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Domrazek K, Jurka P. Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals. Animals (Basel) 2024; 14:1578. [PMID: 38891625 PMCID: PMC11171117 DOI: 10.3390/ani14111578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.
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Affiliation(s)
- Kinga Domrazek
- Institute of Veterinary Medicine, Warsaw University of Life Sciences—SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland;
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Petroff RL, Dolinoy DC, Wang K, Montrose L, Padmanabhan V, Peterson KE, Ruden DM, Sartor MA, Svoboda LK, Téllez-Rojo MM, Goodrich JM. Translational toxicoepigenetic Meta-Analyses identify homologous gene DNA methylation reprogramming following developmental phthalate and lead exposure in mouse and human offspring. ENVIRONMENT INTERNATIONAL 2024; 186:108575. [PMID: 38507935 PMCID: PMC11463831 DOI: 10.1016/j.envint.2024.108575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
Although toxicology uses animal models to represent real-world human health scenarios, a critical translational gap between laboratory-based studies and epidemiology remains. In this study, we aimed to understand the toxicoepigenetic effects on DNA methylation after developmental exposure to two common toxicants, the phthalate di(2-ethylhexyl) phthalate (DEHP) and the metal lead (Pb), using a translational paradigm that selected candidate genes from a mouse study and assessed them in four human birth cohorts. Data from mouse offspring developmentally exposed to DEHP, Pb, or control were used to identify genes with sex-specific sites with differential DNA methylation at postnatal day 21. Associations of human infant DNA methylation in homologous mouse genes with prenatal DEHP or Pb were examined with a meta-analysis. Differential methylation was observed on 6 cytosines (adjusted-p < 0.05) and 90 regions (adjusted-p < 0.001). This translational approach offers a unique method that can detect conserved epigenetic differences that are developmentally susceptible to environmental toxicants.
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Affiliation(s)
- Rebekah L Petroff
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Kai Wang
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Luke Montrose
- Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA; Obstetrics and Gynecology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Karen E Peterson
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Douglas M Ruden
- Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Maureen A Sartor
- Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Martha M Téllez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca, Mexico
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.
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3
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Petroff RL, Cavalcante RG, Colacino JA, Goodrich JM, Jones TR, Lalancette C, Morgan RK, Neier K, Perera BPU, Rygiel CA, Svoboda LK, Wang K, Sartor MA, Dolinoy DC. Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice. Front Cell Dev Biol 2023; 11:1198148. [PMID: 37384255 PMCID: PMC10294071 DOI: 10.3389/fcell.2023.1198148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. Methods: To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n = 5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. Results: DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Discussion: Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in adult DNA hydroxymethylation that was specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.
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Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Raymond G. Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Tamara R. Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Claudia Lalancette
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Rachel K. Morgan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Bambarendage P. U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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Jiang X, Yang Z, Wang S, Deng S. “Big Data” Approaches for Prevention of the Metabolic Syndrome. Front Genet 2022; 13:810152. [PMID: 35571045 PMCID: PMC9095427 DOI: 10.3389/fgene.2022.810152] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolic syndrome (MetS) is characterized by the concurrence of multiple metabolic disorders resulting in the increased risk of a variety of diseases related to disrupted metabolism homeostasis. The prevalence of MetS has reached a pandemic level worldwide. In recent years, extensive amount of data have been generated throughout the research targeted or related to the condition with techniques including high-throughput screening and artificial intelligence, and with these “big data”, the prevention of MetS could be pushed to an earlier stage with different data source, data mining tools and analytic tools at different levels. In this review we briefly summarize the recent advances in the study of “big data” applications in the three-level disease prevention for MetS, and illustrate how these technologies could contribute tobetter preventive strategies.
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Affiliation(s)
- Xinping Jiang
- Department of United Ultrasound, The First Hospital of Jilin University, Changchun, China
| | - Zhang Yang
- Department of Vascular Surgery, The First Hospital of Jilin University, Changchun, China
| | - Shuai Wang
- Department of Vascular Surgery, The First Hospital of Jilin University, Changchun, China
| | - Shuanglin Deng
- Department of Oncological Neurosurgery, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Shuanglin Deng,
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Pozo MR, Meredith GW, Entcheva E. Human iPSC-Cardiomyocytes as an Experimental Model to Study Epigenetic Modifiers of Electrophysiology. Cells 2022; 11:200. [PMID: 35053315 PMCID: PMC8774228 DOI: 10.3390/cells11020200] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/31/2021] [Accepted: 01/01/2022] [Indexed: 02/04/2023] Open
Abstract
The epigenetic landscape and the responses to pharmacological epigenetic regulators in each human are unique. Classes of epigenetic writers and erasers, such as histone acetyltransferases, HATs, and histone deacetylases, HDACs, control DNA acetylation/deacetylation and chromatin accessibility, thus exerting transcriptional control in a tissue- and person-specific manner. Rapid development of novel pharmacological agents in clinical testing-HDAC inhibitors (HDACi)-targets these master regulators as common means of therapeutic intervention in cancer and immune diseases. The action of these epigenetic modulators is much less explored for cardiac tissue, yet all new drugs need to be tested for cardiotoxicity. To advance our understanding of chromatin regulation in the heart, and specifically how modulation of DNA acetylation state may affect functional electrophysiological responses, human-induced pluripotent stem-cell-derived cardiomyocyte (hiPSC-CM) technology can be leveraged as a scalable, high-throughput platform with ability to provide patient-specific insights. This review covers relevant background on the known roles of HATs and HDACs in the heart, the current state of HDACi development, applications, and any adverse cardiac events; it also summarizes relevant differential gene expression data for the adult human heart vs. hiPSC-CMs along with initial transcriptional and functional results from using this new experimental platform to yield insights on epigenetic control of the heart. We focus on the multitude of methodologies and workflows needed to quantify responses to HDACis in hiPSC-CMs. This overview can help highlight the power and the limitations of hiPSC-CMs as a scalable experimental model in capturing epigenetic responses relevant to the human heart.
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Affiliation(s)
| | | | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC 20052, USA; (M.R.P.); (G.W.M.)
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Allen MC, Moog NK, Buss C, Yen E, Gustafsson HC, Sullivan EL, Graham AM. Co-occurrence of preconception maternal childhood adversity and opioid use during pregnancy: Implications for offspring brain development. Neurotoxicol Teratol 2021; 88:107033. [PMID: 34601061 PMCID: PMC8578395 DOI: 10.1016/j.ntt.2021.107033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/11/2022]
Abstract
Understanding of the effects of in utero opioid exposure on neurodevelopment is a priority given the recent dramatic increase in opioid use among pregnant individuals. However, opioid abuse does not occur in isolation-pregnant individuals abusing opioids often have a significant history of adverse experiences in childhood, among other co-occurring factors. Understanding the specific pathways in which these frequently co-occurring factors may interact and cumulatively influence offspring brain development in utero represents a priority for future research in this area. We highlight maternal history of childhood adversity (CA) as one such co-occurring factor that is more prevalent among individuals using opioids during pregnancy and which is increasingly shown to affect offspring neurodevelopment through mechanisms beginning in utero. Despite the high incidence of CA history in pregnant individuals using opioids, we understand very little about the effects of comorbid prenatal opioid exposure and maternal CA history on fetal brain development. Here, we first provide an overview of current knowledge regarding effects of opioid exposure and maternal CA on offspring neurodevelopment that may occur during gestation. We then outline potential mechanistic pathways through which these factors might have interactive and cumulative influences on offspring neurodevelopment as a foundation for future research in this area.
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Affiliation(s)
- Madeleine C Allen
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States
| | - Nora K Moog
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Psychology, Luisenstrasse 57, 10117 Berlin, Germany
| | - Claudia Buss
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Psychology, Luisenstrasse 57, 10117 Berlin, Germany; Development, Health and Disease Research Program, University of California, Irvine, 837 Health Sciences Drive, Irvine, California 92697, United States
| | - Elizabeth Yen
- Department of Pediatrics, Tufts Medical Center, Boston, MA 02111, United States
| | - Hanna C Gustafsson
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States
| | - Elinor L Sullivan
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States; Division of Neuroscience, Oregon National Primate Research Center, 505 NW 185(th) Ave., Beaverton, OR 97006, United States; Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States
| | - Alice M Graham
- Department of Psychiatry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States.
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Salas LA, Peres LC, Thayer ZM, Smith RWA, Guo Y, Chung W, Si J, Liang L. A transdisciplinary approach to understand the epigenetic basis of race/ethnicity health disparities. Epigenomics 2021; 13:1761-1770. [PMID: 33719520 PMCID: PMC8579937 DOI: 10.2217/epi-2020-0080] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/07/2020] [Indexed: 11/21/2022] Open
Abstract
Health disparities correspond to differences in disease burden and mortality among socially defined population groups. Such disparities may emerge according to race/ethnicity, socioeconomic status and a variety of other social contexts, and are documented for a wide range of diseases. Here, we provide a transdisciplinary perspective on the contribution of epigenetics to the understanding of health disparities, with a special emphasis on disparities across socially defined racial/ethnic groups. Scientists in the fields of biological anthropology, bioinformatics and molecular epidemiology provide a summary of theoretical, statistical and practical considerations for conducting epigenetic health disparities research, and provide examples of successful applications from cancer research using this approach.
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Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA
| | - Lauren C Peres
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Zaneta M Thayer
- Department of Anthropology, Dartmouth College, Hanover, NH 03755, USA
| | - Rick WA Smith
- Department of Anthropology, Dartmouth College, Hanover, NH 03755, USA
- The William H. Neukom Institute for Computational Science, Dartmouth College, Hanover, NH 03755, USA
| | | | - Wonil Chung
- Department of Statistics & Actuarial Science, Soongsil University, Seoul, 06478, Korea
- Program in Genetic Epidemiology & Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jiahui Si
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics & Epidemiology, Peking University School of Public Health, Beijing, 100191, China
| | - Liming Liang
- Program in Genetic Epidemiology & Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Chevin LM, Leung C, Le Rouzic A, Uller T. Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map. Genetica 2021; 150:209-221. [PMID: 34617196 DOI: 10.1007/s10709-021-00135-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.
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Affiliation(s)
- Luis-Miguel Chevin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Christelle Leung
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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Lin B, Hui J, Mao H. Nanopore Technology and Its Applications in Gene Sequencing. BIOSENSORS-BASEL 2021; 11:bios11070214. [PMID: 34208844 PMCID: PMC8301755 DOI: 10.3390/bios11070214] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 12/14/2022]
Abstract
In recent years, nanopore technology has become increasingly important in the field of life science and biomedical research. By embedding a nano-scale hole in a thin membrane and measuring the electrochemical signal, nanopore technology can be used to investigate the nucleic acids and other biomacromolecules. One of the most successful applications of nanopore technology, the Oxford Nanopore Technology, marks the beginning of the fourth generation of gene sequencing technology. In this review, the operational principle and the technology for signal processing of the nanopore gene sequencing are documented. Moreover, this review focuses on the applications using nanopore gene sequencing technology, including the diagnosis of cancer, detection of viruses and other microbes, and the assembly of genomes. These applications show that nanopore technology is promising in the field of biological and biomedical sensing.
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Affiliation(s)
- Bo Lin
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; (B.L.); (J.H.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianan Hui
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; (B.L.); (J.H.)
| | - Hongju Mao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China; (B.L.); (J.H.)
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-21-62511070-8707
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Chenarani N, Emamjomeh A, Allahverdi A, Mirmostafa S, Afsharinia MH, Zahiri J. Bioinformatic tools for DNA methylation and histone modification: A survey. Genomics 2021; 113:1098-1113. [PMID: 33677056 DOI: 10.1016/j.ygeno.2021.03.004] [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: 05/22/2020] [Revised: 10/10/2020] [Accepted: 03/02/2021] [Indexed: 01/19/2023]
Abstract
Epigenetic inheritance occurs due to different mechanisms such as chromatin and histone modifications, DNA methylation and processes mediated by non-coding RNAs. It leads to changes in gene expressions and the emergence of new traits in different organisms in many diseases such as cancer. Recent advances in experimental methods led to the identification of epigenetic target sites in various organisms. Computational approaches have enabled us to analyze mass data produced by these methods. Next-generation sequencing (NGS) methods have been broadly used to identify these target sites and their patterns. By using these patterns, the emergence of diseases could be prognosticated. In this study, target site prediction tools for two major epigenetic mechanisms comprising histone modification and DNA methylation are reviewed. Publicly accessible databases are reviewed as well. Some suggestions regarding the state-of-the-art methods and databases have been made, including examining patterns of epigenetic changes that are important in epigenotypes detection.
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Affiliation(s)
- Nasibeh Chenarani
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran; Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Bioinformatics, Faculty of Basic Sciences, University of Zabol, Zabol, Iran.
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - SeyedAli Mirmostafa
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Hossein Afsharinia
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran; Department of Neuroscience, University of California, San Diego, USA.
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11
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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12
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Fetal programming in dairy cows: Effect of heat stress on progeny fertility and associations with the hypothalamic-pituitary-adrenal axis functions. Anim Reprod Sci 2020; 216:106348. [PMID: 32414470 DOI: 10.1016/j.anireprosci.2020.106348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 01/15/2023]
Abstract
Ambient temperatures that result in body temperatures beyond those of the thermo-neutral zone for dairy cattle can lead to reduced reproductive efficiencies that have negative effects on economic and productive efficiencies of dairy farms. In addition, in pregnant cows, ambient temperature-induced heat stress leads to modifications in the epigenome of the developing embryo, which, in turn, could lead to phenotypic variations in the sexually mature animal and its offspring. In the mammalian response to stress, adrenocorticotropic hormone stimulates the synthesis and secretion of glucocorticoids, which may have detrimental effects on the hypothalamic-pituitary-gonadal axis and the female estrous cycle. The aim of this review is to describe the effects of ambient heat stress on the reproductive system of dairy cattle and its potential trans-generational effects. There are many heat stress occurrences in dairy cattle during a large portion of the year in many countries and there is an increase in incidence with the onset of global warming. These heat stress conditions make it possible that the embryo/fetus of cows may be affected when heat stress conditions prevail in ways that there is impaired fertility of the sexually mature cows that develop from these embryos/fetuses. This is the outcome because of molecular changes in ovarian glucocorticoid response caused by epigenetic modifications established during fetal development.
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Angers B, Perez M, Menicucci T, Leung C. Sources of epigenetic variation and their applications in natural populations. Evol Appl 2020; 13:1262-1278. [PMID: 32684958 PMCID: PMC7359850 DOI: 10.1111/eva.12946] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/13/2022] Open
Abstract
Epigenetic processes manage gene expression and products in a real‐time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet‐hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.
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Affiliation(s)
- Bernard Angers
- Department of biological sciences Université de Montréal Montreal Quebec Canada
| | - Maëva Perez
- Department of biological sciences Université de Montréal Montreal Quebec Canada
| | - Tatiana Menicucci
- Department of biological sciences Université de Montréal Montreal Quebec Canada
| | - Christelle Leung
- CEFE CNRS Université de Montpellier Université Paul Valéry Montpellier 3 EPHE Montpellier France
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Bhat RS, Rockey J, Shirasawa K, Tilak IS, Brijesh Patil MP, Reddy Lachagari VB. DNA methylation and expression analyses reveal epialleles for the foliar disease resistance genes in peanut (Arachis hypogaea L.). BMC Res Notes 2020; 13:20. [PMID: 31910887 PMCID: PMC6947992 DOI: 10.1186/s13104-020-4883-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 01/02/2020] [Indexed: 01/02/2023] Open
Abstract
Objective Low DNA sequence polymorphism despite enormous phenotypic variations in peanut indicates the possible role of epigenetic variations. An attempt was made to analyze genome-wide DNA methylation pattern and its influence on gene expression across 11 diverse genotypes of peanut. Results The genotypes were subjected to bisulfite sequencing after 21 days of sowing (DAS). CHG regions showed the highest (30,537,376) DNA methylation followed by CpG (30,356,066) and CHH (15,993,361) across 11 genotypes. The B sub-genome exhibited higher DNA methylation sites (46,294,063) than the A sub-genome (30,415,166). Overall, the DNA methylation was more frequent in inter-genic regions than in the genic regions. The genes showing altered methylation and expression between the parent (TMV 2) and its EMS-derived mutant (TMV 2-NLM) were identified. Foliar disease resistant genotypes showed significant differential DNA methylation at 766 sites corresponding to 25 genes. Of them, two genes (Arahy.1XYC2X on chromosome 01 and Arahy.00Z2SH on chromosome 17) coding for senescence-associated protein showed differential expression with resistant genotypes recording higher fragments per kilobase of transcript per million mapped reads (FPKM) at their epialleles. Overall, the study indicated the variation in the DNA methylation pattern among the diverse genotypes of peanut and its influence of gene expression.
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Affiliation(s)
- R S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005, India.
| | - J Rockey
- AgriGenome Labs Pvt. Ltd., Kochi, Kerala, 682 042, India
| | - Kenta Shirasawa
- Department of Frontier Research, Kazusa DNA Research Institute, Chiba, 292-0818, Japan
| | - I S Tilak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005, India
| | - M P Brijesh Patil
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005, India
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15
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Payá-Milans M, Poza-Viejo L, Martín-Uriz PS, Lara-Astiaso D, Wilkinson MD, Crevillén P. Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. Gigascience 2019; 8:giz147. [PMID: 31800038 PMCID: PMC6892454 DOI: 10.1093/gigascience/giz147] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/24/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Genome-wide maps of histone modifications have been obtained for several plant species. However, most studies focus on model systems and do not enforce FAIR data management principles. Here we study the H3K27me3 epigenome and associated transcriptome of Brassica rapa, an important vegetable cultivated worldwide. FINDINGS We performed H3K27me3 chromatin immunoprecipitation followed by high-throughput sequencing and transcriptomic analysis by 3'-end RNA sequencing from B. rapa leaves and inflorescences. To analyze these data we developed a Reproducible Epigenomic Analysis pipeline using Galaxy and Jupyter, packaged into Docker images to facilitate transparency and reuse. We found that H3K27me3 covers roughly one-third of all B. rapa protein-coding genes and its presence correlates with low transcript levels. The comparative analysis between leaves and inflorescences suggested that the expression of various floral regulatory genes during development depends on H3K27me3. To demonstrate the importance of H3K27me3 for B. rapa development, we characterized a mutant line deficient in the H3K27 methyltransferase activity. We found that braA.clf mutant plants presented pleiotropic alterations, e.g., curly leaves due to increased expression and reduced H3K27me3 levels at AGAMOUS-like loci. CONCLUSIONS We characterized the epigenetic mark H3K27me3 at genome-wide levels and provide genetic evidence for its relevance in B. rapa development. Our work reveals the epigenomic landscape of H3K27me3 in B. rapa and provides novel genomics datasets and bioinformatics analytical resources. We anticipate that this work will lead the way to further epigenomic studies in the complex genome of Brassica crops.
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Affiliation(s)
- Miriam Payá-Milans
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Laura Poza-Viejo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Patxi San Martín-Uriz
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - David Lara-Astiaso
- Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Avenida Pío XII 55, 31008, Pamplona, Spain
| | - Mark D Wilkinson
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón (Madrid), Spain
| | - Pedro Crevillén
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223, Pozuelo de Alarcón (Madrid), Spain
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16
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Iliopoulos I, Ananiadou S, Danchin A, Ioannidis JPA, Katsikis PD, Ouzounis CA, Promponas VJ. Hypothesis, analysis and synthesis, it's all Greek to me. eLife 2019; 8:e43514. [PMID: 30782313 PMCID: PMC6382348 DOI: 10.7554/elife.43514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
The linguistic foundations of science and technology include many terms that have been borrowed from ancient languages. In the case of terms with origins in the Greek language, the modern meaning can often differ significantly from the original one. Here we use the PubMed database to demonstrate the prevalence of words of Greek origin in the language of modern science, and call for scientists to exercise care when coining new terms.
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Affiliation(s)
- Ioannis Iliopoulos
- Division of Basic Sciences, School of MedicineUniversity of CreteHeraklionGreece
| | - Sophia Ananiadou
- School of Computer ScienceUniversity of ManchesterManchesterUnited Kingdom
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié-SalpêtrièreParisFrance
- School of Biomedical Sciences, Li Ka Shing Faculty of MedicineUniversity of Hong KongSAR Hong KongChina
| | - John PA Ioannidis
- Meta-Research Innovation Center at StanfordStanford UniversityStanfordUnited States
| | - Peter D Katsikis
- Department of ImmunologyErasmus University Medical CenterRotterdamNetherlands
| | - Christos A Ouzounis
- Biological Computation & Process Lab, Chemical Process & Energy Resources InstituteCentre for Research & Technology HellasThessalonicaGreece
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological SciencesUniversity of CyprusNicosiaCyprus
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17
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Li Q, Cassese A, Guindani M, Vannucci M. Bayesian negative binomial mixture regression models for the analysis of sequence count and methylation data. Biometrics 2018; 75:183-192. [DOI: 10.1111/biom.12962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 05/01/2018] [Accepted: 07/01/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Qiwei Li
- Department of Clinical SciencesUniversity of Texas Southwestern Medical Center Dallas Texas U.S.A
| | - Alberto Cassese
- Department of Methodology and StatisticsFaculty of Psychology and NeuroscienceMaastricht University Maastricht, The Netherlands
| | - Michele Guindani
- Department of StatisticsUniversity of California Irvine California U.S.A
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18
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Shim J, Banerjee S, Qiu H, Smithe KKH, Estrada D, Bello J, Pop E, Schulten K, Bashir R. Detection of methylation on dsDNA using nanopores in a MoS 2 membrane. NANOSCALE 2017; 9:14836-14845. [PMID: 28795735 PMCID: PMC5890527 DOI: 10.1039/c7nr03092d] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Methylation at the 5-carbon position of the cytosine nucleotide base in DNA has been shown to be a reliable diagnostic biomarker for carcinogenesis. Early detection of methylation and intervention could drastically increase the effectiveness of therapy and reduce the cancer mortality rate. Current methods for detecting methylation involve bisulfite genomic sequencing, which are cumbersome and demand a large sample size of bodily fluids to yield accurate results. Hence, more efficient and cost effective methods are desired. Based on our previous work, we present a novel nanopore-based assay using a nanopore in a MoS2 membrane, and the methyl-binding protein (MBP), MBD1x, to detect methylation on dsDNA. We show that the dsDNA translocation was effectively slowed down using an asymmetric concentration of buffer and explore the possibility of profiling the position of methylcytosines on the DNA strands as they translocate through the 2D membrane. Our findings advance us one step closer towards the possible use of nanopore sensing technology in medical applications such as cancer detection.
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Affiliation(s)
- Jiwook Shim
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028
- Corresponding Authors: Jiwook Shim, Ph.D., Department of Biomedical Engineering, Henry M. Rowan College of Engineering, owan University, 201 Mullica Hill Road, Glassboro, NJ 08028, U.S.A., , Phone: 856-256-5393, Rashid Bashir, Ph.D., Department of Bioengineering, University of Illinois at Urbana – Champaign, 1270 Digital Computer Laboratory, Urbana, IL 61801, , Phone: 217-333-1867
| | - Shouvik Banerjee
- Department of Material Science and Engineering, University of Illinois at Urbana – Champaign, Urbana, IL 61801
| | - Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, 210016, China
| | - Kirby K. H. Smithe
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305
| | - David Estrada
- Department of Material Science and Engineering, Boise State University, Boise, ID 83725
| | - Julian Bello
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028
| | - Eric Pop
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana – Champaign, Urbana, IL 61801
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana – Champaign, Urbana, IL 61801
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana – Champaign, Urbana, IL 61801
- Carle Illinois College of Medicine, University of Illinois at Urbana – Champaign, Urbana, IL 61801
- Corresponding Authors: Jiwook Shim, Ph.D., Department of Biomedical Engineering, Henry M. Rowan College of Engineering, owan University, 201 Mullica Hill Road, Glassboro, NJ 08028, U.S.A., , Phone: 856-256-5393, Rashid Bashir, Ph.D., Department of Bioengineering, University of Illinois at Urbana – Champaign, 1270 Digital Computer Laboratory, Urbana, IL 61801, , Phone: 217-333-1867
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19
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Epigenetic mechanisms of alcoholism and stress-related disorders. Alcohol 2017; 60:7-18. [PMID: 28477725 DOI: 10.1016/j.alcohol.2017.01.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/30/2016] [Accepted: 01/03/2017] [Indexed: 12/20/2022]
Abstract
Stress-related disorders, such as anxiety, early life stress, and posttraumatic stress disorder appear to be important factors in promoting alcoholism, as alcohol consumption can temporarily attenuate the negative affective symptoms of these disorders. Several molecules involved in signaling pathways may contribute to the neuroadaptation induced during alcohol dependence and stress disorders, and among these, brain-derived neurotrophic factor (BDNF), corticotropin releasing factor (CRF), neuropeptide Y (NPY) and opioid peptides (i.e., nociceptin and dynorphin) are involved in the interaction of stress and alcohol. In fact, alterations in the expression and function of these molecules have been associated with the pathophysiology of stress-related disorders and alcoholism. In recent years, various studies have focused on the epigenetic mechanisms that regulate chromatin architecture, thereby modifying gene expression. Interestingly, epigenetic modifications in specific brain regions have been shown to be associated with the neurobiology of psychiatric disorders, including alcoholism and stress. In particular, the enzymes responsible for chromatin remodeling (i.e., histone deacetylases and methyltransferases, DNA methyltransferases) have been identified as common molecular mechanisms for the interaction of stress and alcohol and have become promising therapeutic targets to treat or prevent alcoholism and associated emotional disorders.
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Abstract
Liver fibrosis arises because prolonged injury combined with excessive scar deposition within hepatic parenchyma arising from overactive wound healing response mediated by activated myofibroblasts. Fibrosis is the common end point for any type of chronic liver injury including alcoholic liver disease, nonalcoholic fatty liver disease, viral hepatitis, and cholestatic liver diseases. Although genetic influences are important, it is epigenetic mechanisms that have been shown to orchestrate many aspects of fibrogenesis in the liver. New discoveries in the field are leading toward the development of epigenetic biomarkers and targeted therapies. This review considers epigenetic mechanisms as well as recent advances in epigenetic programming in the context of hepatic fibrosis.
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Key Words
- CLD, chronic liver disease
- Chronic Liver Disease
- CpG, cytosine-phospho-guanine
- DNA Methylation
- DNMT, DNA methyltransferase
- Epigenetics
- HDAC, histone deacetylase
- HSC, hepatic stellate cell
- Histone Modifications
- Liver Fibrosis
- NAFLD, nonalcoholic fatty liver disease
- PPAR, peroxisome proliferator activated receptor
- TET, Ten Eleven Translocation
- miRNA, microRNA
- ncRNA, non-coding RNA
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Affiliation(s)
| | - Jelena Mann
- Correspondence Address correspondence to: Jelena Mann, PhD, Institute of Cellular Medicine, Faculty of Medical Sciences, 4th Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH United Kingdom. fax: +44-191-208-0723.Institute of Cellular MedicineFaculty of Medical Sciences4th FloorWilliam Leech BuildingNewcastle UniversityFramlington PlaceNewcastle upon TyneNE2 4HH United Kingdom
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21
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DNA methylation-based variation between human populations. Mol Genet Genomics 2016; 292:5-35. [PMID: 27815639 DOI: 10.1007/s00438-016-1264-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022]
Abstract
Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.
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22
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Cao YY, Qu YJ, He SX, Li Y, Bai JL, Jin YW, Wang H, Song F. Association between SMN2 methylation and disease severity in Chinese children with spinal muscular atrophy. J Zhejiang Univ Sci B 2016; 17:76-82. [PMID: 26739529 DOI: 10.1631/jzus.b1500072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The homozygous loss of the survival motor neuron 1 (SMN1) gene is the primary cause of spinal muscular atrophy (SMA), a neuromuscular degenerative disease. A genetically similar gene, SMN2, which is not functionally equivalent in all SMA patients, modifies the clinical SMA phenotypes. We analyzed the methylation levels of 4 CpG islands (CGIs) in SMN2 in 35 Chinese children with SMA by MassARRAY. We found that three CpG units located in CGI 1 (nucleotides (nt) -871, -735) and CGI 4 (nt +999) are significantly hypomethylated in SMA type III compared with type I or II children after receiving Bonferroni correction. In addition to the differentially methylated CpG unit of nt -871, the methylation level of the nt -290/-288/-285 unit was negatively correlated with the expression of SMN2 full-length transcripts (SMN2-fl). In addition, the methylation level at nt +938 was inversely proportional to the ratio of SMN2-fl and lacking exon 7 transcripts (SMN2-Δ7, fl/Δ7), and was not associated with the SMN2 transcript levels. Thus, we can conclude that SMN2 methylation may regulate the SMA disease phenotype by modulating its transcription.
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Affiliation(s)
- Yan-yan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yu-jin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Sheng-xi He
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yan Li
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jin-Ll Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yu-wei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
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23
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Exploring genetic moderators and epigenetic mediators of contextual and family effects: From Gene × Environment to epigenetics. Dev Psychopathol 2016; 28:1333-1346. [PMID: 27692009 DOI: 10.1017/s0954579416000882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the current manuscript, we provide an overview of a research program at the University of Georgia's Center for Family Research designed to expand upon rapid and ongoing developments in the fields of genetics and epigenetics. By placing those developments in the context of translational research on family and community determinants of health and well-being among rural African Americans, we hope to identify novel, modifiable environments and biological processes. In the first section of the article, we review our earlier work on genotypic variation effects on the association between family context and mental and physical health outcomes as well as differential responses to family-based intervention. We then transition to discuss our more recent research on the association of family and community environments with epigenetic processes. In this second section of the article, we begin by briefly reviewing terminology and basic considerations before describing evidence that early environments may influence epigenetic motifs that potentially serve as mediators of long-term effects of early family and community environments on longer term health outcomes. We also provide evidence that genotype may sometimes influence epigenetic outcomes. Finally, we describe our recent efforts to use genome-wide characterization of epigenetic patterns to better understand the biological impact of protective parenting on long-term shifts in inflammatory processes and its potential implications for young adult health. As will be clear, research on epigenetics as a mediator of the connections between family/community processes and a range of health outcomes is still in its infancy, but the potential to develop important insights regarding mechanisms linking modifiable environments to biological processes and long-term health outcomes already is coming into view.
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24
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Shim S, Shim J, Taylor WR, Kosari F, Vasmatzis G, Ahlquist DA, Bashir R. Magnetophoretic-based microfluidic device for DNA Concentration. Biomed Microdevices 2016; 18:28. [DOI: 10.1007/s10544-016-0051-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Ouni M, Belot MP, Castell AL, Fradin D, Bougnères P. The P2 promoter of the IGF1 gene is a major epigenetic locus for GH responsiveness. THE PHARMACOGENOMICS JOURNAL 2016; 16:102-6. [PMID: 25869012 PMCID: PMC4746489 DOI: 10.1038/tpj.2015.26] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/02/2015] [Accepted: 02/09/2015] [Indexed: 02/02/2023]
Abstract
Short children using growth hormone (GH) to accelerate their growth respond to this treatment with a variable efficacy. The causes of this individual variability are multifactorial and could involve epigenetics. Quantifying the impact of epigenetic variation on response to treatments is an emerging challenge. Here we show that methylation of a cluster of CGs located within the P2 promoter of the insulin-like growth factor 1 (IGF1) gene, notably CG-137, is inversely closely correlated with the response of growth and circulating IGF1 to GH administration. For example, variability in CG-137 methylation contributes 25% to variance of growth response to GH. Methylation of CGs in the P2 promoter is negatively associated with the increased transcriptional activity of P2 promoter in patients' mononuclear blood cells following GH administration. Our observation indicates that epigenetics is a major determinant of GH signaling (physiology) and of individual responsiveness to GH treatment (pharmacoepigenetics).
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Affiliation(s)
- M Ouni
- Institut National de la Santé et de la Recherche Médicale U986, Paris Sud University, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - M P Belot
- Institut National de la Santé et de la Recherche Médicale U986, Paris Sud University, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - A L Castell
- Department of Pediatric Endocrinology and Diabetes, Paris Sud University, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - D Fradin
- Institut National de la Santé et de la Recherche Médicale U986, Paris Sud University, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - P Bougnères
- Institut National de la Santé et de la Recherche Médicale U986, Paris Sud University, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Department of Pediatric Endocrinology and Diabetes, Paris Sud University, Bicêtre Hospital, Le Kremlin-Bicêtre, France
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26
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Ganie SA, Dey N, Mondal TK. Promoter methylation regulates the abundance of osa-miR393a in contrasting rice genotypes under salinity stress. Funct Integr Genomics 2015; 16:1-11. [PMID: 26319531 DOI: 10.1007/s10142-015-0460-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/28/2015] [Accepted: 08/02/2015] [Indexed: 01/03/2023]
Abstract
MicroRNAs (miRNAs) are important molecules that regulate gene expression under salinity stress. Despite their evolutionary conservation, these regulatory elements have been shown to behave differently in different plant species under a particular environmental stress. In this study, we investigated the behavior of salt responsive osa-miR393a and its target gene (TIR1, LOC_Os05g05800) in salt-tolerant (FL478) and salt-sensitive (IR29) rice genotypes. It was found that the mature and precursor sequences of osa-miR393a as well as its cleavage site in TIR1 were conserved among salt tolerant and sensitive genotypes. Promoters of different salt-responsive miRNAs were also found to be less variable between salt-tolerant and salt-susceptible genotypes. Analysis of gene expression, promoter methylation, and cis-element abundance showed that osa-miR393a behaves differently in FL478 and IR29. Salt stress altered the expression pattern of osa-miR393a-TIR1 module in a time-dependent manner in the roots and shoots of two genotypes. Promoter methylation of this regulatory module was also altered at different time points under salt stress. Expression analysis in two genotypes indicated the overall down-regulation of osa-miR393a and up-regulation of TIR1 in FL478 and their reciprocal regulation in IR29. The expression results were complemented by the differential promoter methylation and cis-element abundance of this regulatory module. Together, the results of transcript abundance and promoter methylation of osa-miR393a-TIR1 module signified the association between these two processes which is reported for the first time in plants to the best of our knowledge.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India
| | - Narottam Dey
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731 235, West Bengal, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, IARI Campus, New Delhi, 110012, India.
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Ouni M, Gunes Y, Belot MP, Castell AL, Fradin D, Bougnères P. The IGF1 P2 promoter is an epigenetic QTL for circulating IGF1 and human growth. Clin Epigenetics 2015; 7:22. [PMID: 25789079 PMCID: PMC4363053 DOI: 10.1186/s13148-015-0062-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/19/2015] [Indexed: 12/28/2022] Open
Abstract
Background Even if genetics play an important role, individual variation in stature remains unexplained at the molecular level. Indeed, genome-wide association study (GWAS) have revealed hundreds of variants that contribute to the variability of height but could explain only a limited part of it, and no single variant accounts for more than 0.3% of height variance. At the interface of genetics and environment, epigenetics contributes to phenotypic diversity. Quantifying the impact of epigenetic variation on quantitative traits, an emerging challenge in humans, has not been attempted for height. Since insulin-like growth factor 1 (IGF1) controls postnatal growth, we tested whether the CG methylation of the two promoters (P1 and P2) of the IGF1 gene is a potential epigenetic contributor to the individual variation in circulating IGF1 and stature in growing children. Results Child height was closely correlated with serum IGF1. The methylation of a cluster of six CGs located within the proximal part of the IGF1 P2 promoter showed a strong negative association with serum IGF1 and growth. The highest association was for CG-137 methylation, which contributed 13% to the variance of height and 10% to serum IGF1. CG methylation (studied in children undergoing surgery) was approximately 50% lower in liver and growth plates, indicating that the IGF1 promoters are tissue-differentially methylated regions (t-DMR). CG methylation was inversely correlated with the transcriptional activity of the P2 promoter in mononuclear blood cells and in transfection experiments, suggesting that the observed association of methylation with the studied traits reflects true biological causality. Conclusions Our observations introduce epigenetics among the individual determinants of child growth and serum IGF1. The P2 promoter of the IGF1 gene is the first epigenetic quantitative trait locus (QTLepi) reported in humans. The CG methylation of the P2 promoter takes place among the multifactorial factors explaining the variation in human stature. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0062-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meriem Ouni
- Institut National de la Santé et de la Recherche Médicale U986, Bicêtre Hospital, Paris Sud University, 80 rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France
| | - Yasemin Gunes
- Institut National de la Santé et de la Recherche Médicale U986, Bicêtre Hospital, Paris Sud University, 80 rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France
| | - Marie-Pierre Belot
- Institut National de la Santé et de la Recherche Médicale U986, Bicêtre Hospital, Paris Sud University, 80 rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France
| | - Anne-Laure Castell
- Department of Pediatric Endocrinology and Diabetes, I3E Pole, Bicêtre Hospital, Paris Sud University, rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France
| | - Delphine Fradin
- Institut National de la Santé et de la Recherche Médicale U986, Bicêtre Hospital, Paris Sud University, 80 rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France
| | - Pierre Bougnères
- Institut National de la Santé et de la Recherche Médicale U986, Bicêtre Hospital, Paris Sud University, 80 rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France ; Department of Pediatric Endocrinology and Diabetes, I3E Pole, Bicêtre Hospital, Paris Sud University, rue du Général Leclerc Le Kremlin-Bicêtre, Paris, 94276 France
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Shim J, Kim Y, Humphreys GI, Nardulli AM, Kosari F, Vasmatzis G, Taylor WR, Ahlquist DA, Myong S, Bashir R. Nanopore-based assay for detection of methylation in double-stranded DNA fragments. ACS NANO 2015; 9:290-300. [PMID: 25569824 DOI: 10.1021/nn5045596] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
DNA methylation is an epigenetic modification of DNA in which methyl groups are added at the 5-carbon position of cytosine. Aberrant DNA methylation, which has been associated with carcinogenesis, can be assessed in various biological fluids and potentially can be used as markers for detection of cancer. Analytically sensitive and specific assays for methylation targeting low-abundance and fragmented DNA are needed for optimal clinical diagnosis and prognosis. We present a nanopore-based direct methylation detection assay that circumvents bisulfite conversion and polymerase chain reaction amplification. Building on our prior work, we used methyl-binding proteins (MBPs), which selectively label the methylated DNA. The nanopore-based assay selectively detects methylated DNA/MBP complexes through a 19 nm nanopore with significantly deeper and prolonged nanopore ionic current blocking, while unmethylated DNA molecules were not detectable due to their smaller diameter. Discrimination of hypermethylated and unmethylated DNA on 90, 60, and 30 bp DNA fragments was demonstrated using sub-10 nm nanopores. Hypermethylated DNA fragments fully bound with MBPs are differentiated from unmethylated DNA at 2.1- to 6.5-fold current blockades and 4.5- to 23.3-fold transport durations. Furthermore, these nanopore assays can detect the CpG dyad in DNA fragments and could someday profile the position of methylated CpG sites on DNA fragments.
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Affiliation(s)
- Jiwook Shim
- Department of Bioengineering, ‡Micro and Nanotechnology Laboratory, and §Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign Urbana, Illinois 61801, United States
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Kyzar EJ, Pandey SC. Molecular mechanisms of synaptic remodeling in alcoholism. Neurosci Lett 2015; 601:11-9. [PMID: 25623036 DOI: 10.1016/j.neulet.2015.01.051] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 01/21/2023]
Abstract
Alcohol use and alcohol addiction represent dysfunctional brain circuits resulting from neuroadaptive changes during protracted alcohol exposure and its withdrawal. Alcohol exerts a potent effect on synaptic plasticity and dendritic spine formation in specific brain regions, providing a neuroanatomical substrate for the pathophysiology of alcoholism. Epigenetics has recently emerged as a critical regulator of gene expression and synaptic plasticity-related events in the brain. Alcohol exposure and withdrawal induce changes in crucial epigenetic processes in the emotional brain circuitry (amygdala) that may be relevant to the negative affective state defined as the "dark side" of addiction. Here, we review the literature concerning synaptic plasticity and epigenetics, with a particular focus on molecular events related to dendritic remodeling during alcohol abuse and alcoholism. Targeting epigenetic processes that modulate synaptic plasticity may yield novel treatments for alcoholism.
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Affiliation(s)
- Evan J Kyzar
- Department of Psychiatry, University of Illinois at Chicago, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Subhash C Pandey
- Department of Psychiatry, University of Illinois at Chicago, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, USA.
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Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep 2014; 4:6546. [PMID: 25306978 PMCID: PMC4194443 DOI: 10.1038/srep06546] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/15/2014] [Indexed: 12/21/2022] Open
Abstract
DNA methylation is a key epigenetic modification in mammals and plays important roles in muscle development. We sampled longissimus dorsi muscle (LDM) from a well-known elite native breed of Chinese Qinchuan cattle living within the same environment but displaying distinct skeletal muscle at the fetal and adult stages. We generated and provided a genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA for fetal and adult muscle studies. Integration analysis revealed a total of 77 and 1,054 negatively correlated genes with methylation in the promoter and gene body regions, respectively, in both the fetal and adult bovine libraries. Furthermore, we identified expression patterns of high-read genes that exhibit a negative correlation between methylation and expression from nine different tissues at multiple developmental stages of bovine muscle-related tissue or organs. In addition, we validated the MeDIP-Seq results by bisulfite sequencing PCR (BSP) in some of the differentially methylated promoters. Together, these results provide valuable data for future biomedical research and genomic and epigenomic studies of bovine skeletal muscle that may help uncover the molecular basis underlying economically valuable traits in cattle. This comprehensive map also provides a solid basis for exploring the epigenetic mechanisms of muscle growth and development.
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Laffita-Mesa JM, Bauer P. Herencia epigenética (metilación del ácido desoxirribonucleico): contexto clínico en neurodegeneraciones y gen ATXN2. Med Clin (Barc) 2014; 143:360-5. [DOI: 10.1016/j.medcli.2013.11.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/31/2013] [Accepted: 11/14/2013] [Indexed: 12/19/2022]
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Dynamic Alu methylation during normal development, aging, and tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:784706. [PMID: 25243180 PMCID: PMC4163490 DOI: 10.1155/2014/784706] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 08/16/2014] [Indexed: 12/15/2022]
Abstract
DNA methylation primarily occurs on CpG dinucleotides and plays an important role in transcriptional regulations during tissue development and cell differentiation. Over 25% of CpG dinucleotides in the human genome reside within Alu elements, the most abundant human repeats. The methylation of Alu elements is an important mechanism to suppress Alu transcription and subsequent retrotransposition. Decades of studies revealed that Alu methylation is highly dynamic during early development and aging. Recently, many environmental factors were shown to have a great impact on Alu methylation. In addition, aberrant Alu methylation has been documented to be an early event in many tumors and Alu methylation levels have been associated with tumor aggressiveness. The assessment of the Alu methylation has become an important approach for early diagnosis and/or prognosis of cancer. This review focuses on the dynamic Alu methylation during development, aging, and tumor genesis. The cause and consequence of Alu methylation changes will be discussed.
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Safi SZ, Qvist R, Yan GOS, Ismail ISB. Differential expression and role of hyperglycemia induced oxidative stress in epigenetic regulation of β1, β2 and β3-adrenergic receptors in retinal endothelial cells. BMC Med Genomics 2014; 7:29. [PMID: 24885710 PMCID: PMC4050418 DOI: 10.1186/1755-8794-7-29] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 05/20/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Aberrant epigenetic profiles are concomitant with a spectrum of developmental defects and diseases. Role of methylation is an increasingly accepted factor in the pathophysiology of diabetes and its associated complications. This study aims to examine the correlation between oxidative stress and methylation of β1, β2 and β3-adrenergic receptors and to analyze the differential variability in the expression of these genes under hyperglycemic conditions. METHODS Human retinal endothelial cells were cultured in CSC complete medium in normal (5 mM) or high (25 mM) glucose to mimic a diabetic condition. Reverse transcription PCR and Western Blotting were performed to examine the expression of β1, β2 and β3-adrenergic receptors. For detections, immunocytochemistry was used. Bisulfite sequencing method was used for promoter methylation analysis. Apoptosis was determined by the terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) assay. Dichlorodihydrofluorescein diacetate (DCFH-DA) assay was used to measure reactive oxygen species (ROS) production in the cells. RESULTS β1 and β3-adrenergic receptors were expressed in retinal endothelial cells while β2-adrenergic receptor was not detectable both at protein and mRNA levels. Hyperglycemia had no significant effect on β1 and β2-adrenergic receptors methylation and expression however β3-adrenergic receptors showed a significantly higher expression (p < 0.05) and methylation (p < 0.01) in high and low glucose concentration respectively. Apoptosis and oxidative stress were inversely correlated with β3-adrenergic receptors methylation with no significant effect on β1 and β2-adrenergic receptors. β2-adrenergic receptor was hypermethylated with halted expression. CONCLUSION Our study demonstrates that β1 and β3-adrenergic receptors expressed in human retinal endothelial cells. Oxidative stress and apoptosis are inversely proportional to the extent of promoter methylation, suggesting that methylation loss might be due to oxidative stress-induced DNA damage.
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Affiliation(s)
- Sher Zaman Safi
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Rajes Qvist
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Gracie Ong Siok Yan
- Department of Anesthesiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ikram Shah Bin Ismail
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Liu Z, Jiang R, Yuan S, Wang N, Feng Y, Hu G, Zhu X, Huang K, Ma J, Xu G, Liu Q, Xue Z, Fan G. Integrated analysis of DNA methylation and RNA transcriptome during in vitro differentiation of human pluripotent stem cells into retinal pigment epithelial cells. PLoS One 2014; 9:e91416. [PMID: 24638073 PMCID: PMC3956675 DOI: 10.1371/journal.pone.0091416] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 02/12/2014] [Indexed: 12/22/2022] Open
Abstract
Using the paradigm of in vitro differentiation of hESCs/iPSCs into retinal pigment epithelial (RPE) cells, we have recently profiled mRNA and miRNA transcriptomes to define a set of RPE mRNA and miRNA signature genes implicated in directed RPE differentiation. In this study, in order to understand the role of DNA methylation in RPE differentiation, we profiled genome-scale DNA methylation patterns using the method of reduced representation bisulfite sequencing (RRBS). We found dynamic waves of de novo methylation and demethylation in four stages of RPE differentiation. Integrated analysis of DNA methylation and RPE transcriptomes revealed a reverse-correlation between levels of DNA methylation and expression of a subset of miRNA and mRNA genes that are important for RPE differentiation and function. Gene Ontology (GO) analysis suggested that genes undergoing dynamic methylation changes were related to RPE differentiation and maturation. We further compared methylation patterns among human ESC- and iPSC-derived RPE as well as primary fetal RPE (fRPE) cells, and discovered that specific DNA methylation pattern is useful to classify each of the three types of RPE cells. Our results demonstrate that DNA methylation may serve as biomarkers to characterize the cell differentiation process during the conversion of human pluripotent stem cells into functional RPE cells.
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Affiliation(s)
- Zhenshan Liu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Suzhou Institute of Tongji University, Suzhou, Jiangsu, China
| | - Rongfeng Jiang
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Songtao Yuan
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Na Wang
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yun Feng
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ganlu Hu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xianmin Zhu
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Kevin Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jieliang Ma
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Guotong Xu
- Tongji Eye Institute and Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China
| | - Qinghuai Liu
- Department of Ophthalmology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- * E-mail: (QL); (ZX); (GF)
| | - Zhigang Xue
- Department of Regenerative Medicine, Translational Center for Stem Cell Research, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Suzhou Institute of Tongji University, Suzhou, Jiangsu, China
- * E-mail: (QL); (ZX); (GF)
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Advanced Institute of Translational Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, China
- * E-mail: (QL); (ZX); (GF)
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Dolinoy DC, Faulk C. Introduction: The use of animals models to advance epigenetic science. ILAR J 2014; 53:227-31. [PMID: 23744962 DOI: 10.1093/ilar.53.3-4.227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2200, USA.
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Abstract
The healthy adult is the result of successful interaction between the maternal environment and the developing fetal epigenome. The Barker hypothesis first suggested that in utero exposure to the maternal environment impacts adult health and disease. Since the origin of this theory, numerous studies have lent further support. Epigenomic alteration involves DNA methylation and histone modifications. Pregnancy, when the epigenome is typically actively programmed, is a vulnerable time, when exposures may have the most profound epigenetic effect. Recent advances have allowed an understanding of the extent and mechanism by which environmental exposures alter the epigenome of the fetus. Healthcare providers who treat and counsel reproductive-age women are in a unique position to protect against these epigenetic alterations and therefore prevent adverse impact on the developing fetus that may manifest throughout life.
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Affiliation(s)
- Lawrence N Odom
- Division of Reproductive Endocrinology and Infertility, Yale School of Medicine, Yale University, 333 Cedar Street, New Haven, CT 06520, USA
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Abstract
This review highlights emerging areas of interest in public health genomics. First, we describe recent advances in newborn screening (NBS), with a focus on the practice and policy implications of current and future efforts to expand NBS programs (e.g., via next-generation sequencing). Next, we detail research findings from the rapidly progressing field of epigenetics and epigenomics, highlighting ways in which our emerging understanding in these areas could guide future intervention and research efforts in public health. We close by considering various ethical, legal, and social issues posed by recent developments in public health genomics; these include policies to regulate access to personal genomic information, the need to enhance genetic literacy in both health professionals and the public, and challenges in ensuring that the benefits (and burdens) of genomic discoveries and applications are equitably distributed. We also note needs for future genomic research that integrates across basic and social sciences.
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Affiliation(s)
- J Scott Roberts
- Department of Health Behavior & Health Education University of Michigan School of Public Health
| | - Dana Dolinoy
- Department of Environmental Health Sciences University of Michigan School of Public Health
| | - Beth Tarini
- Child Health Evauation & Research Unit Division of Pediatrics University of Michigan Health System
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Gu T, Gu HF, Hilding A, Sjöholm LK, Ostenson CG, Ekström TJ, Brismar K. Increased DNA methylation levels of the insulin-like growth factor binding protein 1 gene are associated with type 2 diabetes in Swedish men. Clin Epigenetics 2013; 5:21. [PMID: 24246027 PMCID: PMC3843565 DOI: 10.1186/1868-7083-5-21] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/30/2013] [Indexed: 12/31/2022] Open
Abstract
Background Prospective studies have shown that low levels of circulating insulin-like growth factor binding protein-1 (IGFBP-1) are associated with the risk of type 2 diabetes. In the present study, we investigated DNA methylation in the IGFBP1 gene to evaluate its changes in relation to serum IGFBP-1 levels in type 2 diabetes. Results A total of 406 Swedish men, including age-matched normal glucose tolerance subjects and type 2 diabetes patients either newly diagnosed or undergoing treatment, were selected from the Stockholm Diabetes Prevention Program. IGFBP1 methylation levels in genomic DNA extracted from peripheral blood were analysed by bisulfite pyrosequencing. Serum IGFBP-1 levels were measured by radio-immunoassay. We found that IGFBP1 DNA methylation levels were higher in both newly diagnosed and treated type 2 diabetes patients with a mean diabetes duration of 3 years compared with subjects with normal glucose tolerance (19.8% and 20.2% vs. 16.9%, P < 0.001 for both). Serum levels of IGFBP-1 in newly diagnosed and in treated type 2 diabetes patients were lower compared with healthy individuals (18 μg/l both vs. 24 μg/l, P = 0.011, P < 0.001). IGFBP1 methylation levels but not serum IGFBP-1 levels in type 2 diabetes patients were independent of body mass index. Newly diagnosed patients with a family history of diabetes (FHD) had higher IGFBP1 methylation levels than those without FHD (20.3% vs. 18.6%, P = 0.017). Conclusions This study provides the first evidence that changes in DNA methylation of the IGFBP1 gene are associated with type 2 diabetes in Swedish men and suggests that increased IGFBP1 DNA methylation and decreased IGFBP-1 serum levels are features of type 2 diabetes with a short duration.
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Affiliation(s)
- Tianwei Gu
- Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, Department of Endocrinology, Karolinska University Hospital, Stockholm SE-17176, Sweden.
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Detection and quantification of methylation in DNA using solid-state nanopores. Sci Rep 2013; 3:1389. [PMID: 23474808 PMCID: PMC3593219 DOI: 10.1038/srep01389] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 02/06/2013] [Indexed: 12/24/2022] Open
Abstract
Epigenetic modifications in eukaryotic genomes occur primarily in the form of 5-methylcytosine (5 mC). These modifications are heavily involved in transcriptional repression, gene regulation, development and the progression of diseases including cancer. We report a new single-molecule assay for the detection of DNA methylation using solid-state nanopores. Methylation is detected by selectively labeling methylation sites with MBD1 (MBD-1x) proteins, the complex inducing a 3 fold increase in ionic blockage current relative to unmethylated DNA. Furthermore, the discrimination of methylated and unmethylated DNA is demonstrated in the presence of only a single bound protein, thereby giving a resolution of a single methylated CpG dinucleotide. The extent of methylation of a target molecule could also be coarsely quantified using this novel approach. This nanopore-based methylation sensitive assay circumvents the need for bisulfite conversion, fluorescent labeling, and PCR and could therefore prove very useful in studying the role of epigenetics in human disease.
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Martin FL. Epigenetic influences in the aetiology of cancers arising from breast and prostate: a hypothesised transgenerational evolution in chromatin accessibility. ISRN ONCOLOGY 2013; 2013:624794. [PMID: 23431470 PMCID: PMC3574745 DOI: 10.1155/2013/624794] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 12/26/2012] [Indexed: 01/12/2023]
Abstract
Epidemiological studies have consistently supported the notion that environmental and/or dietary factors play a central role in the aetiology of cancers of the breast and prostate. However, for more than five decades investigators have failed to identify a single cause-and-effect factor, which could be implicated; identification of a causative entity would allow the implementation of an intervention strategy in at-risk populations. This suggests a more complex pathoaetiology for these cancer sites, compared to others. When one examines the increases or decreases in incidence of specific cancers amongst migrant populations, it is notable that disease arising in colon or stomach requires one or at most two generations to exhibit a change in incidence to match that of high-incidence regions, whereas for breast or prostate cancer, at least three generations are required. This generational threshold could suggest a requirement for nonmutation-driven epigenetic alterations in the F0/F1 generations (parental/offspring adopting a more westernized lifestyle), which then predisposes the inherited genome of subsequent generations to mutagenic/genotoxic alterations leading to the development of sporadic cancer in these target sites. As such, individual susceptibility to carcinogen insult would not be based per se on polymorphisms in activating/detoxifying/repair enzymes, but on elevated accessibility of crucial target genes (e.g., oncogenes, tumour suppressor genes) or hotspots therein to mutation events. This could be termed a genomic susceptibility organizational structure (SOS). Several exposures including alcohol and heavy metals are epigens (i.e., modifiers of the epigenome), whereas others are mutagenic/genotoxic, for example, heterocyclic aromatic amines; humans are continuously and variously exposed to mixtures of these agents. Within such a transgenerational multistage model of cancer development, determining the interaction between epigenetic modification to generate a genomic SOS and genotoxic insult will facilitate a new level of understanding in the aetiology of cancer.
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Affiliation(s)
- Francis L. Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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Romero IG, Ruvinsky I, Gilad Y. Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet 2012; 13:505-16. [PMID: 22705669 DOI: 10.1038/nrg3229] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The hypothesis that differences in gene regulation have an important role in speciation and adaptation is more than 40 years old. With the advent of new sequencing technologies, we are able to characterize and study gene expression levels and associated regulatory mechanisms in a large number of individuals and species at an unprecedented resolution and scale. We have thus gained new insights into the evolutionary pressures that shape gene expression levels and have developed an appreciation for the relative importance of evolutionary changes in different regulatory genetic and epigenetic mechanisms. The current challenge is to link gene regulatory changes to adaptive evolution of complex phenotypes. Here we mainly focus on comparative studies in primates and how they are complemented by studies in model organisms.
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Affiliation(s)
- Irene Gallego Romero
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
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Can the battle against tuberculosis gain from epigenetic research? Trends Microbiol 2012; 20:220-6. [PMID: 22464289 DOI: 10.1016/j.tim.2012.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/29/2012] [Accepted: 03/02/2012] [Indexed: 12/24/2022]
Abstract
A healthy immune system needs to be highly plastic to cope with host defense and surveillance. What mechanisms provide this plasticity? Considering the threat of infectious diseases to a large part of the world's population, can these mechanisms possibly be of use in the ongoing battle against infectious diseases? Against the backdrop of the pandemic nature of tuberculosis, we discuss whether and how epigenetic mechanisms can shed light on our understanding of infectious disease, and if epigenetic marks can be employed to monitor latent infection, disease reactivation or treatment response.
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Su Z, Xia J, Zhao Z. Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome. BMC Genomics 2011; 12 Suppl 5:S15. [PMID: 22369656 PMCID: PMC3287497 DOI: 10.1186/1471-2164-12-s5-s15] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND DNA methylation in the 5' promoter regions of genes and microRNA (miRNA) regulation at the 3' untranslated regions (UTRs) are two major epigenetic regulation mechanisms in most eukaryotes. Both DNA methylation and miRNA regulation can suppress gene expression and their corresponding protein product; thus, they play critical roles in cellular processes. Although there have been numerous investigations of gene regulation by methylation changes and miRNAs, there is no systematic genome-wide examination of their coordinated effects in any organism. RESULTS In this study, we investigated the relationship between promoter methylation at the transcription level and miRNA regulation at the post-transcription level by taking advantage of recently released human methylome data and high quality miRNA and other gene annotation data. We found methylation level in the promoter regions and expression level was negatively correlated. Then, we showed that miRNAs tended to target the genes with a low DNA methylation level in their promoter regions. We further demonstrated that this observed pattern was not attributed to the gene expression level, expression broadness, or the number of transcription factor binding sites. Interestingly, we found miRNA target sites were significantly enriched in the genes located in differentially methylated regions or partially methylated domains. Finally, we explored the features of DNA methylation and miRNA regulation in cancer genes and found cancer genes tended to have low methylation level and more miRNA target sites. CONCLUSION This is the first genome-wide investigation of the combined regulation of gene expression. Our results supported a complementary regulation between DNA methylation (transcriptional level) and miRNA function (post-transcriptional level) in the human genome. The results were helpful for our understanding of the evolutionary forces towards organisms' complexity beyond traditional sequence level investigation.
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Affiliation(s)
- Zhixi Su
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Xie L, Weichel B, Ohm JE, Zhang K. An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver. BMC SYSTEMS BIOLOGY 2011; 5 Suppl 3:S4. [PMID: 22784623 PMCID: PMC3287572 DOI: 10.1186/1752-0509-5-s3-s4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs. normal etc., we still lack sufficient knowledge of the role that differential methylation plays during normal cellular differentiation and tissue specification. We also need thorough, genome level studies to determine the meaning of methylation of individual CpG dinucleotides in terms of gene expression. Results In this study, we have used (insert statistical method here) to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylation arraysand compared those to gene expression by RNA sequencing. We have identified unique signatures of global DNA methylation for human heart, kidney and liver, and showed that DNA methylation data can be used to correctly classify various tissues. It indicates that DNA methylation reflects tissue specificity and may play an important role in tissue differentiation. The integrative analysis of methylation and RNA-Seq data showed that gene methylation and its transcriptional levels were comprehensively correlated. The location of methylation markers in terms of distance to transcription start site and CpG island showed no effects on the regulation of gene expression by DNA methylation in normal tissues. Conclusions This study showed that an integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.
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Affiliation(s)
- Linglin Xie
- Department of Biochemistry and Molecular Biology, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
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Burwell RG, Dangerfield PH, Moulton A, Grivas TB. Adolescent idiopathic scoliosis (AIS), environment, exposome and epigenetics: a molecular perspective of postnatal normal spinal growth and the etiopathogenesis of AIS with consideration of a network approach and possible implications for medical therapy. SCOLIOSIS 2011; 6:26. [PMID: 22136338 PMCID: PMC3293085 DOI: 10.1186/1748-7161-6-26] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/02/2011] [Indexed: 12/22/2022]
Abstract
Genetic factors are believed to play an important role in the etiology of adolescent idiopathic scoliosis (AIS). Discordant findings for monozygotic (MZ) twins with AIS show that environmental factors including different intrauterine environments are important in etiology, but what these environmental factors may be is unknown. Recent evidence for common chronic non-communicable diseases suggests epigenetic differences may underlie MZ twin discordance, and be the link between environmental factors and phenotypic differences. DNA methylation is one important epigenetic mechanism operating at the interface between genome and environment to regulate phenotypic plasticity with a complex regulation across the genome during the first decade of life. The word exposome refers to the totality of environmental exposures from conception onwards, comprising factors in external and internal environments. The word exposome is used here also in relation to physiologic and etiopathogenetic factors that affect normal spinal growth and may induce the deformity of AIS. In normal postnatal spinal growth we propose a new term and concept, physiologic growth-plate exposome for the normal processes particularly of the internal environments that may have epigenetic effects on growth plates of vertebrae. In AIS, we propose a new term and concept pathophysiologic scoliogenic exposome for the abnormal processes in molecular pathways particularly of the internal environment currently expressed as etiopathogenetic hypotheses; these are suggested to have deforming effects on the growth plates of vertebrae at cell, tissue, structure and/or organ levels that are considered to be epigenetic. New research is required for chromatin modifications including DNA methylation in AIS subjects and vertebral growth plates excised at surgery. In addition, consideration is needed for a possible network approach to etiopathogenesis by constructing AIS diseasomes. These approaches may lead through screening, genetic, epigenetic, biochemical, metabolic phenotypes and pharmacogenomic research to identify susceptible individuals at risk and modulate abnormal molecular pathways of AIS. The potential of epigenetic-based medical therapy for AIS cannot be assessed at present, and must await new research derived from the evaluation of epigenetic concepts of spinal growth in health and deformity. The tenets outlined here for AIS are applicable to other musculoskeletal growth disorders including infantile and juvenile idiopathic scoliosis.
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Affiliation(s)
- R Geoffrey Burwell
- Centre for Spinal Studies and Surgery, Nottingham University Hospitals Trust, Queen's Medical Centre Campus, Derby Road, Nottingham, NG7 2UH, UK
| | - Peter H Dangerfield
- University of Liverpool, Ashton Street, L69 3GE, UK
- Staffordshire University, Leek Road, Stoke-on-Trent, ST4 2DF. UK
- Royal Liverpool Children's Hospital, Eaton Road, Liverpool, L12 2AP, UK
| | - Alan Moulton
- Department of Orthopaedic Surgery, King's Mill Hospital, Sutton Road, Mansfield NG17 4JL, UK
| | - Theodoros B Grivas
- Department of Trauma and Orthopedics, "Tzanio" General Hospital, Tzani and Afendouli 1 st, Piraeus 18536, Greece.co.uk
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Raleigh SM. Epigenetic regulation of the ACE gene might be more relevant to endurance physiology than the I/D polymorphism. J Appl Physiol (1985) 2011; 112:1082-3. [PMID: 22096122 DOI: 10.1152/japplphysiol.00828.2011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Stuart M Raleigh
- Division of Health and Life Science, University of Northampton, Northampton, United Kingdom.
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Klemcke HG, Joe B, Rose R, Ryan KL. Life or death? A physiogenomic approach to understand individual variation in responses to hemorrhagic shock. Curr Genomics 2011; 12:428-42. [PMID: 22379396 PMCID: PMC3178911 DOI: 10.2174/138920211797248574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/29/2011] [Accepted: 07/06/2011] [Indexed: 11/22/2022] Open
Abstract
Severe hemorrhage due to trauma is a major cause of death throughout the world. It has often been observed that some victims are able to withstand hemorrhage better than others. For decades investigators have attempted to identify physiological mechanisms that distinguish survivors from nonsurvivors for the purpose of providing more informed therapies. As an alternative approach to address this issue, we have initiated a research program to identify genes and genetic mechanisms that contribute to this phenotype of survival time after controlled hemorrhage. From physiogenomic studies using inbred rat strains, we have demonstrated that this phenotype is a heritable quantitative trait, and is therefore a complex trait regulated by multiple genes. Our work continues to identify quantitative trait loci as well as potential epigenetic mechanisms that might influence survival time after severe hemorrhage. Our ultimate goal is to improve survival to traumatic hemorrhage and attendant shock via regulation of genetic mechanisms and to provide knowledge that will lead to genetically-informed personalized treatments.
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Affiliation(s)
- Harold G Klemcke
- U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234, USA
| | - Bina Joe
- Physiological Genomics Laboratory, Department of Physiology and Pharmacology, University of Toledo College of Medicine, Toledo, OH 43614, USA
| | - Rajiv Rose
- U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234, USA
| | - Kathy L Ryan
- U.S. Army Institute of Surgical Research, Fort Sam Houston, TX 78234, USA
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Herrmann A, Haake A, Ammerpohl O, Martin-Guerrero I, Szafranski K, Stemshorn K, Nothnagel M, Kotsopoulos SK, Richter J, Warner J, Olson J, Link DR, Schreiber S, Krawczak M, Platzer M, Nürnberg P, Siebert R, Hampe J. Pipeline for large-scale microdroplet bisulfite PCR-based sequencing allows the tracking of hepitype evolution in tumors. PLoS One 2011; 6:e21332. [PMID: 21750708 PMCID: PMC3130030 DOI: 10.1371/journal.pone.0021332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 05/27/2011] [Indexed: 12/26/2022] Open
Abstract
Cytosine methylation provides an epigenetic level of cellular plasticity that is important for development, differentiation and cancerogenesis. We adopted microdroplet PCR to bisulfite treated target DNA in combination with second generation sequencing to simultaneously assess DNA sequence and methylation. We show measurement of methylation status in a wide range of target sequences (total 34 kb) with an average coverage of 95% (median 100%) and good correlation to the opposite strand (rho = 0.96) and to pyrosequencing (rho = 0.87). Data from lymphoma and colorectal cancer samples for SNRPN (imprinted gene), FGF6 (demethylated in the cancer samples) and HS3ST2 (methylated in the cancer samples) serve as a proof of principle showing the integration of SNP data and phased DNA-methylation information into “hepitypes” and thus the analysis of DNA methylation phylogeny in the somatic evolution of cancer.
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Affiliation(s)
- Alexander Herrmann
- Institute of Internal Medicine I, Christian-Albrechts University, Kiel, Germany
| | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | | | - Karol Szafranski
- Genome Analysis Group, Fritz-Lipman Institute for Ageing Research, Jena, Germany
| | - Kathryn Stemshorn
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Michael Nothnagel
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | | | - Julia Richter
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Jason Warner
- RainDance Technologies, Lexington, Massachusetts, United States of America
| | - Jeff Olson
- RainDance Technologies, Lexington, Massachusetts, United States of America
| | - Darren R. Link
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Internal Medicine I, Christian-Albrechts University, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Matthias Platzer
- Genome Analysis Group, Fritz-Lipman Institute for Ageing Research, Jena, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts University, Kiel, Germany
| | - Jochen Hampe
- Institute of Internal Medicine I, Christian-Albrechts University, Kiel, Germany
- * E-mail:
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