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Therapeutic targets for endothelial dysfunction in vascular diseases. Arch Pharm Res 2019; 42:848-861. [PMID: 31420777 DOI: 10.1007/s12272-019-01180-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022]
Abstract
Vascular endothelial cells are located on the surface of the blood vessels. It has been recognized as an important barrier to the regulation of vascular homeostasis by regulating the blood flow of micro- or macrovascular vessels. Indeed, endothelial dysfunction is an initial stage of vascular diseases and is an important prognostic indicator of cardiovascular and metabolic diseases such as atherosclerosis, hypertension, heart failure, or diabetes. Therefore, in order to develop therapeutic targets for vascular diseases, it is important to understand the key factors involved in maintaining endothelial function and the signaling pathways affecting endothelial dysfunction. The purpose of this review is to describe the function and underlying signaling pathway of oxidative stress, inflammatory factors, shear stress, and epigenetic factors in endothelial dysfunction, and introduce recent therapeutic targets for the treatment of cardiovascular diseases.
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52
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Arjun HA, Elancheran R, Manikandan N, Lakshmithendral K, Ramanathan M, Bhattacharjee A, Lokanath NK, Kabilan S. Design, Synthesis, and Biological Evaluation of (E)-N'-((1-Chloro-3,4-Dihydronaphthalen-2-yl)Methylene)Benzohydrazide Derivatives as Anti-prostate Cancer Agents. Front Chem 2019; 7:474. [PMID: 31355179 PMCID: PMC6636335 DOI: 10.3389/fchem.2019.00474] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/20/2019] [Indexed: 01/09/2023] Open
Abstract
Prostate Cancer (PCa) is the most frequently diagnosed cancer in men in their late '50s. PCa growth is mainly due to the activation of the androgen receptor by androgens. The treatment for PCa may involve surgery, hormonal therapy, and oral chemotherapeutic drugs. A structural based molecular docking approach revealed the findings of (E)-N'-((1-chloro-3,4-dihydronaphthalen-2-yl)methylene)benzohydrazide derivatives, where the possible binding modes of the compounds with protein (PDB ID: 3V49) are shown. The compounds (6a-k) were synthesized and characterized by using conventional methods. The compounds, 6g, 6j, and 6k were reconfirmed through single crystal X-ray diffraction (XRD). Further, the compounds (6a-k) and standard drug were evaluated against human prostate cancer cell lines, LNCaP and PC-3 and the non-cancerous cell line, 3T3. Among these compounds, 6g and 6j showed higher cytotoxicity, and 6g exhibited dose-dependent activity and reduced cell viability. The mechanism of action was observed through the induced apoptosis and was further confirmed by western blot and ELISA. Molecular dynamics simulation studies were carried out to calculate the interaction and the stability of the protein-ligand complex in motion. ADME properties were predicted for all the tested compounds. These findings may give vital information for further development.
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Affiliation(s)
- H. A. Arjun
- Drug Discovery Lab, Department of Chemistry, Annamalai University, Chidambaram, India
| | | | - N. Manikandan
- Department of Pharmacology, PSG College of Pharmacy, Coimbatore, India
| | - K. Lakshmithendral
- Drug Discovery Lab, Department of Chemistry, Annamalai University, Chidambaram, India
| | | | - Atanu Bhattacharjee
- Computational Biology Laboratory, Department of Biotechnology & Bioinformatics, North Eastern Hill University, Shillong, India
| | - N. K. Lokanath
- Department of Physics, University of Mysore, Mysore, India
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Wei K, Ma L, Zhang T. Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend. PeerJ 2019; 7:e7204. [PMID: 31275764 PMCID: PMC6598670 DOI: 10.7717/peerj.7204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/29/2019] [Indexed: 02/04/2023] Open
Abstract
It is vital to understand the conservation and evolution of gene promoter sequences in order to understand environmental adaptation. The level of promoter conservation varies greatly between housekeeping (HK) and tissue-specific (TS) genes, denoting differences in the strength of the evolutionary constraints. Here, we analyzed promoter conservation and evolution to exploit differential regulation between HK and TS genes. The analysis of conserved elements showed CpG islands, short tandem repeats and G-quadruplex sequences are highly enriched in HK promoters relative to TS promoters. In addition, the type and density of regulatory motifs in TS promoters are much higher than HK promoters, indicating that TS genes show more complex regulatory patterns than HK genes. Moreover, the evolutionary dynamics of promoters showed similar evolutionary trend to coding sequences. HK promoters suffer more stringent selective pressure in the long-term evolutionary process. HK genes tend to show increased upstream sequence conservation due to stringent selection pressures acting on the promoter regions. The specificity of TS gene expression may be due to complex regulatory motifs acting in different tissues or conditions. The results from this study can be used to deepen our understanding of adaptive evolution.
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Affiliation(s)
- Kai Wei
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China.,Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Byern, Germany
| | - Lei Ma
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
| | - Tingting Zhang
- College of Life Science, Shihezi University, Shihezi, Xinjiang, China
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LMP2A induces DNA methylation and expression repression of AQP3 in EBV-associated gastric carcinoma. Virology 2019; 534:87-95. [PMID: 31220652 DOI: 10.1016/j.virol.2019.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/14/2019] [Accepted: 06/11/2019] [Indexed: 12/27/2022]
Abstract
Epstein-Barr virus (EBV)-associated gastric carcinoma (EBVaGC) is a unique type of gastric carcinomas that promoter hypermethylation of tumor-related genes is extremely frequent to be found. Aquaporin 3 (AQP3) is a small membrane transport protein that plays a crucial role in cancer progression and metastasis. However, there is no experimental study on the expression of AQP3 in EBVaGC and the regulation mechanism of EBV on AQP3. In this study, the loss of AQP3 was contributed by the hypermethylation status of AQP3 promoter in EBVaGC which was caused by elevated expression of DNMT3a. In addition, stable and transient transfection system in SGC7901 showed that viral latent membrane protein 2A (LMP2A) activated phosphorylated ERK and up-regulated DNMT3a. Taken together, LMP2A induced the phosphorylation of ERK, which activated DNMT3a transcription and caused AQP3 expression loss through CpG island methylation of AQP3 promoter in EBVaGC.
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55
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Choi SH, Ryu TH, Kim JI, Lee S, Lee SS, Kim JH. Mutation in DDM1 inhibits the homology directed repair of double strand breaks. PLoS One 2019; 14:e0211878. [PMID: 30742642 PMCID: PMC6370192 DOI: 10.1371/journal.pone.0211878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/23/2019] [Indexed: 11/19/2022] Open
Abstract
In all organisms, DNA damage must be repaired quickly and properly, as it can be lethal for cells. Because eukaryotic DNA is packaged into nucleosomes, the structural units of chromatin, chromatin modification is necessary during DNA damage repair and is achieved by histone modification and chromatin remodeling. Chromatin remodeling proteins therefore play important roles in the DNA damage response (DDR) by modifying the accessibility of DNA damage sites. Here, we show that mutation in a SWI2/SNF2 chromatin remodeling protein (DDM1) causes hypersensitivity in the DNA damage response via defects in single-strand annealing (SSA) repair of double-strand breaks (DSBs) as well as in the initial steps of homologous recombination (HR) repair. ddm1 mutants such as ddm1-1 and ddm1-2 exhibited increased root cell death and higher DSB frequency compared to the wild type after gamma irradiation. Although the DDM1 mutation did not affect the expression of most DDR genes, it did cause substantial decrease in the frequency of SSA as well as partial inhibition in the γ-H2AX and Rad51 induction, the initial steps of HR. Furthermore, global chromatin structure seemed to be affected by DDM1 mutations. These results suggest that DDM1 is involved in the homology directed repair such as SSA and HR, probably by modifying chromatin structure.
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Affiliation(s)
- Seung Hee Choi
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Tae Ho Ryu
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, Republic of Korea
- Department of Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Jeong-Il Kim
- Department of Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Sungbeom Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, Republic of Korea
- Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, Republic of Korea
- Department of Radiation Biotechnology and Applied Radioisotope Science, University of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Jin-Hong Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Jeollabuk-do, Republic of Korea
- * E-mail:
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Abdi A, Khabazi A, Sakhinia E, Alipour S, Talei M, Babaloo Z. Evaluation of SOCS1 methylation in patients with Behcet's disease. Immunol Lett 2018; 203:15-20. [PMID: 29990515 DOI: 10.1016/j.imlet.2018.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/26/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Epigenetic discusses to inherited changes in mitosis and meiosis in the gene expression pattern which is independent of primary DNA sequence. Since, SOCS1 hyper-methylation can activate JAK / STAT signaling pathway and activation of this pathway can directly affect the impact of different cytokines on cell function and subsequently lead to pathophysiology of diseases, in particular autoimmune diseases that interact directly with the amount of cytokines and due to the fact that the cause and pathology of Behcet's disease (BD) have not ever been completely determined. So, the purpose of this study was to evaluate the methylation pattern of SOCS1 gene in patients with BD and compare them with healthy group. METHODOLOGY This study was a case-control study in which 50 patients with BD and 60 subjects as healthy group participated. Blood samples were collected from all participants and then Peripheral Blood Mononuclear Cells (PBMCs) were isolated through Ficoll method. After extraction of DNA by Salting out method and its analysis with Nano-drop, the methylation level of SOCS1 was examined using qMS-PCR technique. RESULTS Findings about methylation and gene expression in SOCS1 gene showed that the level of SOCS1 methylation was increased in patient groups compared with healthy subjects (control group) which the increase was statistically significant (p-value<0.05). Also, the results of gene expression revealed that the fold change of SOCS1 gene expression was decreased in patient group compared with healthy subjects which the decrease was statistically significant (p-value<0.05). DISCUSSION AND CONCLUSION According to the results of this study, it can be suggested that the DNA methylation of SOCS1 gene is likely to affect the gene expression and thereby contribute to the pathogenesis of Behcet's disease.
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Affiliation(s)
- Ali Abdi
- Immunology Research Center, Tabriz University of Medical Sciences, Iran; Department of Immunology Medicine faculty, Tabriz University of Medical Sciences, Iran
| | - Alireza Khabazi
- Connective Tissue Disease Research Center, Tabriz University of medical science, Iran
| | - Ebrahim Sakhinia
- Dept. of Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahriar Alipour
- Dept. of Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz university of Medical Sciences, Iran
| | - Mahsa Talei
- Immunology Research Center, Tabriz University of Medical Sciences, Iran; Department of Immunology Medicine faculty, Tabriz University of Medical Sciences, Iran
| | - Zohreh Babaloo
- Immunology Research Center, Tabriz University of Medical Sciences, Iran; Department of Immunology Medicine faculty, Tabriz University of Medical Sciences, Iran.
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Wichnieski C, Maheshwari K, Souza LC, Nieves F, Tartari T, Garlet GP, Carneiro E, Letra A, Silva RM. DNA methylation profiles of immune response-related genes in apical periodontitis. Int Endod J 2018; 52:5-12. [PMID: 29904933 DOI: 10.1111/iej.12966] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/12/2018] [Indexed: 12/27/2022]
Abstract
AIM To investigate the DNA methylation profiles of immune response-related genes in apical periodontitis (AP) lesions. METHODOLOGY The methylation profiles on the cytosine-phosphate-guanine (CpG) regions of 22 gene promoters involved in inflammation and autoimmunity were assessed in 60 human AP lesions and 24 healthy periodontal ligaments (controls) using a pathway-specific real-time polymerase chain reaction array (EpiTect® Methyl Signature PCR Array Human Inflammatory Response). Differentially methylated genes were subsequently assessed for their mRNA expression. Data analyses (One-way anova, Tukey's multiple comparisons tests and Mann-Whitney tests) were performed using GraphPad Prism 6 software. P values ≤ 0.05 were considered statistically significant. RESULTS Significant DNA hypermethylation was observed for CXCL3 and FADD gene promoters in AP lesions when compared to control tissues (P < 0.001) and among other genes (P < 0.05). In contrast, IL12B and IL4R were associated with significant hypomethylation in comparison to other genes (P < 0.05). IL12B, IL4R, CXCL3 and FADD had differential mRNA expression in AP lesions and controls (P < 0.001). CONCLUSIONS Differential methylation profiles of immune response-related genes, such as FADD, CXCL3, IL12B and IL4R, may have an influence on individual AP susceptibility and patient treatment outcomes, through their potential contributions to altered expression of disease-relevant genes. Methylation and/or genetic variations in additional genes may also contribute to the dynamics of AP development and should be considered in future studies.
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Affiliation(s)
- C Wichnieski
- Department of Endodontics, Pontifical Catholic University of Parana, Curitiba, Brazil.,Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - K Maheshwari
- Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA
| | - L C Souza
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA
| | - F Nieves
- Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA
| | - T Tartari
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Endodontics, School of Dentistry of Bauru, University of São Paulo (FOB/USP), São Paulo, Brazil
| | - G P Garlet
- Department of Biological Sciences, School of Dentistry of Bauru, University of São Paulo (FOB/USP), Bauru, São Paulo, Brazil
| | - E Carneiro
- Department of Endodontics, Pontifical Catholic University of Parana, Curitiba, Brazil
| | - A Letra
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA.,Department of Diagnostic and Biomedical Sciences, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - R M Silva
- Department of Endodontics, School of Dentistry at Houston, University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, University of Texas School of Dentistry at Houston, Houston, TX, USA
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Dery KJ, Silver C, Yang L, Shively JE. Interferon regulatory factor 1 and a variant of heterogeneous nuclear ribonucleoprotein L coordinately silence the gene for adhesion protein CEACAM1. J Biol Chem 2018; 293:9277-9291. [PMID: 29720400 DOI: 10.1074/jbc.ra117.001507] [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: 12/15/2017] [Revised: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
The adhesion protein carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) is widely expressed in epithelial cells as a short cytoplasmic isoform (S-iso) and in leukocytes as a long cytoplasmic isoform (L-iso) and is frequently silenced in cancer by unknown mechanisms. Previously, we reported that interferon response factor 1 (IRF1) biases alternative splicing (AS) to include the variable exon 7 (E7) in CEACAM1, generating long cytoplasmic isoforms. We now show that IRF1 and a variant of heterogeneous nuclear ribonucleoprotein L (Lv1) coordinately silence the CEACAM1 gene. RNAi-mediated Lv1 depletion in IRF1-treated HeLa and melanoma cells induced significant CEACAM1 protein expression, reversed by ectopic Lv1 expression. The Lv1-mediated CEACAM1 repression resided in residues Gly71-Gly89 and Ala38-Gly89 in Lv1's N-terminal extension. ChIP analysis of IRF1- and FLAG-tagged Lv1-treated HeLa cells and global treatment with the global epigenetic modifiers 5-aza-2'-deoxycytidine and trichostatin A indicated that IRF1 and Lv1 together induce chromatin remodeling, restricting IRF1 access to the CEACAM1 promoter. In interferon γ-treated HeLa cells, the transcription factor SP1 did not associate with the CEACAM1 promoter, but binding by upstream transcription factor 1 (USF1), a known CEACAM1 regulator, was greatly enhanced. ChIP-sequencing revealed that Lv1 overexpression in IRF1-treated cells induces transcriptional silencing across many genes, including DCC (deleted in colorectal carcinoma), associated with CEACAM5 in colon cancer. Notably, IRF1, but not IRF3 and IRF7, affected CEACAM1 expression via translational repression. We conclude that IRF1 and Lv1 coordinately regulate CEACAM1 transcription, alternative splicing, and translation and may significantly contribute to CEACAM1 silencing in cancer.
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Affiliation(s)
- Kenneth J Dery
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - Craig Silver
- Department of Biological Sciences, California State Polytechnic University, Pomona, California 91768, and
| | - Lu Yang
- The Integrative Genomics and Bioinformatics Core, Beckman Research Institute of the City of Hope, Duarte, California 91010
| | - John E Shively
- From the Department of Molecular Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010,
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DNA Tumor Virus Regulation of Host DNA Methylation and Its Implications for Immune Evasion and Oncogenesis. Viruses 2018; 10:v10020082. [PMID: 29438328 PMCID: PMC5850389 DOI: 10.3390/v10020082] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses have evolved various mechanisms to evade host immunity and ensure efficient viral replication and persistence. Several DNA tumor viruses modulate host DNA methyltransferases for epigenetic dysregulation of immune-related gene expression in host cells. The host immune responses suppressed by virus-induced aberrant DNA methylation are also frequently involved in antitumor immune responses. Here, we describe viral mechanisms and virus–host interactions by which DNA tumor viruses regulate host DNA methylation to evade antiviral immunity, which may contribute to the generation of an immunosuppressive microenvironment during cancer development. Recent trials of immunotherapies have shown promising results to treat multiple cancers; however, a significant number of non-responders necessitate identifying additional targets for cancer immunotherapies. Thus, understanding immune evasion mechanisms of cancer-causing viruses may provide great insights for reversing immune suppression to prevent and treat associated cancers.
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60
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Gene expression regulation by heat-shock proteins: the cardinal roles of HSF1 and Hsp90. Biochem Soc Trans 2017; 46:51-65. [PMID: 29273620 DOI: 10.1042/bst20170335] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 10/21/2017] [Accepted: 10/27/2017] [Indexed: 12/31/2022]
Abstract
The ability to permit gene expression is managed by a set of relatively well known regulatory mechanisms. Nonetheless, this property can also be acquired during a life span as a consequence of environmental stimuli. Interestingly, some acquired information can be passed to the next generation of individuals without modifying gene information, but instead by the manner in which cells read and process such information. Molecular chaperones are classically related to the proper preservation of protein folding and anti-aggregation properties, but one of them, heat-shock protein 90 (Hsp90), is a refined sensor of protein function facilitating the biological activity of properly folded client proteins that already have a preserved tertiary structure. Interestingly, Hsp90 can also function as a critical switch able to regulate biological responses due to its association with key client proteins such as histone deacetylases or DNA methylases. Thus, a growing amount of evidence has connected the action of Hsp90 to post-translational modifications of soluble nuclear factors, DNA, and histones, which epigenetically affect gene expression upon the onset of an unfriendly environment. This response is commanded by the activation of the transcription factor heat-shock factor 1 (HSF1). Even though numerous stresses of diverse nature are known to trigger the stress response by activation of HSF1, it is still unknown whether there are different types of molecular sensors for each type of stimulus. In the present review, we will discuss various aspects of the regulatory action of HSF1 and Hsp90 on transcriptional regulation, and how this regulation may affect genetic assimilation mechanisms and the health of individuals.
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Singh P, Srivas S, Thakur MK. Epigenetic Regulation of Memory-Therapeutic Potential for Disorders. Curr Neuropharmacol 2017; 15:1208-1221. [PMID: 28393704 PMCID: PMC5725549 DOI: 10.2174/1570159x15666170404144522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/03/2017] [Accepted: 03/25/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Memory is a vital function which declines in different physiological and pathological conditions such as aging and neurodegenerative diseases. Research in the past has reported that memory formation and consolidation require the precise expression of synaptic plasticity genes. However, little is known about the regulation of these genes. Epigenetic modification is now a well established mechanism that regulates synaptic plasticity genes and neuronal functions including memory. Therefore, we have reviewed the epigenetic regulation of memory and its therapeutic potential for memory dysfunction during aging and neurological disorders. METHOD Research reports and online contents relevant to epigenetic regulation of memory during physiological and pathological conditions have been compiled and discussed. RESULTS Epigenetic modifications include mainly DNA methylation and hydroxymethylation, histone acetylation and methylation which involve chromatin modifying enzymes. These epigenetic marks change during memory formation and impairment due to dementia, aging and neurodegeneration. As the epigenetic modifications are reversible, they can be modulated by enzyme inhibitors leading to the recovery of memory. CONCLUSION Epigenetic modifications could be exploited as a potential therapeutic target to recover memory disorders during aging and pathological conditions.
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Affiliation(s)
- Padmanabh Singh
- Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Sweta Srivas
- Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - M K Thakur
- Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
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Houfflyn S, Matthys C, Soubry A. Male Obesity: Epigenetic Origin and Effects in Sperm and Offspring. CURRENT MOLECULAR BIOLOGY REPORTS 2017; 3:288-296. [PMID: 29387521 PMCID: PMC5768668 DOI: 10.1007/s40610-017-0083-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW The prevalence of obesity has increased substantially in the current generations of Western countries, and the burden of obesity-related complications has been growing steadily. In men, obesity is not only a major risk factor for serious chronic diseases, concern is growing that the reproductive capacity, and more particularly, their offspring's health may be affected. Obesity-related impaired spermatogenesis is associated with a decrease in microscopic and molecular sperm characteristics and pregnancy success. We hypothesize that epigenetics is an important mediator explaining interactions between an obesogenic environment and sperm/offspring outcomes. RECENT FINDINGS Recent studies have explored inter- and transgenerational epigenetic effects in sperm cells and in offspring. Father-to-child effects have been reported in relation to preconceptional nutritional and life-style related factors. SUMMARY Here, we summarize the current understanding about obesity and molecular or epigenetic underlying mechanisms in sperm. We identify the obesogenic environment of the father before conception as a potential origin of health or disease in the offspring and include it as part of a new concept, the Paternal Origins of Health and Disease (POHaD).
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Affiliation(s)
- Sam Houfflyn
- Epidemiology Research Unit, Department of Public Health and Primary Care, University of Leuven, 3000 Leuven, Belgium
| | - Christophe Matthys
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven University, Leuven, Belgium
| | - Adelheid Soubry
- Epidemiology Research Unit, Department of Public Health and Primary Care, University of Leuven, 3000 Leuven, Belgium
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Sagarkar S, Mahajan S, Choudhary AG, Borkar CD, Kokare DM, Sakharkar AJ. Traumatic stress-induced persistent changes in DNA methylation regulate neuropeptide Y expression in rat jejunum. Neurogastroenterol Motil 2017; 29. [PMID: 28418087 DOI: 10.1111/nmo.13074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/22/2017] [Accepted: 02/26/2017] [Indexed: 01/20/2023]
Abstract
BACKGROUND Stress-induced chronic neuropsychiatric conditions such as anxiety are often co-morbid with gastrointestinal malfunctions. While we find enduring anxiety-like symptoms following minimal traumatic brain injury (MTBI) in rats, gastrointestinal consequences of MTBI remain elusive. METHODS In this study, we examined the effects of MTBI on a major gut peptide, neuropeptide Y (NPY) and gut motility. DNA methylation was studied as a possible epigenetic mechanism operative in the regulation of NPY expression in the gut. KEY RESULTS Minimal traumatic brain injury reduced the gut motility 48 hours and 30 days after trauma. The expression of DNA methyltransferase isoforms (DNMT1, DNMT3a, and DNMT3b) was altered in the jejunum 48 hours and 30 days after MTBI. However, the mRNA levels of growth arrest and DNA damage 45 (GADD45) isoforms, GADD45a, and GADD45b, which are believed to be involved in active DNA demethylation, initially decreased at 48 hours but subsequently increased after 30 days of trauma. Similarly, DNA hypomethylation at the NPY promoter region in the jejunum was correlated with the increase in NPY mRNA and protein levels 30 days post-trauma. On the other hand, DNA hypomethylation at 48 hours was associated with a decline in NPY expression. Treatment with 5-azacytidine (5-AzaC), a DNMT inhibitor, retarded DNA methylation and restored the NPY mRNA levels in the jejunum of MTBI-induced rats. CONCLUSIONS & INFERENCES These results suggest that DNA demethylation could be operative as an epigenetic mechanism in the long-term regulation of NPY gene expression to alter the gut motility during traumatic stress.
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Affiliation(s)
- S Sagarkar
- Department of Biotechnology, Savitribai Phule Pune University, Pune, India
| | - S Mahajan
- Department of Biotechnology, Savitribai Phule Pune University, Pune, India
| | - A G Choudhary
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj, Nagpur University, Nagpur, India
| | - C D Borkar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj, Nagpur University, Nagpur, India
| | - D M Kokare
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj, Nagpur University, Nagpur, India
| | - A J Sakharkar
- Department of Biotechnology, Savitribai Phule Pune University, Pune, India
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Mahalingaiah PKS, Ponnusamy L, Singh KP. Oxidative stress-induced epigenetic changes associated with malignant transformation of human kidney epithelial cells. Oncotarget 2017; 8:11127-11143. [PMID: 27655674 PMCID: PMC5355252 DOI: 10.18632/oncotarget.12091] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/05/2016] [Indexed: 12/17/2022] Open
Abstract
Renal Cell Carcinoma (RCC) in humans is positively influenced by oxidative stress status in kidneys. We recently reported that adaptive response to low level of chronic oxidative stress induces malignant transformation of immortalized human renal tubular epithelial cells. Epigenetic alterations in human RCC are well documented, but its role in oxidative stress-induced malignant transformation of kidney cells is not known. Therefore, the objective of this study was to evaluate the potential role of epigenetic changes in chronic oxidative stress-induced malignant transformation of HK-2, human renal tubular epithelial cells. The results revealed aberrant expression of epigenetic regulatory genes involved in DNA methylation (DNMT1, DNMT3a and MBD4) and histone modifications (HDAC1, HMT1 and HAT1) in HK-2 cells malignantly transformed by chronic oxidative stress. Additionally, both in vitro soft agar assay and in vivo nude mice study showing decreased tumorigenic potential of malignantly transformed HK-2 cells following treatment with DNA de-methylating agent 5-aza 2’ dC further confirmed the crucial role of DNA hypermethyaltion in oxidative stress-induced malignant transformation. Changes observed in global histone H3 acetylation (H3K9, H3K18, H3K27 and H3K14) and decrease in phospho-H2AX (Ser139) also suggest potential role of histone modifications in increased survival and malignant transformation of HK-2 cells by oxidative stress. In summary, the results of this study suggest that epigenetic reprogramming induced by low levels of oxidative stress act as driver for malignant transformation of kidney epithelial cells. Findings of this study are highly relevant in potential clinical application of epigenetic-based therapeutics for treatments of kidney cancers.
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Affiliation(s)
- Prathap Kumar S Mahalingaiah
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, Texas, USA
| | - Logeswari Ponnusamy
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, Texas, USA
| | - Kamaleshwar P Singh
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, Texas, USA
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65
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Tharmalingam S, Sreetharan S, Kulesza AV, Boreham DR, Tai TC. Low-Dose Ionizing Radiation Exposure, Oxidative Stress and Epigenetic Programing of Health and Disease. Radiat Res 2017; 188:525-538. [PMID: 28753061 DOI: 10.1667/rr14587.1] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ionizing radiation exposure from medical diagnostic imaging has greatly increased over the last few decades. Approximately 80% of patients who undergo medical imaging are exposed to low-dose ionizing radiation (LDIR). Although there is widespread consensus regarding the harmful effects of high doses of radiation, the biological effects of low-linear energy transfer (LET) LDIR is not well understood. LDIR is known to promote oxidative stress, however, these levels may not be large enough to result in genomic mutations. There is emerging evidence that oxidative stress causes heritable modifications via epigenetic mechanisms (DNA methylation, histone modification, noncoding RNA regulation). These epigenetic modifications result in permanent cellular transformations without altering the underlying DNA nucleotide sequence. This review summarizes the major concepts in the field of epigenetics with a focus on the effects of low-LET LDIR (<100 mGy) and oxidative stress on epigenetic gene modification. In this review, we show evidence that suggests that LDIR-induced oxidative stress provides a mechanistic link between LDIR and epigenetic gene regulation. We also discuss the potential implication of LDIR exposure during pregnancy where intrauterine fetal development is highly susceptible to oxidative stress-induced epigenetic programing.
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Affiliation(s)
| | | | - Adomas V Kulesza
- b Department of Biology, McMaster University, Hamilton, Canada, L8S 4K1
| | - Douglas R Boreham
- a Northern Ontario School of Medicine, Laurentian University, Sudbury, Canada, P3E 2C6.,c Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton, Canada, L8S 4K1
| | - T C Tai
- a Northern Ontario School of Medicine, Laurentian University, Sudbury, Canada, P3E 2C6
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66
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Huang Y, He C, Shen C, Guo J, Mubeen S, Yuan J, Yang Z. Toxicity of cadmium and its health risks from leafy vegetable consumption. Food Funct 2017; 8:1373-1401. [PMID: 28232985 DOI: 10.1039/c6fo01580h] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cadmium (Cd) is a highly toxic heavy metal and has spread widely in the environment in recent decades. This review summarizes current knowledge about Cd contamination of leafy vegetables, its toxicity, exposure, health risks, and approaches to reducing its toxicity in humans. Leafy vegetable consumption has been identified as a dominant exposure pathway of Cd in the human body. An overview of Cd pollution in leafy vegetables as well as the main sources of Cd is given. Notable estimated daily intakes and health risks of Cd exposure through vegetable consumption for humans are revealed in occupational exposure areas and even in some reference areas. Vegetable consumption is one of the most significant sources of exposure to Cd, particularly in occupational exposure regions. Therefore, numerous approaches have been developed to minimize the accumulation of Cd in leafy vegetables, among which the breeding of Cd pollution-safe cultivars is one of the most effective tools. Furthermore, dietary supplements from leafy vegetables perform positive roles in alleviating Cd toxicity in humans with regard to the effects of essential mineral elements, vitamins and phytochemicals taken into the human body via leafy vegetable consumption.
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Affiliation(s)
- Yingying Huang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Xingang Xi Road 135, Guangzhou, 510275, China.
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67
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Hong T, Wu F, Fu B, Yuan Y, Xu J, Wang T, Zhou X. 5-Formylcytosine and 5-Carboxylcytosine Significantly Reduce the Catalytic Activity of Hhal DNA Methyltransferase. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tingting Hong
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Fan Wu
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Boshi Fu
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Yushu Yuan
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Tianlu Wang
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, The Institute for Advanced Studies; Wuhan University; Wuhan Hubei 430072 China
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68
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Zhang X, Yang L, Liu X, Nie Z, Wang X, Pan Y, Luo J. Research on the epigenetic regulation mechanism of thePTPN6gene in advanced chronic myeloid leukaemia. Br J Haematol 2017; 178:728-738. [PMID: 28480959 DOI: 10.1111/bjh.14739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/22/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Xiaokun Zhang
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
| | - Lin Yang
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
| | - Xiaojun Liu
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
| | - Ziyuan Nie
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
| | - Xingzhe Wang
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
| | - Yuxia Pan
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
| | - Jianmin Luo
- Department of Hematology; The Second Hospital of Hebei Medical University; Key Laboratory of Hematology; Shijiazhuang Hebei China
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69
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Moon EK, Hong Y, Lee HA, Quan FS, Kong HH. DNA Methylation of Gene Expression in Acanthamoeba castellanii Encystation. THE KOREAN JOURNAL OF PARASITOLOGY 2017; 55:115-120. [PMID: 28506032 PMCID: PMC5450953 DOI: 10.3347/kjp.2017.55.2.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/13/2017] [Accepted: 04/03/2017] [Indexed: 12/04/2022]
Abstract
Encystation mediating cyst specific cysteine proteinase (CSCP) of Acanthamoeba castellanii is expressed remarkably during encystation. However, the molecular mechanism involved in the regulation of CSCP gene expression remains unclear. In this study, we focused on epigenetic regulation of gene expression during encystation of Acanthamoeba. To evaluate methylation as a potential mechanism involved in the regulation of CSCP expression, we first investigated the correlation between promoter methylation status of CSCP gene and its expression. A 2,878 bp of promoter sequence of CSCP gene was amplified by PCR. Three CpG islands (island 1–3) were detected in this sequence using bioinformatics tools. Methylation of CpG island in trophozoites and cysts was measured by bisulfite sequence PCR. CSCP promoter methylation of CpG island 1 (1,633 bp) was found in 8.2% of trophozoites and 7.3% of cysts. Methylation of CpG island 2 (625 bp) was observed in 4.2% of trophozoites and 5.8% of cysts. Methylation of CpG island 3 (367 bp) in trophozoites and cysts was both 3.6%. These results suggest that DNA methylation system is present in CSCP gene expression of Acanthamoeba. In addition, the expression of encystation mediating CSCP is correlated with promoter CpG island 1 hypomethylation.
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Affiliation(s)
- Eun-Kyung Moon
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - Yeonchul Hong
- Department of Parasitology and Tropical Medicine, Kyungpook National University School of Medicine, Daegu 41944, Korea
| | - Hae-Ahm Lee
- Department of Pharmacology, Kyungpook National University School of Medicine, Daegu 41944, Korea
| | - Fu-Shi Quan
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul 02447, Korea
| | - Hyun-Hee Kong
- Department of Parasitology, Dong-A University College of Medicine, Busan 49201, Korea
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70
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Singh P, Thakur MK. Histone Deacetylase 2 Inhibition Attenuates Downregulation of Hippocampal Plasticity Gene Expression during Aging. Mol Neurobiol 2017; 55:2432-2442. [PMID: 28364391 DOI: 10.1007/s12035-017-0490-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/14/2017] [Indexed: 12/31/2022]
Abstract
The brain undergoes several anatomical, biochemical, and molecular changes during aging, which subsequently result in downregulation of synaptic plasticity genes and decline of memory. However, the regulation of these genes during aging is not clearly understood. Previously, we reported that the expression of histone deacetylase (HDAC)2 was upregulated in the hippocampus of old mice and negatively correlated with the decline in recognition memory. As HDAC2 regulates key synaptic plasticity neuronal immediate early genes (IEGs), we have examined their expression and epigenetic regulation. We noted that the expression of neuronal IEGs decreased both at mRNA and protein level in the hippocampus of old mice. To explore the underlying regulation, we analyzed the binding of HDAC2 and level of histone acetylation at the promoter of neuronal IEGs. While the binding of HDAC2 was higher, H3K9 and H3K14 acetylation level was lower at the promoter of these genes in old as compared to young and adult mice. Further, we inhibited HDAC2 non-specifically by sodium butyrate and specifically by antisense oligonucleotide to recover epigenetic modification, expression of neuronal IEGs, and memory in old mice. Inhibition of HDAC2 increased histone H3K9 and H3K14 acetylation level at the promoter of neuronal IEGs, their expression, and recognition memory in old mice as compared to control. Thus, inhibition of HDAC2 can be used as a therapeutic target to recover decline in memory due to aging and associated neurological disorders.
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Affiliation(s)
- Padmanabh Singh
- Biochemistry and Molecular Biology Laboratory, Centre of Advanced Study, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221 005, India
| | - M K Thakur
- Biochemistry and Molecular Biology Laboratory, Centre of Advanced Study, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, 221 005, India.
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71
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Özbayer C, Üstüner D, Ak GA, Saydam F, Metintaş M, Değirmenci İ. Akciğer Kanserli Hastalarda Plazma DNA Metiltransferaz ve Metil-CpG’ye Bağlanan Protein Seviyelerinin Değerlendirilmesi. DICLE MEDICAL JOURNAL 2017. [DOI: 10.5798/dicletip.298604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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72
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Choo DW, Goh SH, Cho YW, Baek HJ, Park EJ, Motoyama N, Kim TH, Kim JY, Kim SS. CHK2 is involved in the p53-independent radiosensitizing effects of valproic acid. Oncol Lett 2017; 13:2591-2598. [PMID: 28454438 PMCID: PMC5403276 DOI: 10.3892/ol.2017.5792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 12/20/2016] [Indexed: 01/10/2023] Open
Abstract
Radiotherapy is an effective treatment for the majority of types of localized solid cancer. However, the risk of side effects to the surrounding normal tissues limits radiotherapeutic approaches. Whilst the mechanism of action of valproic acid, an inhibitor of histone deacetylase, remains unknown, the inhibitor is a potential antineoplastic radiosensitizer. The present study demonstrated the in vitro radiosensitizing effects of valproic acid on the human breast cancer MCF7 cell line, and revealed that valproic acid increased the level of DNA breakage, apoptosis and senescence. In addition, western blot analyses revealed that valproic acid induced tumor suppressor protein (p)53 and p21 expression, and activated checkpoint kinase 2 (CHK2) in MCF7 cells and primary mouse embryonic fibroblasts. Notably, treatment with valproic acid also induced increases in the level of p21 protein levels and CHK2 activity in p53-null colon cancer HCT116 cells. Furthermore, the present study demonstrated that valproic acid-induced radiosensitization was largely dependent on the activity of CHK2. The results of the present study reveal that valproic acid may exhibit clinical utility with respect to increasing the anticancer efficacy of radiotherapy by affecting the level of p53.
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Affiliation(s)
- Dong Wan Choo
- Radiation Medicine Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Sung Ho Goh
- Cancer Genomics Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Young Woo Cho
- Radiation Medicine Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea.,Colgate University, Hamilton, NY 13346, USA
| | - Hye Jung Baek
- Radiation Medicine Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Eun Jung Park
- Cancer Immunology Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Noboru Motoyama
- Department of Cognitive Brain Science, National Centre for Geriatrics and Gerontology, Obu, Aichi 474-8522, Japan.,Department of Aging Research, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tae Hyun Kim
- Radiation Medicine Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Joo Young Kim
- Radiation Medicine Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
| | - Sang Soo Kim
- Radiation Medicine Branch, National Cancer Center, Goyang, Gyeonggi 410-769, Republic of Korea
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73
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Dardir K, Rathnam C, Lee KB. NanoScript: A Versatile Nanoparticle-Based Synthetic Transcription Factor for Innovative Gene Manipulation. Methods Mol Biol 2017; 1570:239-249. [PMID: 28238141 DOI: 10.1007/978-1-4939-6840-4_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Cellular reprogramming and stem cell-based therapies have shown tremendous potential in the field of regenerative medicine. To that end, developing tools to control stem cell fate is an attractive area of research for replacing damaged and diseased cells and reestablishing functional connections for tissue repair. Transcription factor (TFs) proteins are well known to regulate gene expression and direct stem cell fate. Inspired by natural TFs, NanoScript, a nanoparticle (NP)-based platform, mimics TFs to afford control over gene expression and stem cell fate for regenerative medicine. Here, we describe the construction of the NanoScript platform, which is designed with tunable properties to replicate the structure and function of TFs to bind to specific portions of the genome and regulate gene expression in a way that does not involve viral delivery.
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Affiliation(s)
- Kholud Dardir
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Christopher Rathnam
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA.
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74
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Kujirai T, Machida S, Osakabe A, Kurumizaka H. Influence of polynucleosome preparation methods on sedimentation velocity analysis of chromatin. J Biochem 2016; 161:381-388. [DOI: 10.1093/jb/mvw081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/03/2016] [Indexed: 01/09/2023] Open
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75
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Lee S, Moon JH, Song K, Taweechaipaisankul A, Jo YK, Oh HJ, Park SC, Lee BC. Establishment of Transgenic Porcine Fibroblasts Expressing a Human klotho Gene and Its Effects on Gene Expression and Preimplantation Development of Cloned Embryos. DNA Cell Biol 2016; 36:42-49. [PMID: 28004977 DOI: 10.1089/dna.2016.3482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Even though the functions of the klotho gene in aging of small animals such as mice have been well investigated, studies using large animal models such as pigs, which have many similarities to humans, have been limited due to the absence of cell lines or animal models. Therefore, the objective of this study was to generate porcine cell lines overexpressing human klotho (hKlotho) and tetracycline (Tet)-inducible hKlotho and to produce cloned embryos from these cell lines. We designed vectors for hKlotho overexpression (CA-Klotho) under control of CMV enhancer/chicken β-actin (CAG) promoter and Tet-inducible hKlotho overexpression (Tet-Klotho, under control of doxycycline-dependent promoter). The vectors were transfected into porcine fibroblasts then CA-Klotho and Tet-Klotho cell lines were established. The Tet-Klotho (+) cell line was cultured in the presence of doxycycline (2 μg/mL), whereas the Tet-Klotho (-) cell line was cultured without doxycycline. In polymerase chain reaction (PCR) and reverse transcription-PCR (RT-PCR) assays, integration and expression of the hKlotho gene were confirmed in CA-Klotho, Tet-Klotho (+), and Tet-Klotho (-) cell lines. The CA-Klotho cell line was subjected to real-time PCR and showed positively changed expression of genes related to aging and cell survival. Somatic cell nuclear transfer was performed to generate hKlotho overexpression cloned embryos by using CA-Klotho and Tet-Klotho (+) cell lines; blastocyst formation frequency was significantly higher in cloned embryos from CA-Klotho and Tet-Klotho (+) (21.5% and 20.2%, respectively) compared with the control (8.4%). In conclusion, we established hKlotho overexpression and Tet-inducible hKlotho overexpression cell lines and porcine embryos cloned from these cell lines.
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Affiliation(s)
- Sanghoon Lee
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Joon Ho Moon
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Kilyoung Song
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Anukul Taweechaipaisankul
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Young Kwang Jo
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Hyun Ju Oh
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Se Chang Park
- 2 Laboratory of Aquatic Biomedicine, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
| | - Byeong Chun Lee
- 1 Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Research Institute for Veterinary Science, Seoul National University , Seoul, Republic of Korea
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76
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Kong EY, Cheng SH, Yu KN. Zebrafish as an In Vivo Model to Assess Epigenetic Effects of Ionizing Radiation. Int J Mol Sci 2016; 17:ijms17122108. [PMID: 27983682 PMCID: PMC5187908 DOI: 10.3390/ijms17122108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Exposure to ionizing radiations (IRs) is ubiquitous in our environment and can be categorized into “targeted” effects and “non-targeted” effects. In addition to inducing deoxyribonucleic acid (DNA) damage, IR exposure leads to epigenetic alterations that do not alter DNA sequence. Using an appropriate model to study the biological effects of radiation is crucial to better understand IR responses as well as to develop new strategies to alleviate exposure to IR. Zebrafish, Danio rerio, is a scientific model organism that has yielded scientific advances in several fields and recent studies show the usefulness of this vertebrate model in radiation biology. This review briefly describes both “targeted” and “non-targeted” effects, describes the findings in radiation biology using zebrafish as a model and highlights the potential of zebrafish to assess the epigenetic effects of IR, including DNA methylation, histone modifications and miRNA expression. Other in vivo models are included to compare observations made with zebrafish, or to illustrate the feasibility of in vivo models when the use of zebrafish was unavailable. Finally, tools to study epigenetic modifications in zebrafish, including changes in genome-wide DNA methylation, histone modifications and miRNA expression, are also described in this review.
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Affiliation(s)
- Eva Yi Kong
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
| | - Shuk Han Cheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
| | - Kwan Ngok Yu
- Department of Physics and Materials Science, City University of Hong Kong, Hong Kong, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, China.
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77
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Dynamic reprogramming of DNA methylation in SETD2-deregulated renal cell carcinoma. Oncotarget 2016; 7:1927-46. [PMID: 26646321 PMCID: PMC4811507 DOI: 10.18632/oncotarget.6481] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/16/2015] [Indexed: 11/25/2022] Open
Abstract
Clear cell renal cell carcinomas (ccRCCs) harbor frequent mutations in epigenetic modifiers including SETD2, the H3K36me3 writer. We profiled DNA methylation (5mC) across the genome in cell line-based models of SETD2 inactivation and SETD2 mutant primary tumors because 5mC has been linked to H3K36me3 and is therapeutically targetable. SETD2 depleted cell line models (long-term and acute) exhibited a DNA hypermethylation phenotype coinciding with ectopic gains in H3K36me3 centered across intergenic regions adjacent to low expressing genes, which became upregulated upon dysregulation of the epigenome. Poised enhancers of developmental genes were prominent hypermethylation targets. SETD2 mutant primary ccRCCs, papillary renal cell carcinomas, and lung adenocarcinomas all demonstrated a DNA hypermethylation phenotype that segregated tumors by SETD2 genotype and advanced grade. These findings collectively demonstrate that SETD2 mutations drive tumorigenesis by coordinated disruption of the epigenome and transcriptome,and they have important implications for future therapeutic strategies targeting chromatin regulator mutant tumors.
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78
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Kgatle MM, Kalla AA, Islam MM, Sathekge M, Moorad R. Prostate Cancer: Epigenetic Alterations, Risk Factors, and Therapy. Prostate Cancer 2016; 2016:5653862. [PMID: 27891254 PMCID: PMC5116340 DOI: 10.1155/2016/5653862] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/04/2016] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is the most prevalent urological cancer that affects aging men in South Africa, and mechanisms underlying prostate tumorigenesis remain elusive. Research advancements in the field of PCa and epigenetics have allowed for the identification of specific alterations that occur beyond genetics but are still critically important in the pathogenesis of tumorigenesis. Anomalous epigenetic changes associated with PCa include histone modifications, DNA methylation, and noncoding miRNA. These mechanisms regulate and silence hundreds of target genes including some which are key components of cellular signalling pathways that, when perturbed, promote tumorigenesis. Elucidation of mechanisms underlying epigenetic alterations and the manner in which these mechanisms interact in regulating gene transcription in PCa are an unmet necessity that may lead to novel chemotherapeutic approaches. This will, therefore, aid in developing combination therapies that will target multiple epigenetic pathways, which can be used in conjunction with the current conventional PCa treatment.
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Affiliation(s)
- Mankgopo M. Kgatle
- Division of Hepatology and Liver Research, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Observatory, Western Cape 7925, South Africa
| | - Asgar A. Kalla
- Division of Rheumatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Observatory, Western Cape 7925, South Africa
| | - Muhammed M. Islam
- Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, Western Cape 7925, South Africa
| | - Mike Sathekge
- Department of Nuclear Medicine, University of Pretoria and Steve Biko Academic Hospital, Private Bag X169, Pretoria, Gauteng 0001, South Africa
| | - Razia Moorad
- Department of Surgery, Faculty of Health Science, University of Cape Town and Groote Schuur Hospital, Observatory, Western Cape 7925, South Africa
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Mehta R, Singh A, Bókkon I, Nath Mallick B. REM sleep and its Loss-Associated Epigenetic Regulation with Reference to Noradrenaline in Particular. Curr Neuropharmacol 2016; 14:28-40. [PMID: 26813120 PMCID: PMC4787282 DOI: 10.2174/1570159x13666150414185737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/02/2015] [Accepted: 04/11/2015] [Indexed: 01/12/2023] Open
Abstract
Sleep is an essential physiological process, which has been divided into rapid eye movement sleep (REMS) and non-REMS (NREMS) in higher animals. REMS is a unique phenomenon that unlike other sleep-waking states is not under voluntary control. Directly or indirectly it influences or gets influenced by most of the physiological processes controlled by the brain. It has been proposed that REMS serves housekeeping function of the brain. Extensive research has shown that during REMS at least noradrenaline (NA) -ergic neurons must cease activity and upon REMS loss, there are increased levels of NA in the brain, which then induces many of the REMS loss associated acute and chronic effects. The NA level is controlled by many bio-molecules that are regulated at the molecular and transcriptional levels. Similarly, NA can also directly or indirectly modulate the synthesis and levels of many molecules, which in turn may affect physiological processes. The burgeoning field of behavioral neuroepigenetics has gained importance in recent years and explains the regulatory mechanisms underlying several behavioral phenomena. As REMS and its loss associated changes in NA modulate several pathophysiological processes, in this review we have attempted to explain on one hand how the epigenetic mechanisms regulating the gene expression of factors like tyrosine hydroxylase (TH), monoamine oxidase (MAO), noradrenaline transporter (NAT) control NA levels and on the other hand, how NA per se can affect other molecules in neural circuitry at the epigenetic level resulting in behavioral changes in health and diseases. An
understanding of these events will expose the molecular basis of REMS and its loss-associated pathophysiological changes; which are presented as a testable hypothesis for confirmation.
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80
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Zhang W, Han D, Wan P, Pan P, Cao Y, Liu Y, Wu K, Wu J. ERK/c-Jun Recruits Tet1 to Induce Zta Expression and Epstein-Barr Virus Reactivation through DNA Demethylation. Sci Rep 2016; 6:34543. [PMID: 27708396 PMCID: PMC5052586 DOI: 10.1038/srep34543] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
DNA demethylation plays an essential role in the reactivation of Epstein-Barr virus (EBV) from latency infection. However, it is unclear how epigenetic modification is initiated in responding to stimuli. Here, we demonstrate that ERK/c-Jun signaling is involved in DNA demethylation of EBV immediate early (IE) gene Zta in response to 12-O-Tetradecanoylphorbol-13-acetate (TPA) stimulation. Remarkably, Ser73 phosphorylation of c-Jun facilitates Zta promoter demethylation and EBV reactivation, whereas knockdown of c-Jun attenuates Zta demethylation and viral reactivation. More importantly, we reveal for the first time that c-Jun interacts with DNA dioxygenase Tet1 and facilitates Tet1 to bind to Zta promoter. The binding of c-Jun and Tet1 to Zta enhances promoter demethylation, resulting in the activation of Zta, the stimulation of BHRF1 (a lytic early gene) and gp350/220 (a lytic late gene), and ultimately the reactivation of EBV. Knockdown of Tet1 attenuates TPA-induced Zta demethylation and EBV reactivation. Thus, TPA activates ERK/c-Jun signaling, which subsequently facilitates Tet1 to bind to Zta promoter, leading to DNA demethylation, gene expression, and EBV reactivation. This study reveals important roles of ERK/c-Jun signaling and Tet1 dioxygenase in epigenetic modification, and provides new insights into the mechanism underlying the regulation of virus latent and lytic infection.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Dongjie Han
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Pin Wan
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Pan Pan
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yanhua Cao
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingle Liu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kailang Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jianguo Wu
- State Key Laboratory of Virology and College of Life Sciences, Wuhan University, Wuhan 430072, China
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81
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Ianov L, Kumar A, Foster TC. Epigenetic regulation of estrogen receptor α contributes to age-related differences in transcription across the hippocampal regions CA1 and CA3. Neurobiol Aging 2016; 49:79-85. [PMID: 27776265 DOI: 10.1016/j.neurobiolaging.2016.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 10/20/2022]
Abstract
The expression of estrogen receptor alpha (ERα) varies across brain regions and changes with age and according to the previous history of estradiol exposure. ERα is regulated by a number of mechanisms including the level of mRNA (Esr1) expression. For this study, we took advantage of regional differences in hippocampal ERα expression to investigate DNA ERα promoter methylation at CpG dinucleotide sites as a potential epigenetic mechanism for regulating gene expression. Young and aged female Fischer 344 rats were ovariectomized, and Esr1 expression and ERα promoter methylation were examined in hippocampal regions CA1 and CA3, either 3 or 14 weeks following surgery. The results indicate that reduced Esr1 expression in region CA1 relative to CA3 was associated with an increase in DNA methylation in region CA1, particularly for the first CpG site. Additionally, differential methylation of distal CpG sites, 11-17, was associated with altered Esr1 expression during aging or following long-term hormone deprivation. The results support the idea that methylation of site 1 may be the primary regulatory region for cross-regional patterns in ERα expression, while distal sites are modifiable across the life span and may act as a feedback mechanism for ERα activity.
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Affiliation(s)
- Lara Ianov
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Genetics and Genomics Program, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Ashok Kumar
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
| | - Thomas C Foster
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA; Genetics and Genomics Program, Genetics Institute, University of Florida, Gainesville, FL, USA.
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82
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Srivas S, Thakur MK. Epigenetic regulation of neuronal immediate early genes is associated with decline in their expression and memory consolidation in scopolamine-induced amnesic mice. Mol Neurobiol 2016; 54:5107-5119. [PMID: 27553230 DOI: 10.1007/s12035-016-0047-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/08/2016] [Indexed: 01/08/2023]
Abstract
Recently, we reported a correlation of scopolamine mediated decline in memory consolidation with increase in the expression of DNA methyltransferase 1 (DNMT1) and histone deacetylase 2 (HDAC2) in the mouse hippocampus. Memory consolidation is a protein synthesis-dependent process which involves the expression of synaptic plasticity genes, particularly neuronal immediate early genes (IEGs). However, the mechanism of regulation of these genes during decline in memory is poorly understood. Therefore, we have studied the epigenetic regulation of expression of neuronal IEGs in scopolamine-induced amnesic mice. Scopolamine significantly impaired memory consolidation as tested by radial arm maze, and the expression of neuronal IEGs was downregulated in the hippocampus as revealed by qRT-PCR and Western blotting. Further, methylated DNA immunoprecipitation (MeDIP) analysis showed increase in DNA methylation, while chromatin immunoprecipitation (ChIP) revealed decrease in H3K9/14 acetylation at the promoter of neuronal IEGs. Taken together, the present study shows that increased DNA methylation and decreased histone acetylation at the promoter of neuronal IEGs are associated with decline in their expression and memory consolidation during scopolamine-induced amnesia. These findings suggest that the epigenetic regulation through altered DNA methylation and histone acetylation might be explored further to develop potential therapeutic interventions for amnesia.
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Affiliation(s)
- Sweta Srivas
- Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Department of Zoology, Institute of Sciences, Banaras Hindu University, Varanasi, 221 005, India
| | - Mahendra K Thakur
- Biochemistry and Molecular Biology Laboratory, Brain Research Centre, Department of Zoology, Institute of Sciences, Banaras Hindu University, Varanasi, 221 005, India.
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83
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Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H. Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biol 2016; 5:rsob.150128. [PMID: 26446621 PMCID: PMC4632512 DOI: 10.1098/rsob.150128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Fumiya Adachi
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuhiro Arimura
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kazumitsu Maehara
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Faculty of Medicine, Kyushu University, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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84
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Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing RA, Fan C. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biol 2016; 17:92. [PMID: 27154274 PMCID: PMC4858842 DOI: 10.1186/s13059-016-0954-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/14/2016] [Indexed: 01/17/2023] Open
Abstract
Background Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history. Results Our analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes. Conclusions Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0954-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Feng Tao
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Dave Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Seunghee Lee
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,T.T. Chang Genetics Resources Center, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.
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85
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Essebier A, Vera Wolf P, Cao MD, Carroll BJ, Balasubramanian S, Bodén M. Statistical Enrichment of Epigenetic States Around Triplet Repeats that Can Undergo Expansions. Front Neurosci 2016; 10:92. [PMID: 27013954 PMCID: PMC4782033 DOI: 10.3389/fnins.2016.00092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/23/2016] [Indexed: 12/18/2022] Open
Abstract
More than 30 human genetic diseases are linked to tri-nucleotide repeat expansions. There is no known mechanism that explains repeat expansions in full, but changes in the epigenetic state of the associated locus has been implicated in the disease pathology for a growing number of examples. A comprehensive comparative analysis of the genomic features associated with diverse repeat expansions has been lacking. Here, in an effort to decipher the propensity of repeats to undergo expansion and result in a disease state, we determine the genomic coordinates of tri-nucleotide repeat tracts at base pair resolution and computationally establish epigenetic profiles around them. Using three complementary statistical tests, we reveal that several epigenetic states are enriched around repeats that are associated with disease, even in cells that do not harbor expansion, relative to a carefully stratified background. Analysis of over one hundred cell types reveals that epigenetic states generally tend to vary widely between genic regions and cell types. However, there is qualified consistency in the epigenetic signatures of repeats associated with disease suggesting that changes to the chromatin and the DNA around an expanding repeat locus are likely to be similar. These epigenetic signatures may be exploited further to develop models that could explain the propensity of repeats to undergo expansions.
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Affiliation(s)
- Alexandra Essebier
- School of Chemistry and Molecular Biosciences, The University of Queensland St Lucia, QLD, Australia
| | - Patricia Vera Wolf
- School of Chemistry and Molecular Biosciences, The University of Queensland St Lucia, QLD, Australia
| | - Minh Duc Cao
- School of Chemistry and Molecular Biosciences, The University of Queensland St Lucia, QLD, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland St Lucia, QLD, Australia
| | | | - Mikael Bodén
- School of Chemistry and Molecular Biosciences, The University of Queensland St Lucia, QLD, Australia
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86
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Paluch BE, Naqash AR, Brumberger Z, Nemeth MJ, Griffiths EA. Epigenetics: A primer for clinicians. Blood Rev 2016; 30:285-95. [PMID: 26969414 DOI: 10.1016/j.blre.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 02/04/2016] [Accepted: 02/12/2016] [Indexed: 01/08/2023]
Abstract
With recent advances in cellular biology, we now appreciate that modifications to DNA and histones can have a profound impact on transcription and function, even in the absence of changes to DNA sequence. These modifications, now commonly referred to as "epigenetic" alterations, have changed how we understand cell behavior, reprogramming and differentiation and have provided significant insight into the mechanisms underlying carcinogenesis. Epigenetic alterations, to this point, are largely identified by changes in DNA methylation and hydroxymethylation as well as methylation, acetylation, and phosphorylation of histone tails. These modifications enable significant flexibility in gene expression, rather than just turning genes "ON" or "OFF." Herein we describe the epigenetic landscape in the regulation of gene expression with a particular focus on interrogating DNA methylation in myeloid malignancy.
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Affiliation(s)
- Benjamin E Paluch
- Department of Pharmacology, Center for Pharmacology and Genetics Building (CGP), Roswell Park Cancer Institute (RPCI), Elm and Carlton Street, 14263 Buffalo, NY, USA.
| | - Abdul R Naqash
- Catholic Health, State University of New York at Buffalo (SUNY), 2157 Main Street, 14214 Buffalo, NY, USA.
| | - Zachary Brumberger
- University at Buffalo State University of New York, School of Medicine and Biomedical Sciences, 3435 Main Street, 14260 Buffalo, NY, USA
| | - Michael J Nemeth
- Department of Medicine, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA
| | - Elizabeth A Griffiths
- Department of Pharmacology, Center for Pharmacology and Genetics Building (CGP), Roswell Park Cancer Institute (RPCI), Elm and Carlton Street, 14263 Buffalo, NY, USA; Department of Medicine, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA; Leukemia Division, RPCI, Elm and Carlton Street, 14263 Buffalo, NY, USA.
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87
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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: 73] [Impact Index Per Article: 9.1] [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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88
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The role of endothelial mechanosensitive genes in atherosclerosis and omics approaches. Arch Biochem Biophys 2015; 591:111-31. [PMID: 26686737 DOI: 10.1016/j.abb.2015.11.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 12/24/2022]
Abstract
Atherosclerosis is the leading cause of morbidity and mortality in the U.S., and is a multifactorial disease that preferentially occurs in regions of the arterial tree exposed to disturbed blood flow. The detailed mechanisms by which d-flow induces atherosclerosis involve changes in the expression of genes, epigenetic patterns, and metabolites of multiple vascular cells, especially endothelial cells. This review presents an overview of endothelial mechanobiology and its relation to the pathogenesis of atherosclerosis with special reference to the anatomy of the artery and the underlying fluid mechanics, followed by a discussion of a variety of experimental models to study the role of fluid mechanics and atherosclerosis. Various in vitro and in vivo models to study the role of flow in endothelial biology and pathobiology are discussed in this review. Furthermore, strategies used for the global profiling of the genome, transcriptome, miR-nome, DNA methylome, and metabolome, as they are important to define the biological and pathophysiological mechanisms of atherosclerosis. These "omics" approaches, especially those which derive data based on a single animal model, provide unprecedented opportunities to not only better understand the pathophysiology of atherosclerosis development in a holistic and integrative manner, but also to identify novel molecular and diagnostic targets.
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89
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Ferguson LR, Chen H, Collins AR, Connell M, Damia G, Dasgupta S, Malhotra M, Meeker AK, Amedei A, Amin A, Ashraf SS, Aquilano K, Azmi AS, Bhakta D, Bilsland A, Boosani CS, Chen S, Ciriolo MR, Fujii H, Guha G, Halicka D, Helferich WG, Keith WN, Mohammed SI, Niccolai E, Yang X, Honoki K, Parslow VR, Prakash S, Rezazadeh S, Shackelford RE, Sidransky D, Tran PT, Yang ES, Maxwell CA. Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition. Semin Cancer Biol 2015; 35 Suppl:S5-S24. [PMID: 25869442 PMCID: PMC4600419 DOI: 10.1016/j.semcancer.2015.03.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 03/08/2015] [Accepted: 03/13/2015] [Indexed: 02/06/2023]
Abstract
Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.
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Affiliation(s)
| | - Helen Chen
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marisa Connell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada
| | - Giovanna Damia
- Department of Oncology, Instituti di Ricovero e Cura a Carattere Scientifico-Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, United States
| | | | - Alan K Meeker
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates; Faculty of Science, Cairo University, Cairo, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Katia Aquilano
- Department of Biology, Università di Roma Tor Vergata, Rome, Italy
| | - Asfar S Azmi
- Department of Biology, University of Rochester, Rochester, United States
| | - Dipita Bhakta
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Chandra S Boosani
- Department of BioMedical Sciences, Creighton University, Omaha, NE, United States
| | - Sophie Chen
- Department of Research & Development, Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | | | - Hiromasa Fujii
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | - Gunjan Guha
- School of Chemical and BioTechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | | | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Kanya Honoki
- Department of Orthopaedic Surgery, Nara Medical University, Kashihara, Nara, Japan
| | | | - Satya Prakash
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Sarallah Rezazadeh
- Department of Biology, University of Rochester, Rochester, United States
| | - Rodney E Shackelford
- Department of Pathology, Louisiana State University Health Shreveport, Shreveport, LA, United States
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Phuoc T Tran
- Departments of Radiation Oncology & Molecular Radiation Sciences, Oncology and Urology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, United States
| | - Christopher A Maxwell
- Department of Pediatrics, University of British Columbia, Michael Cuccione Childhood Cancer Research Program, Child and Family Research Institute, Vancouver, Canada.
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McKnight RA, Yost CC, Yu X, Wiedmeier JE, Callaway CW, Brown AS, Lane RH, Fung CM. Intrauterine growth restriction perturbs nucleosome depletion at a growth hormone-responsive element in the mouse IGF-1 gene. Physiol Genomics 2015; 47:634-43. [DOI: 10.1152/physiolgenomics.00082.2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/13/2015] [Indexed: 01/08/2023] Open
Abstract
Intrauterine growth restriction (IUGR) is a common human pregnancy complication. IUGR offspring carry significant postnatal risk for early-onset metabolic syndrome, which is associated with persistent reduction in IGF-1 protein expression. We have previously shown that preadolescent IUGR male mice have decreased hepatic IGF-1 mRNA and circulating IGF-1 protein at postnatal day 21, the age when growth hormone (GH) normally upregulates hepatic IGF-1 expression. Here we studied nucleosome occupancy and CpG methylation at a putative growth hormone-responsive element in intron 2 (in2GHRE) of the hepatic IGF-1 gene in normal, sham-operated, and IUGR mice. Nucleosome occupancy and CpG methylation were determined in embryonic stem cells (ESCs) and in liver at postnatal days 14, 21, and 42. For CpG methylation, additional time points out to 2 yr were analyzed. We confirmed the putative mouse in2GHRE was GH-responsive, and in normal mice, a single nucleosome was displaced from the hepatic in2GHRE by postnatal day 21, which exposed two STAT5b DNA binding sites. Nucleosome displacement correlated with developmentally programmed CpG demethylation. Finally, IUGR significantly altered the nucleosome-depleted region (NDR) at the in2GHRE of IGF-1 on postnatal day 21, with either complete absence of the NDR or with a shifted NDR exposing only one of two STAT5b DNA binding sites. An NDR shift was also seen in offspring of sham-operated mothers. We conclude that prenatal insult such as IUGR or anesthesia/surgery could perturb the proper formation of a well-positioned NDR at the mouse hepatic IGF-1 in2GHRE necessary for transitioning to an open chromatin state.
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Affiliation(s)
- Robert A. McKnight
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Christian C. Yost
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Xing Yu
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Julia E. Wiedmeier
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Christopher W. Callaway
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Ashley S. Brown
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Robert H. Lane
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Camille M. Fung
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
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91
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92
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Langlois T, da Costa Reis Monte-Mor B, Lenglet G, Droin N, Marty C, Le Couédic JP, Almire C, Auger N, Mercher T, Delhommeau F, Christensen J, Helin K, Debili N, Fuks F, Bernard OA, Solary E, Vainchenker W, Plo I. TET2 deficiency inhibits mesoderm and hematopoietic differentiation in human embryonic stem cells. Stem Cells 2015; 32:2084-97. [PMID: 24723429 DOI: 10.1002/stem.1718] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 02/26/2014] [Accepted: 03/16/2014] [Indexed: 01/23/2023]
Abstract
Ten-eleven-translocation 2 (TET2) belongs to the TET protein family that catalyzes the conversion of 5-methylcytosine into 5-hydroxymethylcytosine and plays a central role in normal and malignant adult hematopoiesis. Yet the role of TET2 in human hematopoietic development remains largely unknown. Here, we show that TET2 expression is low in human embryonic stem cell (ESC) lines and increases during hematopoietic differentiation. shRNA-mediated TET2 knockdown had no effect on the pluripotency of various ESCs. However, it skewed their differentiation into neuroectoderm at the expense of endoderm and mesoderm both in vitro and in vivo. These effects were rescued by reintroducing the targeted TET2 protein. Moreover, TET2-driven differentiation was dependent on NANOG transcriptional factor. Indeed, TET2 bound to NANOG promoter and in TET2-deficient cells the methylation of the NANOG promoter correlated with a decreased in NANOG expression. The altered differentiation resulting from TET2 knockdown in ESCs led to a decrease in both the number and the cloning capacities of hematopoietic progenitors. These defects were due to an increased apoptosis and an altered gene expression profile, including abnormal expression of neuronal genes. Intriguingly, when TET2 was knockdown in hematopoietic cells, it increased hematopoietic development. In conclusion, our work suggests that TET2 is involved in different stages of human embryonic development, including induction of the mesoderm and hematopoietic differentiation.
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Affiliation(s)
- Thierry Langlois
- Institut National de la Santé et de la Recherche Médicale, UMR 1009, Laboratory of Excellence GR-Ex, 114 rue Edouard Vaillant, Villejuif, Paris, France; Institut Gustave Roussy, Villejuif, Paris, France; Université Paris Sud 11, Orsay, France
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93
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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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94
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Hu Y, Morota G, Rosa GJM, Gianola D. Prediction of Plant Height in Arabidopsis thaliana Using DNA Methylation Data. Genetics 2015; 201:779-93. [PMID: 26253546 PMCID: PMC4596684 DOI: 10.1534/genetics.115.177204] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/02/2015] [Indexed: 12/18/2022] Open
Abstract
Prediction of complex traits using molecular genetic information is an active area in quantitative genetics research. In the postgenomic era, many types of -omic (e.g., transcriptomic, epigenomic, methylomic, and proteomic) data are becoming increasingly available. Therefore, evaluating the utility of this massive amount of information in prediction of complex traits is of interest. DNA methylation, the covalent change of a DNA molecule without affecting its underlying sequence, is one quantifiable form of epigenetic modification. We used methylation information for predicting plant height (PH) in Arabidopsis thaliana nonparametrically, using reproducing kernel Hilbert spaces (RKHS) regression. Also, we used different criteria for selecting smaller sets of probes, to assess how representative probes could be used in prediction instead of using all probes, which may lessen computational burden and lower experimental costs. Methylation information was used for describing epigenetic similarities between individuals through a kernel matrix, and the performance of predicting PH using this similarity matrix was reasonably good. The predictive correlation reached 0.53 and the same value was attained when only preselected probes were used for prediction. We created a kernel that mimics the genomic relationship matrix in genomic best linear unbiased prediction (G-BLUP) and estimated that, in this particular data set, epigenetic variation accounted for 65% of the phenotypic variance. Our results suggest that methylation information can be useful in whole-genome prediction of complex traits and that it may help to enhance understanding of complex traits when epigenetics is under examination.
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Affiliation(s)
- Yaodong Hu
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Gota Morota
- Department of Animal Science, University of Nebraska, Lincoln, Nebraska 68583
| | - Guilherme J M Rosa
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706
| | - Daniel Gianola
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin 53706 Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706 Department of Dairy Science, University of Wisconsin, Madison, Wisconsin 53706
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95
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Lee S, Jin JX, Khoirinaya C, Kim GA, Lee BC. Lanosterol influences cytoplasmic maturation of pig oocytes in vitro and improves preimplantation development of cloned embryos. Theriogenology 2015; 85:575-84. [PMID: 26494176 DOI: 10.1016/j.theriogenology.2015.09.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/18/2015] [Accepted: 09/18/2015] [Indexed: 12/26/2022]
Abstract
Lanosterol is a precursor of meiosis-activating sterols in the cholesterol biosynthetic pathway and induces a physiological signal that instructs the oocyte to reinitiate meiosis. In this study, we examined the effect of lanosterol on IVM of porcine oocytes, specifically on nuclear maturation, cytoplasmic maturation by investigating intracellular glutathione (GSH) levels and lipid content, embryonic development after parthenogenetic activation and somatic cell nuclear transfer (SCNT), and on gene expression in cumulus cells, oocytes, and SCNT-derived blastocysts. There was no significant difference in nuclear maturation rates between the control and treatment groups (10, 50, and 100 μM of lanosterol added to IVM culture medium). Supplementation with 50-μM lanosterol significantly increased lipid content and GSH levels and decreased reactive oxygen species levels compared with the control. In addition, oocytes treated with 50 μM of lanosterol exhibited significantly increased blastocyst formation rates and total cell numbers after parthenogenetic activation (30.3% and 63.9 vs. 21.6% and 36.5, respectively) and SCNT (18.2% and 53.7 vs. 12.6% and 37.5, respectively), when compared with the control group. Cumulus cells treated with 50 μM of lanosterol showed significantly increased 14α-demethylase, Δ14-reductase, and Δ7-reductase mRNA transcript levels. Significantly increased PPARγ, SREBF1, GPX1, and Bcl-2 and decreased Bax transcript levels were observed in mature oocytes treated with 50 μM of lanosterol compared with the control. SCNT blastocysts derived from 50-μM lanosterol-treated oocytes had significantly higher POU5F1, FGFR2, and Bcl-2 transcript levels than control SCNT-derived blastocysts. In conclusion, supplementation with 50 μM of lanosterol during IVM improves preimplantation development of SCNT embryos by elevating lipid content of oocytes, increasing GSH levels, decreasing reactive oxygen species levels, and regulating genes related to the cholesterol biosynthetic pathway in cumulus cells, to lipid metabolism and apoptosis in oocytes, and their developmental potential and apoptosis in blastocysts.
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Affiliation(s)
- Sanghoon Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun-Xue Jin
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Candrani Khoirinaya
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Geon A Kim
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Byeong Chun Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea; Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Kangwon do, Korea.
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96
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Peirs S, Van der Meulen J, Van de Walle I, Taghon T, Speleman F, Poppe B, Van Vlierberghe P. Epigenetics in T-cell acute lymphoblastic leukemia. Immunol Rev 2015; 263:50-67. [PMID: 25510271 DOI: 10.1111/imr.12237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Normal T-cell development is a strictly regulated process in which hematopoietic progenitor cells migrate from the bone marrow to the thymus and differentiate from early T-cell progenitors toward mature and functional T cells. During this maturation process, cooperation between a variety of oncogenes and tumor suppressors can drive immature thymocytes into uncontrolled clonal expansion and cause T-cell acute lymphoblastic leukemia (T-ALL). Despite improved insights in T-ALL disease biology and comprehensive characterization of its genetic landscape, clinical care remained largely similar over the past decades and still consists of high-dose multi-agent chemotherapy potentially followed by hematopoietic stem cell transplantation. Even with such aggressive treatment regimens, which are often associated with considerable side effects, clinical outcome is still extremely poor in a significant subset of T-ALL patients as a result of therapy resistance or hematological relapses. Recent genetic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in T-ALL, suggesting that epigenetic homeostasis is critically required in restraining tumor development in the T-cell lineage. In this review, we provide an overview of the epigenetic regulators that could be implicated in T-ALL disease biology and speculate how the epigenetic landscape of T-ALL could trigger the development of epigenetic-based therapies to further improve the treatment of human T-ALL.
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Affiliation(s)
- Sofie Peirs
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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97
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Carvalho ATP, Gouveia L, Kanna CR, Wärmländer SKTS, Platts JA, Kamerlin SCL. Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation. Epigenetics 2015; 9:1604-12. [PMID: 25625845 PMCID: PMC4622728 DOI: 10.4161/15592294.2014.988043] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding.
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Key Words
- AFM, Atomic Force Microscopy
- DDD, Dickerson-Drew Dodecamer
- DFT, Density Functional Theory
- DNA methylation
- DNA, Deoxyribonucleic Acid
- DNMT, DNA Methyltransferase
- LINEs, Long Interspred Transposable Elements
- MD, Molecular Dynamics
- MM, Molecular Mechanics
- MeCP, Methylated CpG-binding proteins
- PBC, Periodic Boundary Conditions
- QM, Quantum Mechanics
- RDF, Radial Distribution Functions
- RESP, Restrained Electrostatic Potentials Model
- SINEs, Short Interspred Transposable Elements
- SPME, Smooth Particle-Mesh Ewald
- TET, Translocation Proteins
- WT, Wild Type
- epigenetics
- indirect readout
- molecular dynamics
- recognition
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Affiliation(s)
- Alexandra T P Carvalho
- a Science for Life Laboratory; Department of Cell and Molecular Biology ; Uppsala University ; Uppsala , Sweden
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98
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Navarro A, Díaz T, Cordeiro A, Beyá MD, Ferrer G, Fuster D, Martinez A, Monzó M. Epigenetic regulation of microRNA expression in Hodgkin lymphoma. Leuk Lymphoma 2015; 56:2683-9. [PMID: 25586608 DOI: 10.3109/10428194.2014.995650] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Epigenetic mechanisms are crucial for the inactivation of key genes related to the survival of Hodgkin lymphoma (HL) cells, and methylation is a frequent epigenetic mechanism of microRNA silencing. We have examined the methylation-induced silencing of tumor suppressor microRNAs in HL cell lines and confirmed our results in patient lymph nodes. In addition, we evaluated the in vitro effectiveness of 5-aza-2-deoxycytidine (5-Aza-dC) in HL cell lines. Ten microRNAs containing CpG islands in their promoter region were re-expressed in both the L-428 and L-1236 cell lines. Interestingly, miR-34a and miR-203, both known tumor suppressor microRNAs, were found to be methylated in cell lines and in patient samples. 5-Aza-dC treatment resulted in a dose-dependent antiproliferative effect at 72 h in all the HL cell lines. In summary, 5-Aza-dC treatment of HL cell lines inhibits proliferation at high doses and produces re-expression of the tumor suppressor microRNAs at low-intermediate doses.
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Affiliation(s)
- Alfons Navarro
- a Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS , Barcelona , Spain
| | - Tania Díaz
- a Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS , Barcelona , Spain
| | - Anna Cordeiro
- a Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS , Barcelona , Spain
| | - Marina Díaz Beyá
- b Hematology Department, Hospital Clinic Barcelona , Barcelona , Spain
| | - Gerardo Ferrer
- c Laboratory of Translational Hematology, Hospital Clinic, IDIBAPS , Barcelona , Spain
| | - Dolors Fuster
- a Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS , Barcelona , Spain
| | - Antonio Martinez
- d Hematopathology Section, Hospital Clinic, IDIBAPS , Barcelona , Spain
| | - Mariano Monzó
- a Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS , Barcelona , Spain
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99
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Xin F, Susiarjo M, Bartolomei MS. Multigenerational and transgenerational effects of endocrine disrupting chemicals: A role for altered epigenetic regulation? Semin Cell Dev Biol 2015; 43:66-75. [PMID: 26026600 DOI: 10.1016/j.semcdb.2015.05.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 01/21/2023]
Abstract
Increasing evidence has highlighted the critical role of early life environment in shaping the future health outcomes of an individual. Moreover, recent studies have revealed that early life perturbations can affect the health of subsequent generations. Hypothesized mechanisms of multi- and transgenerational inheritance of abnormal developmental phenotypes include epigenetic misregulation in germ cells. In this review, we will focus on the available data demonstrating the ability of endocrine disrupting chemicals (EDCs), including bisphenol A (BPA), phthalates, and parabens, to alter epigenetic marks in rodents and humans. These epigenetic marks include DNA methylation, histone post-translational modifications, and non-coding RNAs. We also review the current evidence for multi- and transgenerational inheritance of abnormal developmental changes in the offspring following EDC exposure. Based on published results, we conclude that EDC exposure can alter the mouse and human epigenome, with variable tissue susceptibilities. Although increasing data suggest that exposure to EDCs is linked to transgenerational inheritance of reproductive, metabolic, or neurological phenotypes, more studies are needed to validate these observations and to elucidate further whether these developmental changes are directly associated with the relevant epigenetic alterations.
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Affiliation(s)
- Frances Xin
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 Smilow Center for Translational Research, Philadelphia, PA 19104, United States; Center of Excellence in Environmental Toxicology, University of Pennsylvania Perelman School of Medicine, 1316 Biomedical Research Building II/III, Philadelphia, PA 19104, United States
| | - Martha Susiarjo
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 Smilow Center for Translational Research, Philadelphia, PA 19104, United States; Center of Excellence in Environmental Toxicology, University of Pennsylvania Perelman School of Medicine, 1316 Biomedical Research Building II/III, Philadelphia, PA 19104, United States
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 Smilow Center for Translational Research, Philadelphia, PA 19104, United States; Center of Excellence in Environmental Toxicology, University of Pennsylvania Perelman School of Medicine, 1316 Biomedical Research Building II/III, Philadelphia, PA 19104, United States.
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100
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Agarwal P, Collier P, Fritz MHY, Benes V, Wiklund HJ, Westermark B, Singh U. CGGBP1 mitigates cytosine methylation at repetitive DNA sequences. BMC Genomics 2015; 16:390. [PMID: 25981527 PMCID: PMC4432828 DOI: 10.1186/s12864-015-1593-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/28/2015] [Indexed: 11/24/2022] Open
Abstract
Background CGGBP1 is a repetitive DNA-binding transcription regulator with target sites at CpG-rich sequences such as CGG repeats and Alu-SINEs and L1-LINEs. The role of CGGBP1 as a possible mediator of CpG methylation however remains unknown. At CpG-rich sequences cytosine methylation is a major mechanism of transcriptional repression. Concordantly, gene-rich regions typically carry lower levels of CpG methylation than the repetitive elements. It is well known that at interspersed repeats Alu-SINEs and L1-LINEs high levels of CpG methylation constitute a transcriptional silencing and retrotransposon inactivating mechanism. Results Here, we have studied genome-wide CpG methylation with or without CGGBP1-depletion. By high throughput sequencing of bisulfite-treated genomic DNA we have identified CGGBP1 to be a negative regulator of CpG methylation at repetitive DNA sequences. In addition, we have studied CpG methylation alterations on Alu and L1 retrotransposons in CGGBP1-depleted cells using a novel bisulfite-treatment and high throughput sequencing approach. Conclusions The results clearly show that CGGBP1 is a possible bidirectional regulator of CpG methylation at Alus, and acts as a repressor of methylation at L1 retrotransposons. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1593-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Prasoon Agarwal
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, Uppsala, 75185, Sweden.
| | - Paul Collier
- EMBL, Core Facilities and Services, Meyerhofsstrasse 1, Heidelberg, D-69117, Germany.
| | - Markus Hsi-Yang Fritz
- EMBL, Core Facilities and Services, Meyerhofsstrasse 1, Heidelberg, D-69117, Germany.
| | - Vladimir Benes
- EMBL, Core Facilities and Services, Meyerhofsstrasse 1, Heidelberg, D-69117, Germany.
| | - Helena Jernberg Wiklund
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, Uppsala, 75185, Sweden.
| | - Bengt Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, Uppsala, 75185, Sweden.
| | - Umashankar Singh
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Rudbeck Laboratory, Dag Hammarskjölds Väg 20, Uppsala, 75185, Sweden.
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