMC6429558 DOI: 10.1016/j.redox.2019.101163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 03/07/2019] [Indexed: 01/22/2023] Open
Abstract
Medulloblastoma (MB) is a common and highly aggressive pediatric brain tumor of a heterogeneous nature. According to transcriptome-based profiling, four molecular subgroups of MB have been revealed, namely WNT, SHH, Group 3 and Group 4. High MYC mRNA expression and MYC gene amplification in MB have been considered as indicators of poor prognosis. However, the role of c-Myc in MB biology is still not well established. In the present study, the effects of c-Myc activation in UW228-MycER MB cell line were investigated using 4-hydroxytamoxifen (4-OHT) induction system. Upon 4-OHT stimulation, an increase in metabolic activity, large-cell/anaplastic (LC/A) phenotype and oxidative stress-mediated DNA damage were observed. However, 53BP1 foci were not implicated in DNA damage response. Instead, cofilin nuclear translocation, changes in F-actin cytoskeleton and the levels of cytoskeletal proteins were shown. Moreover, the telomere length was found to be unaffected that may be associated with the upregulation of TRF proteins. Transcription of nascent RNA (synthesis of new rRNA) and the expression of RNA polymerase I-specific transcription initiation factor RRN3/TIF-IA were also elevated. Moreover, increased levels of DNMT2, a modulator of stress responses, were observed. A small fraction of cells responded differently as oncogene-induced senescence was also noticed. We postulate that c-Myc-mediated modulation of genetic stability of MB cells may trigger cellular heterogeneity and affect adaptive responses to changing environment.
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27
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Aliaga B, Bulla I, Mouahid G, Duval D, Grunau C. Universality of the DNA methylation codes in Eucaryotes. Sci Rep 2019; 9:173. [PMID: 30655579 PMCID: PMC6336885 DOI: 10.1038/s41598-018-37407-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/24/2018] [Indexed: 12/26/2022] Open
Abstract
Genetics and epigenetics are tightly linked heritable information classes. Question arises if epigenetics provides just a set of environment dependent instructions, or whether it is integral part of an inheritance system. We argued that in the latter case the epigenetic code should share the universality quality of the genetic code. We focused on DNA methylation. Since availability of DNA methylation data is biased towards model organisms we developed a method that uses kernel density estimations of CpG observed/expected ratios to infer DNA methylation types in any genome. We show here that our method allows for robust prediction of mosaic and full gene body methylation with a PPV of 1 and 0.87, respectively. We used this prediction to complement experimental data, and applied hierarchical clustering to identify methylation types in ~150 eucaryotic species covering different body plans, reproduction types and living conditions. Our analysis indicates that there are only four gene body methylation types. These types do not follow phylogeny (i.e. phylogenetically distant clades can have identical methylation types) but they are consistent within clades. We conclude that the gene body DNA methylation codes have universality similar to the universality of the genetic code and should consequently be considered as part of the inheritance system.
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Affiliation(s)
- Benoît Aliaga
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - Ingo Bulla
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
- Institute for Mathematics and Informatics, University of Greifswald, Greifswald, Germany
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Gabriel Mouahid
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - David Duval
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - Christoph Grunau
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France.
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28
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Abhyankar V, Kaduskar B, Kamat SS, Deobagkar D, Ratnaparkhi GS. Drosophila DNA/RNA methyltransferase contributes to robust host defense in aging animals by regulating sphingolipid metabolism. ACTA ACUST UNITED AC 2018; 221:jeb.187989. [PMID: 30254027 DOI: 10.1242/jeb.187989] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/17/2018] [Indexed: 12/20/2022]
Abstract
Drosophila methyltransferase (Mt2) has been implicated in the methylation of both DNA and tRNA. In this study, we demonstrate that loss of Mt2 activity leads to an age-dependent decline of immune function in the adult fly. A newly eclosed adult has mild immune defects that are exacerbated in a 15 day old Mt2-/- fly. The age-dependent effects appear to be systemic, including disturbances in lipid metabolism, changes in cell shape of hemocytes and significant fold-changes in levels of transcripts related to host defense. Lipid imbalance, as measured by quantitative lipidomics, correlates with immune dysfunction, with high levels of immunomodulatory lipids, sphingosine-1-phosphate (S1P) and ceramides, along with low levels of storage lipids. Activity assays on fly lysates confirm the age-dependent increase in S1P and concomitant reduction of S1P lyase activity. We hypothesize that Mt2 functions to regulate genetic loci such as S1P lyase and this regulation is essential for robust host defense as the animal ages. Our study uncovers novel links between age--dependent Mt2 function, innate immune response and lipid homeostasis.
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Affiliation(s)
- Varada Abhyankar
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Bhagyashree Kaduskar
- Department of Biology, Indian Institute of Science Education & Research (IISER), Pune 411008, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education & Research (IISER), Pune 411008, India
| | - Deepti Deobagkar
- Department of Zoology, Savitribai Phule Pune University, Pune 411007, India .,Center of Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Girish S Ratnaparkhi
- Department of Biology, Indian Institute of Science Education & Research (IISER), Pune 411008, India
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29
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Angelova MT, Dimitrova DG, Dinges N, Lence T, Worpenberg L, Carré C, Roignant JY. The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. Front Bioeng Biotechnol 2018; 6:46. [PMID: 29707539 PMCID: PMC5908907 DOI: 10.3389/fbioe.2018.00046] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 01/19/2023] Open
Abstract
Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.
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Affiliation(s)
- Margarita T Angelova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Nadja Dinges
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Tina Lence
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Lina Worpenberg
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Clément Carré
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Jean-Yves Roignant
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
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30
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Conflict in the Intracellular Lives of Endosymbionts and Viruses: A Mechanistic Look at Wolbachia-Mediated Pathogen-blocking. Viruses 2018; 10:v10040141. [PMID: 29561780 PMCID: PMC5923435 DOI: 10.3390/v10040141] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/14/2018] [Accepted: 03/20/2018] [Indexed: 12/16/2022] Open
Abstract
At the forefront of vector control efforts are strategies that leverage host-microbe associations to reduce vectorial capacity. The most promising of these efforts employs Wolbachia, a maternally transmitted endosymbiotic bacterium naturally found in 40% of insects. Wolbachia can spread through a population of insects while simultaneously inhibiting the replication of viruses within its host. Despite successes in using Wolbachia-transfected mosquitoes to limit dengue, Zika, and chikungunya transmission, the mechanisms behind pathogen-blocking have not been fully characterized. Firstly, we discuss how Wolbachia and viruses both require specific host-derived structures, compounds, and processes to initiate and maintain infection. There is significant overlap in these requirements, and infection with either microbe often manifests as cellular stress, which may be a key component of Wolbachia’s anti-viral effect. Secondly, we discuss the current understanding of pathogen-blocking through this lens of cellular stress and develop a comprehensive view of how the lives of Wolbachia and viruses are fundamentally in conflict with each other. A thorough understanding of the genetic and cellular determinants of pathogen-blocking will significantly enhance the ability of vector control programs to deploy and maintain effective Wolbachia-mediated control measures.
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31
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Lewinska A, Adamczyk-Grochala J, Kwasniewicz E, Wnuk M. Downregulation of methyltransferase Dnmt2 results in condition-dependent telomere shortening and senescence or apoptosis in mouse fibroblasts. J Cell Physiol 2017; 232:3714-3726. [PMID: 28177119 DOI: 10.1002/jcp.25848] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 01/05/2023]
Abstract
Dnmt2 is a highly conserved methyltransferase of uncertain biological function(s). As Dnmt2 was considered as a driver of fruit fly longevity and a modulator of stress response, we decided to evaluate the role of Dnmt2 during stress-induced premature senescence in NIH3T3 mouse fibroblasts. Stable knockdown of Dnmt2 resulted in hydrogen peroxide-mediated sensitivity and apoptosis, whereas in the control conditions, senescence was induced. Cellular senescence was accompanied by elevated levels of p53 and p21, decreased telomere length and telomerase activity, increased production of reactive oxygen species and protein carbonylation, and DNA damage. Dnmt2 silencing also promoted global DNA and RNA hypermethylation, and upregulation of methyltransferases, namely Dnmt1, Dnmt3a, and Dnmt3b. Taken together, we show for the first time that Dnmt2 may promote lifespan in the control conditions and survival during stress conditions in mouse fibroblasts.
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Affiliation(s)
- Anna Lewinska
- Laboratory of Cell Biology, University of Rzeszow, Kolbuszowa, Poland
| | | | - Ewa Kwasniewicz
- Laboratory of Cell Biology, University of Rzeszow, Kolbuszowa, Poland
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Kolbuszowa, Poland
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32
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Tuorto F, Lyko F. Genome recoding by tRNA modifications. Open Biol 2017; 6:rsob.160287. [PMID: 27974624 PMCID: PMC5204126 DOI: 10.1098/rsob.160287] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/14/2016] [Indexed: 11/12/2022] Open
Abstract
RNA modifications are emerging as an additional regulatory layer on top of the primary RNA sequence. These modifications are particularly enriched in tRNAs where they can regulate not only global protein translation, but also protein translation at the codon level. Modifications located in or in the vicinity of tRNA anticodons are highly conserved in eukaryotes and have been identified as potential regulators of mRNA decoding. Recent studies have provided novel insights into how these modifications orchestrate the speed and fidelity of translation to ensure proper protein homeostasis. This review highlights the prominent modifications in the tRNA anticodon loop: queuosine, inosine, 5-methoxycarbonylmethyl-2-thiouridine, wybutosine, threonyl-carbamoyl-adenosine and 5-methylcytosine. We discuss the functional relevance of these modifications in protein translation and their emerging role in eukaryotic genome recoding during cellular adaptation and disease.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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33
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Lewinska A, Adamczyk-Grochala J, Kwasniewicz E, Deregowska A, Semik E, Zabek T, Wnuk M. Reduced levels of methyltransferase DNMT2 sensitize human fibroblasts to oxidative stress and DNA damage that is accompanied by changes in proliferation-related miRNA expression. Redox Biol 2017; 14:20-34. [PMID: 28843151 PMCID: PMC5568885 DOI: 10.1016/j.redox.2017.08.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023] Open
Abstract
Methyltransferase DNMT2 is suggested to be involved in the regulation of numerous processes, however its biological significance and underlying molecular mechanisms remain elusive. In the present study, we have used WI-38 and BJ human fibroblasts as an in vitro model system to investigate the effects of siRNA-based DNMT2 silencing. DNMT2-depleted cells were found to be sensitive to oxidative stress conditions as judged by increased production of reactive oxygen species and susceptible to DNA damage that resulted in the inhibition of cell proliferation. DNMT2 silencing promoted upregulation of proliferation-related and tumor suppressor miRNAs, namely miR-28-3p, miR-34a-3p, miR-30b-5p, miR-29b-3p, miR-200c-3p, miR-28-5p, miR-379-5p, miR-382-5p, miR-194-5p, miR-193b-3p and miR-409-3p. Moreover, DNMT2 silencing induced cellular senescence and DNMT2 levels were elevated in replicatively senescent cells. Taken together, we found that DNMT2 may take part in the regulation of cell proliferation and longevity in human fibroblasts and speculate that the manipulation of DNMT2 levels that limits cell proliferation may be potentially useful anticancer strategy. DNMT2 silencing promotes oxidative stress and DNA damage in human fibroblasts. DNMT2 silencing results in upregulation of proliferation-related miRNAs. DNMT2 silencing inhibits cell proliferation and induces cellular senescence. DNMT2 levels are elevated during replicative senescence. DNMT2 is a novel regulator of cell proliferation and longevity in human fibroblasts.
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Affiliation(s)
- Anna Lewinska
- Laboratory of Cell Biology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | | | - Ewa Kwasniewicz
- Laboratory of Cell Biology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Anna Deregowska
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland; Department of Genetics, University of Rzeszow, Rzeszow, Poland
| | - Ewelina Semik
- Laboratory of Genomics, National Research Institute of Animal Production, Balice n. Cracow, Poland
| | - Tomasz Zabek
- Laboratory of Genomics, National Research Institute of Animal Production, Balice n. Cracow, Poland
| | - Maciej Wnuk
- Department of Genetics, University of Rzeszow, Rzeszow, Poland
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Bhattacharya T, Newton ILG, Hardy RW. Wolbachia elevates host methyltransferase expression to block an RNA virus early during infection. PLoS Pathog 2017; 13:e1006427. [PMID: 28617844 PMCID: PMC5472326 DOI: 10.1371/journal.ppat.1006427] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/22/2017] [Indexed: 01/08/2023] Open
Abstract
Wolbachia pipientis is an intracellular endosymbiont known to confer host resistance against RNA viruses in insects. However, the causal mechanism underlying this antiviral defense remains poorly understood. To this end, we have established a robust arthropod model system to study the tripartite interaction involving Sindbis virus and Wolbachia strain wMel within its native host, Drosophila melanogaster. By leveraging the power of Drosophila genetics and a parallel, highly tractable D. melanogaster derived JW18 cell culture system, we determined that in addition to reducing infectious virus production, Wolbachia negatively influences Sindbis virus particle infectivity. This is further accompanied by reductions in viral transcript and protein levels. Interestingly, unchanged ratio of proteins to viral RNA copies suggest that Wolbachia likely does not influence the translational efficiency of viral transcripts. Additionally, expression analyses of candidate host genes revealed D. melanogaster methyltransferase gene Mt2 as an induced host factor in the presence of Wolbachia. Further characterization of viral resistance in Wolbachia-infected flies lacking functional Mt2 revealed partial recovery of virus titer relative to wild-type, accompanied by complete restoration of viral RNA and protein levels, suggesting that Mt2 acts at the stage of viral genome replication. Finally, knockdown of Mt2 in Wolbachia uninfected JW18 cells resulted in increased virus infectivity, thus demonstrating its previously unknown role as an antiviral factor against Sindbis virus. In conclusion, our findings provide evidence supporting the role of Wolbachia-modulated host factors towards RNA virus resistance in arthropods, alongside establishing Mt2's novel antiviral function against Sindbis virus in D. melanogaster.
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Affiliation(s)
- Tamanash Bhattacharya
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Irene L. G. Newton
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Richard W. Hardy
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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35
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Shamsi MB, Firoz AS, Imam SN, Alzaman N, Samman MA. Epigenetics of human diseases and scope in future therapeutics. J Taibah Univ Med Sci 2017; 12:205-211. [PMID: 31435241 PMCID: PMC6695077 DOI: 10.1016/j.jtumed.2017.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/19/2017] [Accepted: 04/24/2017] [Indexed: 12/31/2022] Open
Abstract
Epigenetics is the study of nucleotide modifications that are heritable and act as regulatory mechanisms without changing the nucleotide sequence of the genome. Exogenous cues such as environment, lifestyle, nutrition, stress, and psychological factors affect epigenetic mechanisms. This mechanism is in concordance with the genetic information that plays an important role during prenatal and postnatal life of an individual. Recent epigenetic studies have revealed the potential of epigenetics in elucidating the mechanisms of different diseases. In this review, we discuss basic epigenetic mechanisms and their roles in health and disease. In addition, reported aberrations in epigenetic regulation for some common human diseases are described. Finally, we address some epigenetic approaches that have shown potential for targeted treatment of diseases.
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Affiliation(s)
- Monis B Shamsi
- Center for Genetics & Inherited Diseases, Taibah University, Almadinah Almunawwarah, KSA
| | - Abdul S Firoz
- Center for Genetics & Inherited Diseases, Taibah University, Almadinah Almunawwarah, KSA
| | - Syed N Imam
- Department of Anatomy, College of Medicine, Taibah University, Almadinah Almunawwarah, KSA
| | - Naweed Alzaman
- Department of Internal Medicine, College of Medicine, Taibah University, Almadinah Almunawwarah, KSA
| | - Muhammad A Samman
- Center for Genetics & Inherited Diseases, Taibah University, Almadinah Almunawwarah, KSA
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36
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Wei H, Jiang S, Chen L, He C, Wu S, Peng H. Characterization of Cytosine Methylation and the DNA Methyltransferases of Toxoplasma gondii. Int J Biol Sci 2017; 13:458-470. [PMID: 28529454 PMCID: PMC5436566 DOI: 10.7150/ijbs.18644] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/22/2017] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a key epigenetic modification which confers phenotypic plasticity and adaptation. Cyst-forming strains of Toxoplasma gondii undergo tachyzoite to bradyzoite conversion after initial acute infection of a host, and the reverse conversion may occur in immune-suppressed hosts. The formation of m5C is catalyzed by DNA methyltransferase (DNMT). We identified two functional DNA methyltransferases, TgDNMTa and TgDNMTb, in T. gondii that may mediate DNA methylation. The recombinant proteins showed intrinsic methyltransferase activity; both have higher transcription levels in bradyzoites than that in tachyzoites. We performed genome-wide analysis of DNA methylation in tachyzoites and bradyzoites. The results showed more methylation sites in bradyzoites than that in tachyzoites. The most significantly enriched GO-terms of genes with DNA methylation were associated with basal cellular processes such as energy metabolism and parasite resistance to host immunity. Tachyzoite proliferation in parasitophorous vacuoles (PV) can be inhibited by the DNA methyltransferase inhibitor 5-azacytidine, a chemical analogue of the nucleotide cytosine that can inactivate DNA methyltransferases. These findings provide the first confirmation of DNA methylation in T. gondii.
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Affiliation(s)
- Haixia Wei
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Shichen Jiang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Longfei Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Cheng He
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Shuizhen Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
| | - Hongjuan Peng
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, and Key Laboratory of Prevention and Control for Emerging Infectious Diseases of Guangdong Higher Institutes, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, 510515, P.R. China
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Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification. Biomolecules 2017; 7:biom7010014. [PMID: 28208632 PMCID: PMC5372726 DOI: 10.3390/biom7010014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.
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Neves M, Ribeiro J, Medeiros R, Sousa H. Genetic polymorphism in DNMTs and gastric cancer: A systematic review and meta-analysis. Porto Biomed J 2016; 1:164-172. [PMID: 32258570 DOI: 10.1016/j.pbj.2016.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
Highlights Single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs) modulate protein expression and affect DNA methylation.Aberrant DNA methylation, have been associated with gastric carcinogenesis.DNMT2 rs11254413 is associated with protection for GC development.DNMT3A rs7560488, DNMT3A rs36012910 and, specially, DNMT1 rs16999593 are associated with increased susceptibility for GC development. Abstract Epigenetics alterations, including aberrant DNA methylation, have been associated with gastric carcinogenesis. Single nucleotide polymorphisms (SNPs) in DNA methyltransferases (DNMTs) may influence protein expression and therefore affect DNA regulation and susceptibility for Gastric Cancer (GC).We have performed a systematic review and meta-analysis involving 11 studies and a total of 24 SNPs in DNMTs were analyzed. According to literature, only 4 SNPs, DNMT1 rs16999593, DNMT2 rs11254413 and DNMT3A rs7560488 and DNMT3A rs36012910, were associated with GC. DNMT1 rs16999593 and DNMT3A rs7560488C allele and DNMT3A rs36012910 G allele showed an increased risk for GC. On the other hand, DNMT2 rs11254413 G allele presented a protective effect for GC. Additionally, the meta-analysis evaluated the SNPs analyzed in more than one study (n = 6). Results revealed that only DNMT1 rs16999593 had a statistically significant association with GC development (OR = 1.31; 95% CI = 1.08-1.60; p = 0.006 for TC + CC genotypes).Our study suggests that DNMT2 rs11254413, DNMT3A rs7560488, DNMT3A rs36012910 and, specially, DNMT1 rs16999593 may have an association with GC development. Nevertheless, further studies are need using different populations to clarify this association with GC risk.
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Affiliation(s)
- Marco Neves
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal
| | - Joana Ribeiro
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Research Department, Portuguese League Against Cancer (LPCC-NRNorte), Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Research Department, Portuguese League Against Cancer (LPCC-NRNorte), Porto, Portugal.,Abel Salazar Institute for the Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
| | - Hugo Sousa
- Molecular Oncology and Viral Pathology Group, Research Centre (CI-IPOP), Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Faculty of Medicine of University of Porto, Alameda Prof. Hernâni Monteiro, Porto, Portugal.,Virology Service, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal
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Falckenhayn C, Carneiro VC, de Mendonça Amarante A, Schmid K, Hanna K, Kang S, Helm M, Dimopoulos G, Fantappié MR, Lyko F. Comprehensive DNA methylation analysis of the Aedes aegypti genome. Sci Rep 2016; 6:36444. [PMID: 27805064 PMCID: PMC5090363 DOI: 10.1038/srep36444] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/17/2016] [Indexed: 01/03/2023] Open
Abstract
Aedes aegypti mosquitoes are important vectors of viral diseases. Mosquito host factors play key roles in virus control and it has been suggested that dengue virus replication is regulated by Dnmt2-mediated DNA methylation. However, recent studies have shown that Dnmt2 is a tRNA methyltransferase and that Dnmt2-dependent methylomes lack defined DNA methylation patterns, thus necessitating a systematic re-evaluation of the mosquito genome methylation status. We have now searched the Ae. aegypti genome for candidate DNA modification enzymes. This failed to reveal any known (cytosine-5) DNA methyltransferases, but identified homologues for the Dnmt2 tRNA methyltransferase, the Mettl4 (adenine-6) DNA methyltransferase, and the Tet DNA demethylase. All genes were expressed at variable levels throughout mosquito development. Mass spectrometry demonstrated that DNA methylation levels were several orders of magnitude below the levels that are usually detected in organisms with DNA methylation-dependent epigenetic regulation. Furthermore, whole-genome bisulfite sequencing failed to reveal any evidence of defined DNA methylation patterns. These results suggest that the Ae. aegypti genome is unmethylated. Interestingly, additional RNA bisulfite sequencing provided first evidence for Dnmt2-mediated tRNA methylation in mosquitoes. These findings have important implications for understanding the mechanism of Dnmt2-dependent virus regulation.
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Affiliation(s)
- Cassandra Falckenhayn
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Vitor Coutinho Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Anderson de Mendonça Amarante
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Katharina Schmid
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Katharina Hanna
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Seokyoung Kang
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 21205 Baltimore, MD, USA
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, 21205 Baltimore, MD, USA
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
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40
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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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Khalil H, Tazi M, Caution K, Ahmed A, Kanneganti A, Assani K, Kopp B, Marsh C, Dakhlallah D, Amer AO. Aging is associated with hypermethylation of autophagy genes in macrophages. Epigenetics 2016; 11:381-8. [PMID: 26909551 DOI: 10.1080/15592294.2016.1144007] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Autophagy is a biological process characterized by self-digestion and involves induction of autophagosome formation, leading to degradation of autophagic cargo. Aging is associated with the reduction of autophagy activity leading to neurodegenerative disorders, chronic inflammation, and susceptibility to infection; however, the underlying mechanism is unclear. DNA methylation by DNA methyltransferases reduces the expression of corresponding genes. Since macrophages are major players in inflammation and defense against infection we determined the differences in methylation of autophagy genes in macrophages derived from young and aged mice. We found that promoter regions of Atg5 and LC3B are hypermethylated in macrophages from aged mice and this is accompanied by low gene expression. Treatment of aged mice and their derived macrophages with methyltransferase inhibitor (2)-epigallocatechin-3-gallate (EGCG) or specific DNA methyltransferase 2 (DNMT2) siRNA restored the expression of Atg5 and LC3 in vivo and in vitro. Our study builds a foundation for the development of novel therapeutics aimed to improve autophagy in the elderly population and suggests a role for DNMT2 in DNA methylation activities.
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Affiliation(s)
- Hany Khalil
- a Department of Molecular Biology , Genetic Engineering and Biotechnology Research Institute, University of Sadat City , Sadat City , Egypt
| | - Mia Tazi
- b Department of Microbial Infection and Immunity , Center for Microbial Interface Biology, The Ohio State University , Columbus , OH.,c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
| | - Kyle Caution
- b Department of Microbial Infection and Immunity , Center for Microbial Interface Biology, The Ohio State University , Columbus , OH.,c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
| | - Amr Ahmed
- b Department of Microbial Infection and Immunity , Center for Microbial Interface Biology, The Ohio State University , Columbus , OH.,c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
| | - Apurva Kanneganti
- b Department of Microbial Infection and Immunity , Center for Microbial Interface Biology, The Ohio State University , Columbus , OH.,c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
| | - Kaivon Assani
- d The Research Institute at Nationwide Children's Hospital, The Ohio State University , Columbus , OH
| | - Benjamin Kopp
- d The Research Institute at Nationwide Children's Hospital, The Ohio State University , Columbus , OH
| | - Clay Marsh
- c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
| | - Duaa Dakhlallah
- c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
| | - Amal O Amer
- b Department of Microbial Infection and Immunity , Center for Microbial Interface Biology, The Ohio State University , Columbus , OH.,c The Davis Heart and Lung Research Institute, The Ohio State University , Columbus , OH
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Prolonged Effects of Silver Nanoparticles on p53/p21 Pathway-Mediated Proliferation, DNA Damage Response, and Methylation Parameters in HT22 Hippocampal Neuronal Cells. Mol Neurobiol 2016; 54:1285-1300. [PMID: 26843106 PMCID: PMC5310673 DOI: 10.1007/s12035-016-9688-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/05/2016] [Indexed: 12/31/2022]
Abstract
It is widely accepted that silver nanoparticles (AgNPs) are toxic to biological systems. However, little is known about their actions at molecular level and the cytophysiological effects after AgNP removal. As nanoparticles are suggested a promising tool to transport drugs to the brain for use in neurological conditions, we used HT22 mouse hippocampal neuronal cells as a model to study AgNP-mediated effects after their removal from the cell culture medium. We selected a relatively low concentration of AgNPs, 5 μg/ml, treated the cells for 48 h, and evaluated AgNP-induced cytophysiological effects after 96 h of AgNP removal. AgNP removal did not result in cytotoxicity. In contrast, AgNPs modulated HT22 cell cycle and proliferation and induced oxidative stress and 53BP1 recruitment, which were accompanied by elevated levels of p53 and p21. AgNP-associated diminution in lamin B1 pools did not significantly affect the structure of the nucleus. No disruption in F-actin dynamics was observed upon AgNP treatment. Moreover, we showed for the first time that AgNPs stimulated changes in DNA methylation: the augmentation in 5-methylcytosine (5-mC) and DNMT1, DNMT2, DNMT3a, and DNMT3b levels were observed. The upregulation of DNMT2 may be a part of cellular stress response to AgNP treatment. Taken together, AgNP removal resulted in p53/p21-mediated inhibition of cell proliferation, oxidant-based DNA damage response, and changes in DNA methylation patterns, which suggests that more attention should be paid to the possible outcomes in individuals exposed to nano-sized biomaterials.
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Dasmahapatra AK, Khan IA. Modulation of DNA methylation machineries in Japanese rice fish (Oryzias latipes) embryogenesis by ethanol and 5-azacytidine. Comp Biochem Physiol C Toxicol Pharmacol 2016; 179:174-83. [PMID: 26510680 DOI: 10.1016/j.cbpc.2015.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 01/20/2023]
Abstract
As a sequel of our investigations on the impact of epigenome in inducing fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish, we have investigated on several DNA methylation machinery genes including DNA methyl transferase 3ba (dnmt3ba) and methyl binding proteins (MBPs), namely, mbd1b, mbd3a, mbd3b, and mecp2 at the transcription level. Studies were made during normal development, from 0day post fertilization (dpf) to hatching, and also exposing the fertilized eggs to ethanol or a DNMT inhibitor, 5-azacytidine (5-azaC). We observed that during development, all these genes followed distinct expression patterns, generally high mRNA copies in early phases (0-1dpf) and significantly low mRNA copies prior to or after hatching. Ethanol (100-500mM, 0-2dpf) was unable to alter any of these mRNAs in 2dpf; additional four day (2-6dpf) maintenance of these embryos in ethanol-free environment, on 6dpf, was also unable to establish any significant difference in these mRNA levels in comparison with the corresponding controls. However, continuous exposure of fertilized eggs in 300mM ethanol, 0-6dpf, showed significantly high mRNA copies only in MBPs (mbd1b, mbd3a, mbd3b, mecp2). 5-azaC (2mM) on 2dpf was able to enhance only mbd3b mRNA. Removal of 5-azaC and maintenance of these embryos in clean medium, 2-6dpf, showed significantly enhanced mbd3b and mecp2 mRNAs compared to corresponding controls on 6dpf. Our studies showed that in Japanese rice fish embryogenesis both ethanol and 5-azaC have the potential to specifically modulate the developmental rhythm of DNA methylation machineries.
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Affiliation(s)
- Asok K Dasmahapatra
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, University, MS 38677, USA; Department of BioMolecular Sciences, Division of Pharmacology, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Ikhlas A Khan
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, University, MS 38677, USA; Department of BioMolecular Sciences, Division of Pharmacognosy, School of Pharmacy, University of Mississippi, University, MS 38677, USA
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Zahnow C, Topper M, Stone M, Murray-Stewart T, Li H, Baylin S, Casero R. Inhibitors of DNA Methylation, Histone Deacetylation, and Histone Demethylation: A Perfect Combination for Cancer Therapy. Adv Cancer Res 2016; 130:55-111. [PMID: 27037751 DOI: 10.1016/bs.acr.2016.01.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Epigenetic silencing and inappropriate activation of gene expression are frequent events during the initiation and progression of cancer. These events involve a complex interplay between the hypermethylation of CpG dinucleotides within gene promoter and enhancer regions, the recruitment of transcriptional corepressors and the deacetylation and/or methylation of histone tails. These epigenetic regulators act in concert to block transcription or interfere with the maintenance of chromatin boundary regions. However, DNA/histone methylation and histone acetylation states are reversible, enzyme-mediated processes and as such, have emerged as promising targets for cancer therapy. This review will focus on the potential benefits and synergistic/additive effects of combining DNA-demethylating agents and histone deacetylase inhibitors or lysine-specific demethylase inhibitors together in epigenetic therapy for solid tumors and will highlight what is known regarding the mechanisms of action that contribute to the antitumor response.
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45
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Fan HC, Chi CS, Cheng SN, Lee HF, Tsai JD, Lin SZ, Harn HJ. Targeting New Candidate Genes by Small Molecules Approaching Neurodegenerative Diseases. Int J Mol Sci 2015; 17:E26. [PMID: 26712747 PMCID: PMC4730273 DOI: 10.3390/ijms17010026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/10/2015] [Accepted: 12/21/2015] [Indexed: 02/08/2023] Open
Abstract
Neurodegenerative diseases (NDs) are among the most feared of the disorders that afflict humankind for the lack of specific diagnostic tests and effective treatments. Understanding the molecular, cellular, biochemical changes of NDs may hold therapeutic promise against debilitating central nerve system (CNS) disorders. In the present review, we summarized the clinical presentations and biology backgrounds of NDs, including Parkinson's disease (PD), Huntington's disease (HD), and Alzheimer's disease (AD) and explored the role of molecular mechanisms, including dys-regulation of epigenetic control mechanisms, Ataxia-telangiectasia-mutated protein kinase (ATM), and neuroinflammation in the pathogenesis of NDs. Targeting these mechanisms may hold therapeutic promise against these devastating diseases.
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Affiliation(s)
- Hueng-Chuen Fan
- Department of Pediatrics, Tung's Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan.
- Department of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan.
| | - Ching-Shiang Chi
- Department of Pediatrics, Tung's Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan.
- Department of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan.
| | - Shin-Nan Cheng
- Department of Pediatrics, Tung's Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan.
- Department of Nursing, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan.
| | - Hsiu-Fen Lee
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung 407, Taiwan.
| | - Jeng-Dau Tsai
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan.
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung 402, Taiwan.
| | - Shinn-Zong Lin
- Graduate Institute of Immunology, China Medical University, Taichung 404, Taiwan.
- Center for Neuropsychiatry, China Medical University and Hospital, Taichung 404, Taiwan.
- Department of Neurosurgery, China Medical University Beigang Hospital, Yunlin 651, Taiwan.
| | - Horng-Jyh Harn
- Department of Pathology, China Medical University and Hospital, Taichung 404, Taiwan.
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46
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Duenas-Gonzalez A, Medina-Franco JL, Chavez-Blanco A, Dominguez-Gomez G, Fernández-de Gortari E. Developmental DNA methyltransferase inhibitors in the treatment of gynecologic cancers. Expert Opin Pharmacother 2015; 17:323-38. [PMID: 26559668 DOI: 10.1517/14656566.2016.1118053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION DNA methylation has become an attractive target for the treatment of cancer. DNA methyltransferase inhibitors have proven useful for the treatment of myelodysplastic syndrome and are being evaluated in gynecological neoplasias. AREAS COVERED We provide an overview of the current knowledge on DNA methylation and cancer and the role of DNA methylation in cervical, ovarian and endometrial carcinomas. The results of recent clinical trials with demethylating agents for cervical and ovarian cancer treatment are also discussed. EXPERT OPINION There are few studies of DNA demethylating agents for cervical and ovarian cancer treatment; nevertheless, the results are promising. To accelerate these advances, there are at least two actions that can be simultaneously pursued. One is to greatly increase the number of small clinical exploratory trials with existing demethylating drugs and using methylome analyses to identify predictive factors for response and/or toxicity. The second is finding out epigenetic 'drivers' unique to gynecological cancers and their subtypes, and then proceed to clinical trials in a highly selected population of patients. It is expected that in the future, DNA demethylation could have a role in the treatment of gynecologic cancers.
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Affiliation(s)
- Alfonso Duenas-Gonzalez
- a Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México/Instituto Nacional de Cancerología , Mexico City , Mexico
| | - José L Medina-Franco
- b Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México City , México
| | - Alma Chavez-Blanco
- c Division of Basic Research , Instituto Nacional de Cancerología , Mexico City , México
| | | | - Eli Fernández-de Gortari
- b Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México City , México
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47
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Dasmahapatra AK, Khan IA. DNA methyltransferase expressions in Japanese rice fish (Oryzias latipes) embryogenesis is developmentally regulated and modulated by ethanol and 5-azacytidine. Comp Biochem Physiol C Toxicol Pharmacol 2015; 176-177:1-9. [PMID: 26183885 DOI: 10.1016/j.cbpc.2015.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/03/2015] [Accepted: 07/06/2015] [Indexed: 12/18/2022]
Abstract
We aimed to investigate the impact of the epigenome in inducting fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish embryogenesis. One of the significant events in epigenome is DNA methylation which is catalyzed by DNA methyltransferase (DNMT) enzymes. We analyzed DNMT enzyme mRNA expressions in Japanese rice fish development starting from fertilized eggs to hatching and also in embryos exposed for first 48h of development either to ethanol (300mM) or to 5-azacytidine (5-azaC; 2mM), an inhibitor of DNMT enzyme activity. As observed in FASD phenotypes, 5-azaC exposure was able to induce microcephaly and craniofacial cartilage deformities in Japanese rice fish. Moreover, we have observed that expression of DNMTs (dnmt1, dnmt3aa, and dnmt3bb.1) are developmentally regulated; high mRNA copies were found in early stages (1-2day-post-fertilization, dpf), followed by gradual reduction until hatched. In ethanol-treated embryos, compared to controls, dnmt1 mRNA is in reduced level in 2dpf and in enhanced level in 6dpf embryos. While dnmt3aa and 3bb.1 remained unaltered. In contrast, embryos exposed to 5-azaC have an enhanced level of dnmt1 and dnmt3bb.1 mRNAs both in 2 and 6dpf embryos while dnmt3aa is enhanced only in 6dpf embryos. Moreover, endocannabinoid receptor 1a (cnr1a) mRNA which was found to be reduced by ethanol remained unaltered and cnr1b and cnr2 mRNAs, which were remained unaltered by ethanol, were increased significantly by 5-azaC in 6dpf embryos. This study indicates that the craniofacial defects observed in FASD phenotypes are the results of dysregulations in DNMT expressions.
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MESH Headings
- Abnormalities, Drug-Induced/enzymology
- Abnormalities, Drug-Induced/etiology
- Abnormalities, Drug-Induced/genetics
- Animals
- Azacitidine/toxicity
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- DNA Methyltransferase 3A
- Disease Models, Animal
- Epigenesis, Genetic/drug effects
- Ethanol/toxicity
- Fetal Alcohol Spectrum Disorders/enzymology
- Fetal Alcohol Spectrum Disorders/etiology
- Fetal Alcohol Spectrum Disorders/genetics
- Fish Proteins/genetics
- Fish Proteins/metabolism
- Gene Expression Regulation, Enzymologic
- Oryzias/embryology
- Oryzias/genetics
- Oryzias/metabolism
- RNA, Messenger/metabolism
- Receptor, Cannabinoid, CB1/drug effects
- Receptor, Cannabinoid, CB1/genetics
- Receptor, Cannabinoid, CB1/metabolism
- Receptor, Cannabinoid, CB2/drug effects
- Receptor, Cannabinoid, CB2/genetics
- Receptor, Cannabinoid, CB2/metabolism
- Time Factors
- DNA Methyltransferase 3B
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Affiliation(s)
- Asok K Dasmahapatra
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA; Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS, USA.
| | - Ikhlas A Khan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, USA; Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS, USA
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48
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Müller M, Hartmann M, Schuster I, Bender S, Thüring KL, Helm M, Katze JR, Nellen W, Lyko F, Ehrenhofer-Murray AE. Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Nucleic Acids Res 2015; 43:10952-62. [PMID: 26424849 PMCID: PMC4678861 DOI: 10.1093/nar/gkv980] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/17/2015] [Indexed: 01/13/2023] Open
Abstract
Dnmt2 enzymes are cytosine-5 methyltransferases that methylate C38 of several tRNAs. We report here that the activities of two Dnmt2 homologs, Pmt1 from Schizosaccharomyces pombe and DnmA from Dictyostelium discoideum, are strongly stimulated by prior queuosine (Q) modification of the substrate tRNA. In vivo tRNA methylation levels were stimulated by growth of cells in queuine-containing medium; in vitro Pmt1 activity was enhanced on Q-containing RNA; and queuine-stimulated in vivo methylation was abrogated by the absence of the enzyme that inserts queuine into tRNA, eukaryotic tRNA-guanine transglycosylase. Global analysis of tRNA methylation in S. pombe showed a striking selectivity of Pmt1 for tRNA(Asp) methylation, which distinguishes Pmt1 from other Dnmt2 homologs. The present analysis also revealed a novel Pmt1- and Q-independent tRNA methylation site in S. pombe, C34 of tRNA(Pro). Notably, queuine is a micronutrient that is scavenged by higher eukaryotes from the diet and gut microflora. This work therefore reveals an unanticipated route by which the environment can modulate tRNA modification in an organism.
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Affiliation(s)
- Martin Müller
- Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Mark Hartmann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | | | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Kathrin L Thüring
- Institut für Pharmakologie und Biochemie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Mark Helm
- Institut für Pharmakologie und Biochemie, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Jon R Katze
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Wolfgang Nellen
- Abteilung für Genetik, Universität Kassel, 34132 Kassel, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, 69120 Heidelberg, Germany
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49
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Tuorto F, Herbst F, Alerasool N, Bender S, Popp O, Federico G, Reitter S, Liebers R, Stoecklin G, Gröne HJ, Dittmar G, Glimm H, Lyko F. The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis. EMBO J 2015; 34:2350-62. [PMID: 26271101 PMCID: PMC4570521 DOI: 10.15252/embj.201591382] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/16/2015] [Indexed: 12/17/2022] Open
Abstract
The Dnmt2 enzyme utilizes the catalytic mechanism of eukaryotic DNA methyltransferases to methylate several tRNAs at cytosine 38. Dnmt2 mutant mice, flies, and plants were reported to be viable and fertile, and the biological function of Dnmt2 has remained elusive. Here, we show that endochondral ossification is delayed in newborn Dnmt2-deficient mice, which is accompanied by a reduction of the haematopoietic stem and progenitor cell population and a cell-autonomous defect in their differentiation. RNA bisulfite sequencing revealed that Dnmt2 methylates C38 of tRNA AspGTC, GlyGCC, and ValAAC, thus preventing tRNA fragmentation. Proteomic analyses from primary bone marrow cells uncovered systematic differences in protein expression that are due to specific codon mistranslation by tRNAs lacking Dnmt2-dependent methylation. Our observations demonstrate that Dnmt2 plays an important role in haematopoiesis and define a novel function of C38 tRNA methylation in the discrimination of near-cognate codons, thereby ensuring accurate polypeptide synthesis.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Friederike Herbst
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nader Alerasool
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Sebastian Bender
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Oliver Popp
- Mass Spectrometry Core Unit, MDC, Berlin, Germany
| | - Giuseppina Federico
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | - Sonja Reitter
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center (DKFZ) and Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Reinhard Liebers
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Georg Stoecklin
- Helmholtz Junior Research Group Posttranscriptional Control of Gene Expression, German Cancer Research Center (DKFZ) and Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hermann-Josef Gröne
- Department of Cellular and Molecular Pathology, German Cancer Research Center, Heidelberg, Germany
| | | | - Hanno Glimm
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
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50
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Egg-specific expression of protein with DNA methyltransferase activity in the biocarcinogenic liver fluke Clonorchis sinensis. Parasitology 2015; 142:1228-38. [PMID: 26036304 DOI: 10.1017/s0031182015000566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Despite recent reports regarding the biology of cytosine methylation in Schistosoma mansoni, the impact of the regulatory machinery remains unclear in diverse platyhelminthes. This ambiguity is reinforced by discoveries of DNA methyltransferase 2 (DNMT2)-only organisms and the substrate specificity of DNMT2 preferential to RNA molecules. Here, we characterized a novel DNA methyltransferase, named CsDNMT2, in a liver fluke Clonorchis sinensis. The protein exhibited structural properties conserved in other members of the DNMT2 family. The native and recombinant CsDNMT2 exhibited considerable enzymatic activity on DNA. The spatiotemporal expression of CsDNMT2 mirrored that of 5-methylcytosine (5 mC), both of which were elevated in the C. sinensis eggs. However, CsDNMT2 and 5 mC were marginally detected in other histological regions of C. sinensis adults including ovaries and seminal receptacle. The methylation site seemed not related to genomic loci occupied by progenies of an active long-terminal-repeat retrotransposon. Taken together, our data strongly suggest that C. sinensis has preserved the functional DNA methylation machinery and that DNMT2 acts as a genuine alternative to DNMT1/DNMT3 to methylate DNA in the DNMT2-only organism. The epigenetic regulation would target functional genes primarily involved in the formation and/or maturation of eggs, rather than retrotransposons.
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