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Lin SM, Huang HT, Fang PJ, Chang CF, Satange R, Chang CK, Chou SH, Neidle S, Hou MH. Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation. Nucleic Acids Res 2024; 52:8566-8579. [PMID: 38989613 DOI: 10.1093/nar/gkae594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.
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Affiliation(s)
- Shan-Meng Lin
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiang-Ti Huang
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Pei-Ju Fang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Ho Chou
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan
| | - Stephen Neidle
- School of Pharmacy, University College London, London WC1N 1AX, UK
| | - Ming-Hon Hou
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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Okashita N, Tachibana M. Transcriptional Regulation of the Y-Linked Mammalian Testis-Determining Gene SRY. Sex Dev 2021; 15:351-359. [PMID: 34583357 DOI: 10.1159/000519217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022] Open
Abstract
Mammalian male sex differentiation is triggered during embryogenesis by the activation of the Y-linked testis-determining gene SRY. Since insufficient or delayed expression of SRY results in XY gonadal sex reversal, accurate regulation of SRY is critical for male development in XY animals. In humans, dysregulation of SRY may cause disorders of sex development. Mouse Sry is the most intensively studied mammalian model of sex determination. Sry expression is controlled in a spatially and temporally stringent manner. Several transcription factors play a key role in sex determination as trans-acting factors for Sry expression. In addition, recent studies have shown that several epigenetic modifications of Sry are involved in sex determination as cis-acting factors for Sry expression. Herein, we review the current understanding of transcription factor- and epigenetic modifier-mediated regulation of SRY/Sry expression.
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Affiliation(s)
- Naoki Okashita
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Makoto Tachibana
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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3
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Monti N, Cavallaro RA, Stoccoro A, Nicolia V, Scarpa S, Kovacs GG, Fiorenza MT, Lucarelli M, Aronica E, Ferrer I, Coppedè F, Troen AM, Fuso A. CpG and non-CpG Presenilin1 methylation pattern in course of neurodevelopment and neurodegeneration is associated with gene expression in human and murine brain. Epigenetics 2020; 15:781-799. [PMID: 32019393 PMCID: PMC7518704 DOI: 10.1080/15592294.2020.1722917] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
The Presenilin1 (PSEN1) gene encodes the catalytic peptide of the γ-secretase complex, a key enzyme that cleaves the amyloid-β protein precursor (AβPP), to generate the amyloid-β (Aβ) peptides, involved in Alzheimer's Disease (AD). Other substrates of the γ-secretase, such as E-cadherin and Notch1, are involved in neurodevelopment and haematopoiesis. Gene-specific DNA methylation influences PSEN1 expression in AD animal models. Here we evaluated canonical and non-canonical cytosine methylation patterns of the PSEN1 5'-flanking during brain development and AD progression, in DNA extracted from the frontal cortex of AD transgenic mice (TgCRND8) and post-mortem human brain. Mapping CpG and non-CpG methylation revealed different methylation profiles in mice and humans. PSEN1 expression only correlated with DNA methylation in adult female mice. However, in post-mortem human brain, lower methylation, both at CpG and non-CpG sites, correlated closely with higher PSEN1 expression during brain development and in disease progression. PSEN1 methylation in blood DNA was significantly lower in AD patients than in controls. The present study is the first to demonstrate a temporal correlation between dynamic changes in PSEN1 CpG and non-CpG methylation patterns and mRNA expression during neurodevelopment and AD neurodegeneration. These observations were made possible by the use of an improved bisulphite methylation assay employing primers that are not biased towards non-CpG methylation. Our findings deepen the understanding of γ-secretase regulation and support the hypothesis that epigenetic changes can promote the pathophysiology of AD. Moreover, they suggest that PSEN1 DNA methylation in peripheral blood may provide a biomarker for AD.
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Affiliation(s)
- Noemi Monti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Department of Surgery “P. Valdoni”, Sapienza University of Rome, Rome, Italy
| | | | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Vincenzina Nicolia
- Department of Surgery “P. Valdoni”, Sapienza University of Rome, Rome, Italy
| | - Sigfrido Scarpa
- Department of Surgery “P. Valdoni”, Sapienza University of Rome, Rome, Italy
| | - Gabor G. Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Maria Teresa Fiorenza
- Department of Psychology, Division of Neuroscience, Sapienza University of Rome, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Isidre Ferrer
- Neuropathology, Service of Pathology, Bellvitge University Hospital, Barcelona, Spain
- CIBERNED, Hospitalet De Llobregat, University of Barcelona, Barcelona, Spain
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Aron M. Troen
- Nutrition and Brain Health Laboratory, the Institute of Biochemistry Food and Nutrition Science, the Robert H. Smith Faculty of Agriculture Food and the Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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4
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Xiao W, Liu X, Niu X, Li C, Guo Y, Tan J, Xiong W, Fan L, Li Y. The frequency of CpG and non-CpG methylation of Notch3 gene promoter determines its expression levels in breast cancer cells. Exp Cell Res 2020; 386:111743. [PMID: 31770532 DOI: 10.1016/j.yexcr.2019.111743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 02/05/2023]
Abstract
Notch3 can act as a tumor suppressor in the breast cancer epithelial cells. Unfortunately, Notch3 expression is decreased or lost, especially in triple-negative breast cancer (TNBC) cells, and the reasons remain unclear. Here, we found Notch3 was upregulated in MDA-MB-231 cells with 5-Aza treatment. Two CpG islands were observed in notch3 promoter. Interestingly, bisulfite sequencing exhibited that large amounts of unconverted cytosines were not only followed by guanine, but also adenine, cytosine and thymine, which implied that there simultaneously existed CpG and non-CpG methylation in notch3 promoter. To better analyze the methylation frequency of non-CpG locus, we designed CpG/non-CpG methylation analysis software. The results showed that the methylation frequency of notch3 gene in different breast cancer cell lines was in order T47D, MCF-7, SKBR3, BT-549 and MDA-MB-231. Furthermore, we identified that DNMT3b, DNMT1, DNMT3L, Mecp2 and EZH2 were important regulators of non-CpG locus of notch3 gene. Immunohistochemistry staining revealed a negative correlation between EZH2 and Notch3 from 22 luminal and 26 TNBC cases. In vitro methylation combined luciferase activity assays showed that non-CpG methylation was still crucial cause leading to notch3 transcriptional repression in TNBC. Our findings provide possible explanation for the downregulation or loss of Notch3 expression in TNBC.
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Affiliation(s)
- Wenjun Xiao
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China; Present Address: Health Science Center of Shenzhen University Medical College, Shenzhen, 518055, China
| | - Xiong Liu
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Xia Niu
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Chun Li
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Yuxian Guo
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Junyu Tan
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Wei Xiong
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Liping Fan
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China
| | - Yaochen Li
- The Central Laboratory of Cancer Hospital of Shantou University Medical College, 7 Raoping Road, Shantou, 515031, China.
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5
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Li C, Xiong W, Liu X, Xiao W, Guo Y, Tan J, Li Y. Hypomethylation at non-CpG/CpG sites in the promoter of HIF-1α gene combined with enhanced H3K9Ac modification contribute to maintain higher HIF-1α expression in breast cancer. Oncogenesis 2019; 8:26. [PMID: 30940798 PMCID: PMC6445832 DOI: 10.1038/s41389-019-0135-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/26/2019] [Accepted: 03/18/2019] [Indexed: 02/06/2023] Open
Abstract
HIF-1α has a broad impact on tumors, including enhanced utilization of glucose, tumor cell stemness, migration, metastasis and so on. In pilot study, we found that the expression of HIF-1α significantly increased in breast cancer cell lines and tissue samples with higher malignant behaviors and decreased in luminal subtype breast cancer cells and tissue samples. We analyzed and found there is one large CpG island in HIF-1α promoter around transcription start site, and the hypermethylation occurred at these CpGs and their surrounding non-CpGs sites. Epigenetic events driving tumorigenesis has been characterized. However, knowledge is lacking on the non-CpGs methylation of HIF-1α promoter in breast cancer cells. We validated that non-CpGs methylation can directly regulate HIF-1α expression by luciferase activity assay. We also found DNMT3a and Mecp2 play vital role in methylation at non-CpGs and CpGs sites. In addition, we noticed that H3K9ac modification could promote the transcription of HIF-1α in MDA-MB-231 cells by binding to the region contained hypomethylated non-CpG and CpG sites. Taken together, the hypomethylation status at non-CpG and CpG loci in HIF-1α promoter and H3K9ac modification together contribute to maintain higher HIF-1αactivity in invasive breast cancer cells when compared with the non-invasive breast cancer cells, which may establish a tissue-specific epigenetic modification pattern and point to the new directions for future understanding breast cancer therapy.
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Affiliation(s)
- Chun Li
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
- Department of Pathology, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Wei Xiong
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Xiong Liu
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Wenjun Xiao
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Yuxian Guo
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Junyu Tan
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China
| | - Yaochen Li
- The central laboratory, of Cancer Hospital of Shantou University Medical College, No.7 Raoping Road, Shantou, 515031, China.
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6
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Stévant I, Nef S. Genetic Control of Gonadal Sex Determination and Development. Trends Genet 2019; 35:346-358. [PMID: 30902461 DOI: 10.1016/j.tig.2019.02.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/15/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
Sex determination is the process by which the bipotential gonads develop as either testes or ovaries. With two distinct potential outcomes, the gonadal primordium offers a unique model for the study of cell fate specification and how distinct cell populations diverge from multipotent progenitors. This review focuses on recent advances in our understanding of the genetic programs and epigenetic mechanisms that regulate gonadal sex determination and the regulation of cell fate commitment in the bipotential gonads. We rely primarily on mouse data to illuminate the complex and dynamic genetic programs controlling cell fate decision and sex-specific cell differentiation during gonadal formation and gonadal sex determination.
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Affiliation(s)
- Isabelle Stévant
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva, Switzerland; SIB, Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva, Switzerland.
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Abstract
Mammalian sex determination is triggered by activation of the mammalian sex-determining gene, Sry, in a spatially and temporally controlled manner. Because reduced or delayed Sry expression results in male-to-female sex reversal, male development is highly dependent on the accurate transcription of Sry. SRY dysregulation is a potential cause of human disorders of sex development (DSD). In addition to changes in DNA sequences, gene expression is regulated by epigenetic mechanisms. Epigenetic regulation ensures spatial and temporal accuracy of the expression of developmentally regulated genes. Epigenetic regulation such as histone tail modification, DNA methylation, chromatin remodeling, and non-coding RNA regulation engages several biological processes in multicellular organisms. In recent years, it has been revealed that various types of epigenetic regulation are involved in accurate gonadal differentiation in mammals. In particular, histone modification plays an integral part in sex determination, which is the first step of gonadal differentiation. Here, we focus on the findings on the epigenetic modifications that regulate Sry expression. Finally, we discuss the role of metabolism that potentially alters the epigenetic state in response to environmental cues.
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Affiliation(s)
- Shingo Miyawaki
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan; Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Makoto Tachibana
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan; Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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8
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Yang Y, Workman S, Wilson M. The molecular pathways underlying early gonadal development. J Mol Endocrinol 2018; 62:JME-17-0314. [PMID: 30042122 DOI: 10.1530/jme-17-0314] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 12/30/2022]
Abstract
The body of knowledge surrounding reproductive development spans the fields of genetics, anatomy, physiology and biomedicine, to build a comprehensive understanding of the later stages of reproductive development in humans and animal models. Despite this, there remains much to learn about the bi-potential progenitor structure that the ovary and testis arise from, known as the genital ridge (GR). This tissue forms relatively late in embryonic development and has the potential to form either the ovary or testis, which in turn produce hormones required for development of the rest of the reproductive tract. It is imperative that we understand the genetic networks underpinning GR development if we are to begin to understand abnormalities in the adult. This is particularly relevant in the contexts of disorders of sex development (DSDs) and infertility, two conditions that many individuals struggle with worldwide, with often no answers as to their aetiology. Here, we review what is known about the genetics of GR development. Investigating the genetic networks required for GR formation will not only contribute to our understanding of the genetic regulation of reproductive development, it may in turn open new avenues of investigation into reproductive abnormalities and later fertility issues in the adult.
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Affiliation(s)
- Yisheng Yang
- Y Yang, Anatomy, University of Otago, Dunedin, New Zealand
| | | | - Megan Wilson
- M Wilson , Anatomy, University of Otago, Dunedin, New Zealand
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9
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Garcia-Moreno SA, Plebanek MP, Capel B. Epigenetic regulation of male fate commitment from an initially bipotential system. Mol Cell Endocrinol 2018; 468:19-30. [PMID: 29410272 PMCID: PMC6084468 DOI: 10.1016/j.mce.2018.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/21/2022]
Abstract
A fundamental goal in biology is to understand how distinct cell types containing the same genetic information arise from a single stem cell throughout development. Sex determination is a key developmental process that requires a unidirectional commitment of an initially bipotential gonad towards either the male or female fate. This makes sex determination a unique model to study cell fate commitment and differentiation in vivo. We have focused this review on the accumulating evidence that epigenetic mechanisms contribute to the bipotential state of the fetal gonad and to the regulation of chromatin accessibility during and immediately downstream of the primary sex-determining switch that establishes the male fate.
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Affiliation(s)
| | | | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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10
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Saikia S, Rehman AU, Barooah P, Sarmah P, Bhattacharyya M, Deka M, Deka M, Goswami B, Husain SA, Medhi S. Alteration in the expression of MGMT and RUNX3 due to non-CpG promoter methylation and their correlation with different risk factors in esophageal cancer patients. Tumour Biol 2017; 39:1010428317701630. [PMID: 28468586 DOI: 10.1177/1010428317701630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Promoter methylation reflects in the inactivation of different genes like O6-methylguanine-DNA methyltransferase DNA repair gene and runt-related transcription factor 3, a known tumor suppressor gene in various cancers such as esophageal cancer. The promoter methylation was evaluated for O6-methylguanine-DNA methyltransferase and runt-related transcription factor 3 in CpG, CHH, and CHG context (where H is A, T, or C) by next-generation sequencing. The methylation status was correlated with quantitative messenger RNA expression. In addition, messenger RNA expression was correlated with different risk factors like tobacco, alcohol, betel nut consumption, and smoking habit. CpG methylation of O6-methylguanine-DNA methyltransferase promoter had a positive association in the development of esophageal cancer (p < 0.05), whereas runt-related transcription factor 3 promoter methylation showed no significant association (p = 1.0) to develop esophageal cancer. However, the non-CpG methylation, CHH, and CHG were significantly correlated with O6-methylguanine-DNA methyltransferase (p < 0.05) and runt-related transcription factor 3 (p < 0.05) promoters in the development of esophageal cancer. The number of cytosine converted to thymine (C→T) in O6-methylguanine-DNA methyltransferase promoter showed a significant correlation between cases and controls (p < 0.05), but in runt-related transcription factor 3 no such significant correlation was observed. Besides, messenger RNA expression was found to be significantly correlated with promoter hypermethylation of O6-methylguanine-DNA methyltransferase and runt-related transcription factor 3 in the context of CHG and CHH (p < 0.05). The CpG hypermethylation in O6-methylguanine-DNA methyltransferase showed positive (p < 0.05) association, whereas in runt-related transcription factor 3, it showed contrasting negative association (p = 0.23) with their messenger RNA expression. Tobacco, betel nut consumption, and smoking habits were associated with altered messenger RNA expression of O6-methylguanine-DNA methyltransferase (p < 0.05) and betel nut consumption and smoking habits were associated with runt-related transcription factor 3 (p < 0.05). There was no significant association between messenger RNA expression of O6-methylguanine-DNA methyltransferase and runt-related transcription factor 3 with alcohol consumption (p = 0.32 and p = 0.15). In conclusion, our results suggest that an aberrant messenger RNA expression may be the outcome of CpG, CHG, and CHH methylation in O6-methylguanine-DNA methyltransferase, whereas outcome of CHG and CHH methylation in runt-related transcription factor 3 promoters along with risk factors such as consumption of tobacco, betel nut, and smoking habits in esophageal cancer from Northeast India.
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Affiliation(s)
- Snigdha Saikia
- 1 Department of Bioengineering and Technology, Laboratory of Molecular Virology and Oncology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, India.,2 Department of Gastroenterology, Gauhati Medical College and Hospital, Guwahati, India
| | - Asad Ur Rehman
- 3 Department of Bioscience, Jamia Millia Islamia, New Delhi, India
| | - Prajjalendra Barooah
- 1 Department of Bioengineering and Technology, Laboratory of Molecular Virology and Oncology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, India.,2 Department of Gastroenterology, Gauhati Medical College and Hospital, Guwahati, India
| | - Preeti Sarmah
- 2 Department of Gastroenterology, Gauhati Medical College and Hospital, Guwahati, India
| | - Mallika Bhattacharyya
- 2 Department of Gastroenterology, Gauhati Medical College and Hospital, Guwahati, India
| | - Muktanjalee Deka
- 4 Department of Pathology, Gauhati Medical College and Hospital, Guwahati, India
| | - Manab Deka
- 1 Department of Bioengineering and Technology, Laboratory of Molecular Virology and Oncology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, India
| | - Bhabadev Goswami
- 2 Department of Gastroenterology, Gauhati Medical College and Hospital, Guwahati, India
| | | | - Subhash Medhi
- 1 Department of Bioengineering and Technology, Laboratory of Molecular Virology and Oncology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, India
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11
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Sarkar DK. Male germline transmits fetal alcohol epigenetic marks for multiple generations: a review. Addict Biol 2016; 21:23-34. [PMID: 25581210 DOI: 10.1111/adb.12186] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Alcohol exposure during fetal and early postnatal development can lead to an increased incidence of later life adult-onset diseases. Examples include central nervous system dysfunction, depression, anxiety, hyperactivity, and an inability to deal with stressful situations, increased infection and cancer. Direct effects of alcohol leading to developmental abnormalities often involve epigenetic modifications of genes that regulate cellular functions. Epigenetic marks carried over from the parents are known to undergo molecular programming events that happen early in embryonic development by a wave of DNA demethylation, which leaves the embryo with a fresh genomic composition. The proopiomelanocortin (Pomc) gene controls neuroendocrine-immune functions and is imprinted by fetal alcohol exposure. Recently, this gene has been shown to be hypermethylated through three generations. Additionally, the alcohol epigenetic marks on the Pomc gene are maintained in the male but not in the female germline during this transgenerational transmission. These data suggest that the male-specific chromosome might be involved in transmitting alcohol epigenetic marks through multiple generations.
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Affiliation(s)
- Dipak K. Sarkar
- Rutgers Endocrine Program; Department of Animal Sciences; Rutgers, The State University of New Jersey; Piscataway Township NJ USA
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12
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Larney C, Bailey TL, Koopman P. Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species. BMC DEVELOPMENTAL BIOLOGY 2015; 15:34. [PMID: 26444262 PMCID: PMC4595323 DOI: 10.1186/s12861-015-0085-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Sex determination in mammals requires expression of the Y-linked gene Sry in the bipotential genital ridges of the XY embryo. Even minor delay of the onset of Sry expression can result in XY sex reversal, highlighting the need for accurate gene regulation during sex determination. However, the location of critical regulatory elements remains unknown. Here, we analysed Sry flanking sequences across many species, using newly available genome sequences and computational tools, to better understand Sry's genomic context and to identify conserved regions predictive of functional roles. METHODS Flanking sequences from 17 species were analysed using both global and local sequence alignment methods. Multiple motif searches were employed to characterise common motifs in otherwise unconserved sequence. RESULTS We identified position-specific conservation of binding motifs for multiple transcription factor families, including GATA binding factors and Oct/Sox dimers. In contrast with the landscape of extremely low sequence conservation around the Sry coding region, our analysis highlighted a strongly conserved interval of ~106 bp within the Sry promoter (which we term the Sry Proximal Conserved Interval, SPCI). We further report that inverted repeats flanking murine Sry are much larger than previously recognised. CONCLUSIONS The unusually fast pace of sequence drift on the Y chromosome sharpens the likely functional significance of both the SPCI and the identified binding motifs, providing a basis for future studies of the role(s) of these elements in Sry regulation.
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Affiliation(s)
- Christian Larney
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Timothy L Bailey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Tachibana M. Epigenetics of sex determination in mammals. Reprod Med Biol 2015; 15:59-67. [PMID: 29259422 DOI: 10.1007/s12522-015-0223-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022] Open
Abstract
Epigenetics is the study of changes in gene function that cannot be explained by changes in DNA sequence. A mammalian body contains more than two hundred types of cells. Since all of them are derived from a single fertilized egg, their genotypes are identical. However, the gene expression patterns are different between the cell types, indicating that each cell type has unique own "epigenotype". Epigenetic gene regulation mechanisms essentially contribute to various processes of mammalian development. The essence of epigenetic regulation is the structural change of chromatin to modulate gene activity in a spatiotemporal manner. DNA methylation and histone modifications are the major epigenetic mechanisms. Sex determination is the process for gender establishment. There are two types of sex-determining mechanisms in animals, environmental sex determination (ESD) and genotypic sex determination (GSD). Recent studies have provided some evidence that epigenetic mechanisms play indispensable roles in ESD and GSD. Some fishes undergo ESD, in which DNA methylation is essentially involved. GSD is employed in therian mammals, where Sry (sex-determining region on the Y chromosome) triggers testis differentiation from undifferentiated gonads. Sry expression is tightly regulated in a spatiotemporal manner. A recent study demonstrated that histone modification is involved in Sry regulation. In this review, we discuss the role of epigenetic mechanisms for sex determination in mammals and other vertebrates.
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Affiliation(s)
- Makoto Tachibana
- Department of Enzyme Chemistry, Institute for Enzyme Research Tokushima University 18-15-3 Kuramoto-cho 770-8503 Tokushima Japan
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Fuso A, Ferraguti G, Scarpa S, Ferrer I, Lucarelli M. Disclosing bias in bisulfite assay: MethPrimers underestimate high DNA methylation. PLoS One 2015; 10:e0118318. [PMID: 25692551 PMCID: PMC4333220 DOI: 10.1371/journal.pone.0118318] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/14/2015] [Indexed: 01/18/2023] Open
Abstract
Discordant results obtained in bisulfite assays using MethPrimers (PCR primers designed using MethPrimer software or assuming that non-CpGs cytosines are non methylated) versus primers insensitive to cytosine methylation lead us to hypothesize a technical bias. We therefore used the two kinds of primers to study different experimental models and methylation statuses. We demonstrated that MethPrimers negatively select hypermethylated DNA sequences in the PCR step of the bisulfite assay, resulting in CpG methylation underestimation and non-CpG methylation masking, failing to evidence differential methylation statuses. We also describe the characteristics of “Methylation-Insensitive Primers” (MIPs), having degenerated bases (G/A) to cope with the uncertain C/U conversion. As CpG and non-CpG DNA methylation patterns are largely variable depending on the species, developmental stage, tissue and cell type, a variable extent of the bias is expected. The more the methylome is methylated, the greater is the extent of the bias, with a prevalent effect of non-CpG methylation. These findings suggest a revision of several DNA methylation patterns so far documented and also point out the necessity of applying unbiased analyses to the increasing number of epigenomic studies.
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Affiliation(s)
- Andrea Fuso
- Dept. of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research (CERC)/IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giampiero Ferraguti
- Dept. of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Sigfrido Scarpa
- Dept. of Surgery "P. Valdoni", Sapienza University of Rome, Rome, Italy
| | - Isidre Ferrer
- Institute of Neuropathology, IDIBELL-Bellvitge University Hospital and University of Barcelona, CIBERNED, L'Hospitalet de Llobregat, Spain
| | - Marco Lucarelli
- Dept. of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy; Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
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Bellizzi D, D'Aquila P, Scafone T, Giordano M, Riso V, Riccio A, Passarino G. The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern. DNA Res 2013; 20:537-47. [PMID: 23804556 PMCID: PMC3859322 DOI: 10.1093/dnares/dst029] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 05/30/2013] [Indexed: 11/23/2022] Open
Abstract
DNA methylation is a common epigenetic modification of the mammalian genome. Conflicting data regarding the possible presence of methylated cytosines within mitochondrial DNA (mtDNA) have been reported. To clarify this point, we analysed the methylation status of mtDNA control region (D-loop) on human and murine DNA samples from blood and cultured cells by bisulphite sequencing and methylated/hydroxymethylated DNA immunoprecipitation assays. We found methylated and hydroxymethylated cytosines in the L-strand of all samples analysed. MtDNA methylation particularly occurs within non-C-phosphate-G (non-CpG) nucleotides, mainly in the promoter region of the heavy strand and in conserved sequence blocks, suggesting its involvement in regulating mtDNA replication and/or transcription. We observed DNA methyltransferases within the mitochondria, but the inactivation of Dnmt1, Dnmt3a, and Dnmt3b in mouse embryonic stem (ES) cells results in a reduction of the CpG methylation, while the non-CpG methylation shows to be not affected. This suggests that D-loop epigenetic modification is only partially established by these enzymes. Our data show that DNA methylation occurs in the mtDNA control region of mammals, not only at symmetrical CpG dinucleotides, typical of nuclear genome, but in a peculiar non-CpG pattern previously reported for plants and fungi. The molecular mechanisms responsible for this pattern remain an open question.
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Affiliation(s)
- Dina Bellizzi
- Department of Cell Biology, University of Calabria, Rende 87036, Italy
| | - Patrizia D'Aquila
- Department of Cell Biology, University of Calabria, Rende 87036, Italy
| | - Teresa Scafone
- Department of Cell Biology, University of Calabria, Rende 87036, Italy
| | - Marco Giordano
- Department of Cell Biology, University of Calabria, Rende 87036, Italy
| | - Vincenzo Riso
- Institute of Genetics and Biophysics—Adriano Buzzati Traverso, Napoli 80131, Italy
| | - Andrea Riccio
- Institute of Genetics and Biophysics—Adriano Buzzati Traverso, Napoli 80131, Italy
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Truong M, Yang B, Wagner J, Desotelle J, Jarrard DF. Analysis of promoter non-CG methylation in prostate cancer. Epigenomics 2013; 5:65-71. [PMID: 23414321 DOI: 10.2217/epi.12.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In vertebrates, DNA methylation occurs primarily at CG dinucleotides but recently, non-CG methylation has been found at appreciable levels in embryonic stem cells. MATERIALS & METHODS To assess non-CG methylation in cancer, we compared the extent of non-CG methylation at several biologically important CG islands in prostate cancer and normal cell lines. An assessment of the promoter CG islands EVX1 and FILIP1L demonstrates a fourfold higher rate of non-CG methylation at EVX1 compared with FILIP1L across all cell lines. These loci are densely methylated at CG sites in cancer. RESULTS No significant difference in non-CG methylation was demonstrated between cancer and normal. Treatment of cancer cell lines with 5-azacytidine significantly reduced methylation within EVX1 at CG and CC sites, preferentially. CONCLUSION Non-CG methylation does not correlate with CG methylation at hypermethylated promoter regions in cancer. Furthermore, global inhibition of DNA methyltransferases does not affect all methylated cytosines uniformly.
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Affiliation(s)
- Matthew Truong
- Department of Urology, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
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D'Aquila P, Rose G, Bellizzi D, Passarino G. Epigenetics and aging. Maturitas 2012; 74:130-6. [PMID: 23245587 DOI: 10.1016/j.maturitas.2012.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 11/11/2012] [Indexed: 01/06/2023]
Abstract
Over the past two decades, a growing interest on the research of the biological basis of human longevity has emerged, in order to clarify the intricacy of biological and environmental factors affecting (together with stochastic factors) the quality and the rate of human aging. These researches have outlined a complex scenario in which epigenetic marks, such as DNA methylation and numerous histone modifications, are emerging as important factors of the overall variation in life expectancy. In fact, epigenetic marks, that are responsible of the establishment of specific expression programs and of genome stability, represent a "drawbridge" across genetic, environmental and stochastic factors. In this review we provide an overview on the current knowledge and the general features of the epigenetic modifications characterizing the aging process.
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Affiliation(s)
- Patrizia D'Aquila
- Department of Cell Biology, University of Calabria, 87036 Rende, Italy
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Pulverer W, Wielscher M, Panzer-Grümayer R, Plessl T, Kriegner A, Vierlinger K, Weinhäusel A. The stem cell signature of CHH/CHG methylation is not present in 271 cancer associated 5'UTR gene regions. Biochimie 2012; 94:2345-52. [PMID: 22750649 DOI: 10.1016/j.biochi.2012.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/21/2012] [Indexed: 01/27/2023]
Abstract
UNLABELLED Non-CpG methylation is frequently present in stem cell DNA. We investigated the value of this epigenetic modification in cancerous DNA in order to establish the implications of CHH/CHG methylation for biomarker development. Therefore we used the restriction enzymes BstNI and PspGI within a combined multiplex PCR and targeted microarray approach for the elucidation of non-CpG (CCWGG) methylation. Targeting 544 CCWGG sites in 271 5' gene regions, the CHH/CHG methylation status of the MCF7 breast cancer cell line and blood from healthy volunteers and childhood ALL was analyzed. Statistical analysis of microarray data and subsequent SYBR green based qPCR on DNA digests was applied to confirm the results from the microarray screen. RESULT/CONCLUSION The microarray experiments identified for the MCF7 cell line the genes MSH2 (p < 0.001), EREG (p < 0.001) and HSPA2 (p = 0.029) with CHH/CHG methylation, and in childhood ALL the genes HIST1H2AG (p = 0.003), PGF (p = 0.02), CPEB4 (p = 0.039) and TJP2 (p = 0.04). Validation using qPCR upon restriction digestion did not confirm the presence of CHH/CHG methylation in MCF7 DNA. In ALL samples only TJP2 was found harboring CHH/CHG methylation (p = 0.02). However, applying Bonferroni-correction for multiple testing that qPCR-result was not rated as statistically significant anymore. We concluded that non-CpG methylation in 544 CCWGG sites analyzed did not change in tumor cells. Thus any change of the CHH/CHG methylation pattern is a minor event in tumorigenesis, even if the stem cell markers OCT4, NANOG, STELLAR and GDF3 are expressed like in the MCF7 breast cancer cell line.
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Affiliation(s)
- Walter Pulverer
- AIT - Austrian Institute of Technology GmbH, Health & Environment Department, Molecular Diagnostics, Muthgasse 11/2, A-1190 Vienna, Austria.
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