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Congues F, Wang P, Lee J, Lin D, Shahid A, Xie J, Huang Y. Targeting aryl hydrocarbon receptor to prevent cancer in barrier organs. Biochem Pharmacol 2024; 223:116156. [PMID: 38518996 PMCID: PMC11144369 DOI: 10.1016/j.bcp.2024.116156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/08/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
The skin, lung, and gut are important barrier organs that control how the body reacts to environmental stressors such as ultraviolet (UV) radiation, air pollutants, dietary components, and microorganisms. The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that plays an important role in maintaining homeostasis of barrier organs. AhR was initially discovered as a receptor for environmental chemical carcinogens such as polycyclic aromatic hydrocarbons (PAHs). Activation of AhR pathways by PAHs leads to increased DNA damage and mutations which ultimately lead to carcinogenesis. Ongoing evidence reveals an ever-expanding role of AhR. Recently, AhR has been linked to immune systems by the interaction with the development of natural killer (NK) cells, regulatory T (Treg) cells, and T helper 17 (Th17) cells, as well as the production of immunosuppressive cytokines. However, the role of AhR in carcinogenesis is not as straightforward as we initially thought. Although AhR activation has been shown to promote carcinogenesis in some studies, others suggest that it may act as a tumor suppressor. In this review, we aim to explore the role of AhR in the development of cancer that originates from barrier organs. We also examined the preclinical efficacy data of AhR agonists and antagonists on carcinogenesis to determine whether AhR modulation can be a viable option for cancer chemoprevention.
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Affiliation(s)
- Francoise Congues
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Pengcheng Wang
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA; Department of Stomatology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Joshua Lee
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Daphne Lin
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Ayaz Shahid
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Jianming Xie
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Ying Huang
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA.
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Dhat R, Mongad D, Raji S, Arkat S, Mahapatra NR, Singhal N, Sitasawad SL. Epigenetic modifier alpha-ketoglutarate modulates aberrant gene body methylation and hydroxymethylation marks in diabetic heart. Epigenetics Chromatin 2023; 16:12. [PMID: 37101286 PMCID: PMC10134649 DOI: 10.1186/s13072-023-00489-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/21/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Diabetic cardiomyopathy (DCM) is a leading cause of death in diabetic patients. Hyperglycemic myocardial microenvironment significantly alters chromatin architecture and the transcriptome, resulting in aberrant activation of signaling pathways in a diabetic heart. Epigenetic marks play vital roles in transcriptional reprogramming during the development of DCM. The current study is aimed to profile genome-wide DNA (hydroxy)methylation patterns in the hearts of control and streptozotocin (STZ)-induced diabetic rats and decipher the effect of modulation of DNA methylation by alpha-ketoglutarate (AKG), a TET enzyme cofactor, on the progression of DCM. METHODS Diabetes was induced in male adult Wistar rats with an intraperitoneal injection of STZ. Diabetic and vehicle control animals were randomly divided into groups with/without AKG treatment. Cardiac function was monitored by performing cardiac catheterization. Global methylation (5mC) and hydroxymethylation (5hmC) patterns were mapped in the Left ventricular tissue of control and diabetic rats with the help of an enrichment-based (h)MEDIP-sequencing technique by using antibodies specific for 5mC and 5hmC. Sequencing data were validated by performing (h)MEDIP-qPCR analysis at the gene-specific level, and gene expression was analyzed by qPCR. The mRNA and protein expression of enzymes involved in the DNA methylation and demethylation cycle were analyzed by qPCR and western blotting. Global 5mC and 5hmC levels were also assessed in high glucose-treated DNMT3B knockdown H9c2 cells. RESULTS We found the increased expression of DNMT3B, MBD2, and MeCP2 with a concomitant accumulation of 5mC and 5hmC, specifically in gene body regions of diabetic rat hearts compared to the control. Calcium signaling was the most significantly affected pathway by cytosine modifications in the diabetic heart. Additionally, hypermethylated gene body regions were associated with Rap1, apelin, and phosphatidyl inositol signaling, while metabolic pathways were most affected by hyperhydroxymethylation. AKG supplementation in diabetic rats reversed aberrant methylation patterns and restored cardiac function. Hyperglycemia also increased 5mC and 5hmC levels in H9c2 cells, which was normalized by DNMT3B knockdown or AKG supplementation. CONCLUSION This study demonstrates that reverting hyperglycemic damage to cardiac tissue might be possible by erasing adverse epigenetic signatures by supplementing epigenetic modulators such as AKG along with an existing antidiabetic treatment regimen.
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Affiliation(s)
- Rohini Dhat
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Dattatray Mongad
- NCMR-National Centre for Cell Science (NCCS), Pune, Maharashtra, 411007, India
| | - Sivarupa Raji
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Silpa Arkat
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Nitish R Mahapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Nishant Singhal
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Sandhya L Sitasawad
- National Centre for Cell Science, NCCS Complex, S. P. Pune University, Ganeshkhind, Pune, Maharashtra, 411007, India.
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Palma-Gudiel H, Yu L, Huo Z, Yang J, Wang Y, Gu T, Gao C, De Jager PL, Jin P, Bennett DA, Zhao J. Fine-mapping and replication of EWAS loci harboring putative epigenetic alterations associated with AD neuropathology in a large collection of human brain tissue samples. Alzheimers Dement 2023; 19:1216-1226. [PMID: 35959851 PMCID: PMC9922334 DOI: 10.1002/alz.12761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/07/2022]
Abstract
INTRODUCTION Our previous epigenome-wide association study (EWAS) of Alzheimer's disease (AD) in human brain identified 71 CpGs associated with AD pathology. However, due to low coverage of the Illumina platform, many important CpGs might have been missed. METHODS In a large collection of human brain tissue samples (N = 864), we fine-mapped previous EWAS loci by targeted bisulfite sequencing and examined their associations with AD neuropathology. DNA methylation was also linked to gene expression of the same brain cortex. RESULTS Our targeted sequencing captured 130 CpGs (∼1.2 kb), 93 of which are novel. Of the 130 CpGs, 57 sites (only 17 included in previous EWAS) and 12 gene regions (e.g., ANK1, BIN1, RHBDF2, SPG7, PODXL) were significantly associated with amyloid load. DNA methylation in some regions was associated with expression of nearby genes. DISCUSSION Targeted methylation sequencing can validate previous EWAS loci and discover novel CpGs associated with AD pathology.
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Affiliation(s)
- Helena Palma-Gudiel
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Lei Yu
- Rush Alzheimer’s Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Zhiguang Huo
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Jingyun Yang
- Rush Alzheimer’s Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Yanling Wang
- Rush Alzheimer’s Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Cheng Gao
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, USA
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Min S, Whited JL. Limb blastema formation: How much do we know at a genetic and epigenetic level? J Biol Chem 2023; 299:102858. [PMID: 36596359 PMCID: PMC9898764 DOI: 10.1016/j.jbc.2022.102858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 01/02/2023] Open
Abstract
Regeneration of missing body parts is an incredible ability which is present in a wide number of species. However, this regenerative capability varies among different organisms. Urodeles (salamanders) are able to completely regenerate limbs after amputation through the essential process of blastema formation. The blastema is a collection of relatively undifferentiated progenitor cells that proliferate and repattern to form the internal tissues of a regenerated limb. Understanding blastema formation in salamanders may enable comparative studies with other animals, including mammals, with more limited regenerative abilities and may inspire future therapeutic approaches in humans. This review focuses on the current state of knowledge about how limb blastemas form in salamanders, highlighting both the possible roles of epigenetic controls in this process as well as limitations to scientific understanding that present opportunities for research.
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Affiliation(s)
- Sangwon Min
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
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Yazar V, Dawson VL, Dawson TM, Kang SU. DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2023; 13:145-164. [PMID: 36710687 PMCID: PMC10041453 DOI: 10.3233/jpd-223517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Mani N, Daiya A, Chowdhury R, Mukherjee S, Chowdhury S. Epigenetic adaptations in drug-tolerant tumor cells. Adv Cancer Res 2023; 158:293-335. [PMID: 36990535 DOI: 10.1016/bs.acr.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Traditional chemotherapy against cancer is often severely hampered by acquired resistance to the drug. Epigenetic alterations and other mechanisms like drug efflux, drug metabolism, and engagement of survival pathways are crucial in evading drug pressure. Herein, growing evidence suggests that a subpopulation of tumor cells can often tolerate drug onslaught by entering a "persister" state with minimal proliferation. The molecular features of these persister cells are gradually unraveling. Notably, the "persisters" act as a cache of cells that can eventually re-populate the tumor post-withdrawal drug pressure and contribute to acquiring stable drug-resistant features. This underlines the clinical significance of the tolerant cells. Accumulating evidence highlights the importance of modulation of the epigenome as a critical adaptive strategy for evading drug pressure. Chromatin remodeling, altered DNA methylation, and de-regulation of non-coding RNA expression and function contribute significantly to this persister state. No wonder targeting adaptive epigenetic modifications is increasingly recognized as an appropriate therapeutic strategy to sensitize them and restore drug sensitivity. Furthermore, manipulating the tumor microenvironment and "drug holiday" is also explored to maneuver the epigenome. However, heterogeneity in adaptive strategies and lack of targeted therapies have significantly hindered the translation of epigenetic therapy to the clinics. In this review, we comprehensively analyze the epigenetic alterations adapted by the drug-tolerant cells, the therapeutic strategies employed to date, and their limitations and future prospects.
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Tan B, Zeng J, Meng F, Wang S, Xiao L, Zhao X, Hong L, Zheng E, Wu Z, Li Z, Gu T. Comprehensive analysis of pre-mRNA alternative splicing regulated by m6A methylation in pig oxidative and glycolytic skeletal muscles. BMC Genomics 2022; 23:804. [PMID: 36474138 PMCID: PMC9724443 DOI: 10.1186/s12864-022-09043-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Different types of skeletal myofibers exhibit distinct physiological and metabolic properties that are associated with meat quality traits in livestock. Alternative splicing (AS) of pre-mRNA can generate multiple transcripts from an individual gene by differential selection of splice sites. N6-methyladenosine (m6A) is the most abundant modification in mRNAs, but its regulation for AS in different muscles remains unknown. RESULTS: We characterized AS events and m6A methylation pattern in pig oxidative and glycolytic muscles. A tota1 of 1294 differential AS events were identified, and differentially spliced genes were significantly enriched in processes related to different phenotypes between oxidative and glycolytic muscles. We constructed the regulatory network between splicing factors and corresponding differential AS events and identified NOVA1 and KHDRBS2 as key splicing factors. AS event was enriched in m6A-modified genes, and the methylation level was positively correlated with the number of AS events in genes. The dynamic change in m6A enrichment was associated with 115 differentially skipping exon (SE-DAS) events within 92 genes involving in various processes, including muscle contraction and myofibril assembly. We obtained 23.4% SE-DAS events (27/115) regulated by METTL3-meditaed m6A and experimentally validated the aberrant splicing of ZNF280D, PHE4DIP, and NEB. The inhibition of m6A methyltransferase METTL3 could induce the conversion of oxidative fiber to glycolytic fiber in PSCs. CONCLUSION Our study suggested that m6A modification could contribute to significant difference in phenotypes between oxidative and glycolytic muscles by mediating the regulation of AS. These findings would provide novel insights into mechanisms underlying muscle fiber conversion.
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Affiliation(s)
- Baohua Tan
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Jiekang Zeng
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Fanming Meng
- grid.135769.f0000 0001 0561 6611State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, 510640 Guangzhou, Guangdong People’s Republic of China
| | - Shanshan Wang
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Liyao Xiao
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Xinming Zhao
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Linjun Hong
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Enqin Zheng
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Zhenfang Wu
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, 510642 Guangzhou, China
| | - Zicong Li
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
| | - Ting Gu
- grid.20561.300000 0000 9546 5767National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China ,grid.20561.300000 0000 9546 5767Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642 Guangzhou, China
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Habano W, Miura T, Terashima J, Ozawa S. Aryl hydrocarbon receptor as a DNA methylation reader in the stress response pathway. Toxicology 2022; 470:153154. [PMID: 35301058 DOI: 10.1016/j.tox.2022.153154] [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: 10/05/2021] [Revised: 01/31/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
The aryl hydrocarbon receptor (AhR) mediates various cellular responses upon exposure to exogenous and endogenous stress factors. In these responses, AhR plays a dual role as a stress sensor for detecting various AhR ligands and as a transcription factor that upregulates the expression of downstream effector genes, such as those encoding drug-metabolizing enzymes. As a transcription factor, it selectively binds to the unmethylated form of a specific sequence called the xenobiotic responsive element (XRE). We suggest that AhR is a novel DNA methylation reader, unlike classical methylation readers, such as methyl-CpG-binding protein 2, which binds to methylated sequences. Under physiological conditions of continuous exposure to endogenous AhR ligands, such as kynurenine, methylation states of the individual target XREs must be strictly regulated to select and coordinate the expression of downstream genes responsible for maintaining homeostasis in the body. In contrast, long-term exposure to AhR ligands frequently leads to changes in the methylation patterns around the XRE sequence. These data indicate that AhR may contribute to the adaptive cellular response to various stresses by modulating DNA methylation. Thus, the DNA methylation profile of AhR target genes should be dynamically controlled through a balance between robustness and flexibility under both physiological and stress conditions. AhR is a pivotal player in the regulation of stress response as it shows versatility by functioning as a stress sensor, methylation reader, and putative methylation modulator.
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Affiliation(s)
- Wataru Habano
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan.
| | - Toshitaka Miura
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Jun Terashima
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
| | - Shogo Ozawa
- Division of Pharmacodynamics and Molecular Genetics, Department of Clinical Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Shiwa 028-3694, Iwate, Japan
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Abstract
Neuroepigenetics, a new branch of epigenetics, plays an important role in the regulation of gene expression. Neuroepigenetics is associated with holistic neuronal function and helps in formation and maintenance of memory and learning processes. This includes neurodevelopment and neurodegenerative defects in which histone modification enzymes appear to play a crucial role. These modifications, carried out by acetyltransferases and deacetylases, regulate biologic and cellular processes such as apoptosis and autophagy, inflammatory response, mitochondrial dysfunction, cell-cycle progression and oxidative stress. Alterations in acetylation status of histone as well as non-histone substrates lead to transcriptional deregulation. Histone deacetylase decreases acetylation status and causes transcriptional repression of regulatory genes involved in neural plasticity, synaptogenesis, synaptic and neural plasticity, cognition and memory, and neural differentiation. Transcriptional deactivation in the brain results in development of neurodevelopmental and neurodegenerative disorders. Mounting evidence implicates histone deacetylase inhibitors as potential therapeutic targets to combat neurologic disorders. Recent studies have targeted naturally-occurring biomolecules and micro-RNAs to improve cognitive defects and memory. Multi-target drug ligands targeting HDAC have been developed and used in cell-culture and animal-models of neurologic disorders to ameliorate synaptic and cognitive dysfunction. Herein, we focus on the implications of histone deacetylase enzymes in neuropathology, their regulation of brain function and plausible involvement in the pathogenesis of neurologic defects.
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Höglund A, Henriksen R, Fogelholm J, Churcher AM, Guerrero-Bosagna CM, Martinez-Barrio A, Johnsson M, Jensen P, Wright D. The methylation landscape and its role in domestication and gene regulation in the chicken. Nat Ecol Evol 2020; 4:1713-1724. [PMID: 32958860 DOI: 10.1038/s41559-020-01310-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 08/26/2020] [Indexed: 01/06/2023]
Abstract
Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.
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Affiliation(s)
- Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | | | - Carlos M Guerrero-Bosagna
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.,Evolutionary Biology Centrum, Dept of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden.
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Kouidou S, Malousi A, Andreou AZ. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection: Triggering a Lethal Fight to Keep Control of the Ten-Eleven Translocase (TET)-Associated DNA Demethylation? Pathogens 2020; 9:E1006. [PMID: 33266135 PMCID: PMC7760189 DOI: 10.3390/pathogens9121006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/15/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
The extended and diverse interference of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in multiple host functions and the diverse associated symptoms implicate its involvement in fundamental cellular regulatory processes. The activity of ten-eleven translocase 2 (TET2) responsible for selective DNA demethylation, has been recently identified as a regulator of endogenous virus inactivation and viral invasion, possibly by proteasomal deregulation of the TET2/TET3 activities. In a recent report, we presented a detailed list of factors that can be affected by TET activity, including recognition of zinc finger protein binding sites and bimodal promoters, by enhancing the flexibility of adjacent sequences. In this review, we summarize the TET-associated processes and factors that could account for SARS-CoV-2 diverse symptoms. Moreover, we provide a correlation for the observed virus-induced symptoms that have been previously associated with TET activities by in vitro and in vitro studies. These include early hypoxia, neuronal regulation, smell and taste development, liver, intestinal, and cardiomyocyte differentiation. Finally, we propose that the high mortality of SARS-CoV-2 among adult patients, the different clinical symptoms of adults compared to children, the higher risk of patients with metabolic deregulation, and the low mortality rates among women can all be accounted for by the complex balance of the three enzymes with TET activity, which is developmentally regulated. This activity is age-dependent, related to telomere homeostasis and integrity, and associated with X chromosome inactivation via (de)regulation of the responsible XIST gene expression.
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Affiliation(s)
- Sofia Kouidou
- Lab of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
| | - Andigoni Malousi
- Lab of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece;
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Malousi A, Andreou AZ, Kouidou S. In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors. Epigenetics 2020; 16:503-518. [PMID: 32752914 DOI: 10.1080/15592294.2020.1805693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The presence of 5-hydroxymethyl cytosine in DNA has been previously associated with ageing. Using in silico analysis of normal liver samples we presently observed that in 5-hydroxymethyl cytosine sequences, DNA methylation is dependent on the co-presence of G-quadruplexes and palindromes. This association exhibits discrete patterns depending on G-quadruplex and palindrome densities. DNase-Seq data show that 5-hydroxymethyl cytosine sequences are common among liver nucleosomes (p < 2.2x10-16) and threefold more frequent than nucleosome sequences. Nucleosomes lacking palindromes and potential G-quadruplexes are rare in vivo (1%) and nucleosome occupancy potential decreases with increasing G-quadruplexes. Palindrome distribution is similar to that previously reported in nucleosomes. In low and mixed complexity sequences 5-hydroxymethyl cytosine is frequently located next to three elements: G-quadruplexes or imperfect G-quadruplexes with CpGs, or unstable hairpin loops (TCCCAY6TGGGA) mostly located in antisense strands or finally A-/T-rich segments near these motifs. The high frequencies and selective distribution of pentamer sequences (including TCCCA, TGGGA) probably indicate the positive contribution of 5-hydroxymethyl cytosine to stabilize the formation of structures unstable in the absence of this cytosine modification. Common motifs identified in all total 5-hydroxymethyl cytosine-containing sequences exhibit high homology to recognition sites of several transcription factor families: homeobox, factors involved in growth, mortality/ageing, cancer, neuronal function, vision, and reproduction. We conclude that cytosine hydroxymethylation could play a role in the recognition of sequences with G-quadruplexes/palindromes by forming epigenetically regulated DNA 'springs' and governing expansions or compressions recognized by different transcription factors or stabilizing nucleosomes. The balance of these epigenetic elements is lost in hepatocellular carcinoma.
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Affiliation(s)
- Andigoni Malousi
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Sofia Kouidou
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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13
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Sun X, Tian Y, Wang J, Sun Z, Zhu Y. Genome-wide analysis reveals the association between alternative splicing and DNA methylation across human solid tumors. BMC Med Genomics 2020; 13:4. [PMID: 31906954 PMCID: PMC6945449 DOI: 10.1186/s12920-019-0654-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022] Open
Abstract
Background Dysregulation of alternative splicing (AS) is a critical signature of cancer. However, the regulatory mechanisms of cancer-specific AS events, especially the impact of DNA methylation, are poorly understood. Methods By using The Cancer Genome Atlas (TCGA) SpliceSeq and TCGA data for ten solid tumor types, association analysis was performed to characterize the potential link between cancer-specific AS and DNA methylation. Functional and pathway enrichment analyses were performed, and the protein-protein interaction (PPI) network was constructed with the String website. The prognostic analysis was carried out with multivariate Cox regressions models. Results 15,818 AS events in 3955 annotated genes were identified across ten solid tumor types. The different DNA methylation patterns between tumor and normal tissues at the corresponding alternative spliced exon boundaries were shown, and 51.3% of CpG sites (CpGs) revealed hypomethylated in tumors. Notably, 607 CpGs were found to be highly correlated with 369 cancer-specific AS events after permutation tests. Among them, the hypomethylated CpGs account for 52.7%, and the number of down-regulated exons was 173. Furthermore, we found 38 AS events in 35 genes could serve as new molecular biomarkers to predict patient survival. Conclusions Our study described the relationship between DNA methylation and AS events across ten human solid tumor types and provided new insights into intragenic DNA methylation and exon usage during the AS process.
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Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yiping Tian
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, the State University of New Jersey, New Brunswick, 08901, USA
| | - Zeyuan Sun
- Department of Health Related Social and Behavioral Science, West China School of Public Health, Sichuan University, Chengdu, 610041, China
| | - Yimin Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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Tabish AM, Arif M, Song T, Elbeck Z, Becker RC, Knöll R, Sadayappan S. Association of intronic DNA methylation and hydroxymethylation alterations in the epigenetic etiology of dilated cardiomyopathy. Am J Physiol Heart Circ Physiol 2019; 317:H168-H180. [PMID: 31026178 PMCID: PMC6692731 DOI: 10.1152/ajpheart.00758.2018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/15/2019] [Accepted: 04/22/2019] [Indexed: 01/03/2023]
Abstract
In this study, we investigated the role of DNA methylation [5-methylcytosine (5mC)] and 5-hydroxymethylcytosine (5hmC), epigenetic modifications that regulate gene activity, in dilated cardiomyopathy (DCM). A MYBPC3 mutant mouse model of DCM was compared with wild type and used to profile genomic 5mC and 5hmC changes by Chip-seq, and gene expression levels were analyzed by RNA-seq. Both 5mC-altered genes (957) and 5hmC-altered genes (2,022) were identified in DCM hearts. Diverse gene ontology and KEGG pathways were enriched for DCM phenotypes, such as inflammation, tissue fibrosis, cell death, cardiac remodeling, cardiomyocyte growth, and differentiation, as well as sarcomere structure. Hierarchical clustering of mapped genes affected by 5mC and 5hmC clearly differentiated DCM from wild-type phenotype. Based on these data, we propose that genomewide 5mC and 5hmC contents may play a major role in DCM pathogenesis. NEW & NOTEWORTHY Our data demonstrate that development of dilated cardiomyopathy in mice is associated with significant epigenetic changes, specifically in intronic regions, which, when combined with gene expression profiling data, highlight key signaling pathways involved in pathological cardiac remodeling and heart contractile dysfunction.
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Affiliation(s)
- Ali M Tabish
- Integrated Cardio-Metabolic Centre, Karolinska Institutet , Stockholm , Sweden
| | - Mohammed Arif
- Heart, Lung, Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Taejeong Song
- Heart, Lung, Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Zaher Elbeck
- Integrated Cardio-Metabolic Centre, Karolinska Institutet , Stockholm , Sweden
| | - Richard C Becker
- Heart, Lung, Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati , Cincinnati, Ohio
| | - Ralph Knöll
- Integrated Cardio-Metabolic Centre, Karolinska Institutet , Stockholm , Sweden
- Cardiovascular and Metabolic Disease Innovative Medicines and Early Development Unit, AstraZeneca R&D, Gothenburg , Sweden
| | - Sakthivel Sadayappan
- Heart, Lung, Vascular Institute, Division of Cardiovascular Health and Disease, Department of Internal Medicine, University of Cincinnati , Cincinnati, Ohio
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15
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Ehrlich KC, Lacey M, Ehrlich M. Tissue-specific epigenetics of atherosclerosis-related ANGPT and ANGPTL genes. Epigenomics 2019; 11:169-186. [PMID: 30688091 PMCID: PMC6371847 DOI: 10.2217/epi-2018-0150] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aim: To understand tissue-specific regulation of angiopoietin/angiopoietin-like (ANGPT/ANGPTL) genes (especially the five genes embedded in introns of host genes) and their association with atherosclerosis. Methods: Transcription and epigenomic databases from various normal tissues were examined in the vicinity of ANGPT1, ANGPT2, ANGPTL1, ANGPTL2, ANGPTL3, ANGPTL4 and ANGPTL8. Results: We identified tissue-specific enhancer chromatin regions that are likely to regulate transcription of ANGPT/ANGPTL genes and were intragenic, intergenic or host gene-linked. In addition, we found atherosclerosis-linked differentially methylated regions associated with ANGPT2 and with sequences encoding miR-145, a microRNA that targets ANGPT2 mRNA in cancers. Conclusion: Our findings implicate enhancers as major contributors to tissue-specific expression of ANGPT/ANGPTL genes, which play critical roles in angiogenesis, atherosclerosis, cancer, and inflammatory and metabolic diseases.
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Affiliation(s)
- Kenneth C Ehrlich
- Center for Bioinformatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Melanie Ehrlich
- Center for Bioinformatics & Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.,Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.,Hayward Genetics Center Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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16
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Dynamic alterations in methylation of global DNA and growth-related genes in large yellow croaker (Larimichthys crocea) in response to starvation stress. Comp Biochem Physiol B Biochem Mol Biol 2019; 227:98-105. [DOI: 10.1016/j.cbpb.2018.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
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17
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Gagliardi M, Strazzullo M, Matarazzo MR. DNMT3B Functions: Novel Insights From Human Disease. Front Cell Dev Biol 2018; 6:140. [PMID: 30406101 PMCID: PMC6204409 DOI: 10.3389/fcell.2018.00140] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
DNA methylation plays important roles in gene expression regulation and chromatin structure. Its proper establishment and maintenance are essential for mammalian development and cellular differentiation. DNMT3B is the major de novo DNA methyltransferase expressed and active during the early stage of embryonic development, including implantation. In addition to its well-known role to methylate centromeric, pericentromeric, and subtelomeric repeats, recent observations suggest that DNMT3B acts as the main enzyme methylating intragenic regions of active genes. Although largely studied, much remains unknown regarding how these specific patterns of de novo CpG methylation are established in mammalian cells, and which are the rules governing DNMT3B recruitment and activity. Latest evidence indicates that DNMT3B recruitment is regulated by numerous mechanisms including chromatin modifications, transcription levels, non-coding RNAs, and the presence of DNA-binding factors. DNA methylation abnormalities are a common mark of human diseases involving chromosomal and genomic instabilities, such as inherited disease and cancer. The autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies syndrome, type I (ICF-1), is associated to hypomorphic mutations in DNMT3B gene, while its altered expression has been correlated with the development of tumors. In both cases, this implies that abnormal DNA hypomethylation and hypermethylation patterns affect gene expression and genomic architecture contributing to the pathological states. We will provide an overview of the most recent research aimed at deciphering the molecular mechanisms by which DNMT3B abnormalities are associated with the onset and progression of these pathologies.
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Affiliation(s)
- Miriam Gagliardi
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Max Planck Institute of Psychiatry, Munich, Germany
| | - Maria Strazzullo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
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Malousi A, Andreou AZ, Georgiou E, Tzimagiorgis G, Kovatsi L, Kouidou S. Age-dependent methylation in epigenetic clock CpGs is associated with G-quadruplex, co-transcriptionally formed RNA structures and tentative splice sites. Epigenetics 2018; 13:808-821. [PMID: 30270726 PMCID: PMC6224212 DOI: 10.1080/15592294.2018.1514232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Horvath's epigenetic clock consists of 353 CpGs whose methylation levels can accurately predict the age of individuals. Using bioinformatics analysis, we investigated the conformation, energy characteristics and presence of tentative splice sites of the sequences surrounding the epigenetic clock CpGs, in relation to the median methylation changes in different ages, the presence of CpG islands and their position in genes. Common characteristics in the 100 nt sequences surrounding the epigenetic clock CpGs are G-quadruplexes and/or tentative splice site motifs. Median methylation increases significantly in sequences which adopt less stable structures during transcription. Methylation is higher when CpGs overlap with G-quadruplexes than when they precede them. Median methylation in epigenetic clock CpGs is higher in sequences expressed as single products rather than in multiple products and those containing single donors and multiple acceptors. Age-related methylation variation is significant in sequences without G-quadruplexes, particularly those producing low stability nascent RNA and those with splice sites. CpGs in sequences close to transcription start sites and those which are possibly never expressed (hypothetical proteins) undergo similar extent of age-related median methylation decrease and increase. Preservation of methylation is observed in CpG islands without G-quadruplexes, contrary to CpGs far from CpG islands (open sea). Sequences containing G-quadruplexes and RNA pseudoknots, determining the recognition by H3K27 histone methyltransferase, are hypomethylated. The presented structural DNA and co-transcriptional RNA analysis of epigenetic clock sequences, foreshadows the association of age-related methylation changes with the principle biological processes of DNA and histone methylation, splicing and chromatin silencing.
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Affiliation(s)
- Andigoni Malousi
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | | | - Elisavet Georgiou
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Georgios Tzimagiorgis
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Leda Kovatsi
- c Laboratory of Forensic Medicine & Toxicology , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - Sofia Kouidou
- a Laboratory of Biological Chemistry , Medical School, Aristotle University of Thessaloniki , Thessaloniki , Greece
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Li Y, Fang C, Fu Y, Hu A, Li C, Zou C, Li X, Zhao S, Zhang C, Li C. A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing. DNA Res 2018; 25:421-437. [PMID: 29850846 PMCID: PMC6105124 DOI: 10.1093/dnares/dsy014] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/08/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its limitation of uncertainties about the complete structure of mRNA. Here we combined single-molecule real-time sequencing, Illumina RNA-seq and DNA methylation data to characterize the landscapes of DNA methylation on AS, fusion isoforms formation and lncRNA feature and further to unveil the transcriptome complexity of pig. Our analysis identified an unprecedented scale of high-quality full-length isoforms with over 28,127 novel isoforms from 26,881 novel genes. More than 92,000 novel AS events were detected and intron retention predominated in AS model, followed by exon skipping. Interestingly, we found that DNA methylation played an important role in generating various AS isoforms by regulating splicing sites, promoter regions and first exons. Furthermore, we identified a large of fusion transcripts and novel lncRNAs, and found that DNA methylation of the promoter and gene body could regulate lncRNA expression. Our results significantly improved existed gene models of pig and unveiled that pig AS and epigenetic modify were more complex than previously thought.
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Affiliation(s)
- Yao Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - An Hu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Do social insects support Haig's kin theory for the evolution of genomic imprinting? Epigenetics 2018; 12:725-742. [PMID: 28703654 PMCID: PMC5739101 DOI: 10.1080/15592294.2017.1348445] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although numerous imprinted genes have been described in several lineages, the phenomenon of genomic imprinting presents a peculiar evolutionary problem. Several hypotheses have been proposed to explain gene imprinting, the most supported being Haig's kinship theory. This theory explains the observed pattern of imprinting and the resulting phenotypes as a competition for resources between related individuals, but despite its relevance it has not been independently tested. Haig's theory predicts that gene imprinting should be present in eusocial insects in many social scenarios. These lineages are therefore ideal for testing both the theory's predictions and the mechanism of gene imprinting. Here we review the behavioral evidence of genomic imprinting in eusocial insects, the evidence of a mechanism for genomic imprinting and finally we evaluate recent results showing parent of origin allele specific expression in honeybees in the light of Haig's theory.
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Affiliation(s)
- Mirko Pegoraro
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Hollie Marshall
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Zoë N Lonsdale
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Eamonn B Mallon
- a Department of Genetics and Genome Biology , University of Leicester , UK
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Lardenoije R, Pishva E, Lunnon K, van den Hove DL. Neuroepigenetics of Aging and Age-Related Neurodegenerative Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:49-82. [PMID: 30072060 DOI: 10.1016/bs.pmbts.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current state of play for epigenetic research into neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. We focus on the recent evidence for a potential role of DNA modifications, histone modifications and non-coding RNA in the etiology of these disorders. Finally, we discuss how new technological and bioinformatics advances in the field of epigenetics could further progress our understanding about the underlying mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Roy Lardenoije
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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Murcia O, Jover R, Egoavil C, Perez-Carbonell L, Juárez M, Hernández-Illán E, Rojas E, Alenda C, Balaguer F, Andreu M, Llor X, Castells A, Boland CR, Goel A. TFAP2E Methylation and Expression Status Does Not Predict Response to 5-FU-based Chemotherapy in Colorectal Cancer. Clin Cancer Res 2018. [PMID: 29535127 DOI: 10.1158/1078-0432.ccr-17-2940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Purpose: A recent study reported that 5-fluorouracil (5-FU)-based chemotherapy is less effective in treating patients with advanced colorectal cancer demonstrating hypermethylation of the TFAP2E gene. The aim of our study was to confirm and validate these findings in large, uniformly treated, well-characterized patient cohorts.Experimental Design: Two cohorts of 783 patients with colorectal cancer: 532 from a population-based, multicenter cohort (EPICOLON I) and 251 patients from a clinic-based trial were used to study the effectiveness of TFAP2E methylation and expression as a predictor of response of colorectal cancer patients to 5-FU-based chemotherapy. DNA methylation status of the TFAP2E gene in patients with colorectal cancer was assessed by quantitative bisulfite pyrosequencing analysis. IHC analysis of the TFAP2E protein expression was also performed.Results: Correlation between TFAP2E methylation status and IHC staining was performed in 607 colorectal cancer samples. Among 357 hypermethylated tumors, only 141 (39.6%) exhibited loss of protein expression. Survival was not affected by TFAP2E hypermethylation in stage IV patients [HR, 1.21; 95% confidence interval (CI), 0.79-1.87; log-rank P = 0.6]. In stage II-III cases, disease-free survival was not influenced by TFAP2E hypermethylation status in 5-FU-treated (HR, 0.91; 95% CI, 0.52-1.59; log-rank P = 0.9) as well as in nontreated patients (HR, 0.88; 95% CI, 0.5-1.54; log-rank P = 0.7).Conclusions:TFAP2E hypermethylation does not correlate with loss of its protein expression. Our large, systematic, and comprehensive study indicates that TFAP2E methylation and expression may not play a major role in predicting response to 5-FU-based chemotherapy in patients with colorectal cancer. Clin Cancer Res; 24(12); 2820-7. ©2018 AACR.
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Affiliation(s)
- Oscar Murcia
- Unidad de Gastroenterologia, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain
| | - Rodrigo Jover
- Unidad de Gastroenterologia, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain.
| | - Cecilia Egoavil
- Research Unit, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain.,Department of Pathology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain
| | - Lucia Perez-Carbonell
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Miriam Juárez
- Research Unit, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain
| | - Eva Hernández-Illán
- Research Unit, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain
| | - Estefania Rojas
- Department of Pathology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain
| | - Cristina Alenda
- Department of Pathology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria ISABIAL, Alicante, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Spain
| | | | - Xavier Llor
- Department of Medicine, Yale University Medical Center, New Haven, Connecticut
| | - Antoni Castells
- Gastroenterology Department, Hospital Clinic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - C Richard Boland
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas.
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Kim D, Shivakumar M, Han S, Sinclair MS, Lee YJ, Zheng Y, Olopade OI, Kim D, Lee Y. Population-dependent Intron Retention and DNA Methylation in Breast Cancer. Mol Cancer Res 2018; 16:461-469. [PMID: 29330282 DOI: 10.1158/1541-7786.mcr-17-0227] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 09/15/2017] [Accepted: 11/27/2017] [Indexed: 12/31/2022]
Abstract
Regulation of gene expression by DNA methylation in gene promoter regions is well studied; however, the effects of methylation in the gene body (exons and introns) on gene expression are comparatively understudied. Recently, hypermethylation has been implicated in the inclusion of alternatively spliced exons; moreover, exon recognition can be enhanced by recruiting the methyl-CpG-binding protein (MeCP2) to hypermethylated sites. This study examines whether the methylation status of an intron is correlated with how frequently the intron is retained during splicing using DNA methylation and RNA sequencing data from breast cancer tissue specimens in The Cancer Genome Atlas. Interestingly, hypomethylation of introns is correlated with higher levels of intron expression in mRNA and the methylation level of an intron is inversely correlated with its retention in mRNA from the gene in which it is located. Furthermore, significant population differences were observed in the methylation level of retained introns. In African-American donors, retained introns were not only less methylated compared to European-American donors, but also were more highly expressed. This underscores the need for understanding epigenetic differences in populations and their correlation with breast cancer is an important step toward achieving personalized cancer care.Implications: This research contributes to the understanding of how epigenetic markers in the gene body communicate with the transcriptional machinery to control transcript diversity and differential biological response to changes in methylation status could underlie some of the known, yet unexplained, disparities in certain breast cancer patient populations. Mol Cancer Res; 16(3); 461-9. ©2018 AACR.
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Affiliation(s)
- Dongwook Kim
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Manu Shivakumar
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania
| | - Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Michael S Sinclair
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Young-Ji Lee
- Department of Health and Community Systems, University of Pittsburgh School of Nursing, Pittsburgh, Pennsylvania
| | - Yonglan Zheng
- Department of Medicine, University of Chicago, Chicago, Illinois
| | | | - Dokyoon Kim
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania.
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, Utah.
- Huntsman Cancer Institute, Salt Lake City, Utah
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24
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Gatto S, Gagliardi M, Franzese M, Leppert S, Papa M, Cammisa M, Grillo G, Velasco G, Francastel C, Toubiana S, D’Esposito M, Angelini C, Matarazzo MR. ICF-specific DNMT3B dysfunction interferes with intragenic regulation of mRNA transcription and alternative splicing. Nucleic Acids Res 2017; 45:5739-5756. [PMID: 28334849 PMCID: PMC5449610 DOI: 10.1093/nar/gkx163] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 12/11/2022] Open
Abstract
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown. We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate the genome-scale effects of DNMT3B dysfunction. We highlighted that altered intragenic CpG-methylation impairs multiple aspects of transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing. These defects preferentially associate with changes of intragenic H3K4me3 and at lesser extent of H3K27me3 and H3K36me3. In addition, we highlighted a novel DNMT3B activity in modulating the self-regulatory circuit of sense-antisense pairs and the exon skipping during alternative splicing, through interacting with RNA molecules. Strikingly, altered transcription affects disease relevant genes, as for instance the memory-B cell marker CD27 and PTPRC genes, providing us with biological insights into the ICF1-syndrome pathogenesis. Our genome-scale approach sheds light on the mechanisms still poorly understood of the intragenic function of DNMT3B and DNA methylation in gene expression regulation.
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Affiliation(s)
- Sole Gatto
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Sanford Burnham Prebys Medical Discovery Research Institute, La Jolla, CA, USA
| | - Miriam Gagliardi
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Monica Franzese
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Sylwia Leppert
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
| | - Mariarosaria Papa
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
| | - Marco Cammisa
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta 81100, Italy
| | - Giacomo Grillo
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Guillame Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, Paris 75205, France
| | - Shir Toubiana
- Molecular Medicine Laboratory, Rambam Health Care Campus and Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Maurizio D’Esposito
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Claudia Angelini
- Institute for Applied Mathematics ‘Mauro Picone’, CNR, Naples 80131, Italy
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics ‘Adriano Buzzati-Traverso’, CNR, Naples 80131, Italy
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25
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A saga of cancer epigenetics: linking epigenetics to alternative splicing. Biochem J 2017; 474:885-896. [PMID: 28270561 DOI: 10.1042/bcj20161047] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 12/29/2016] [Accepted: 01/05/2017] [Indexed: 12/14/2022]
Abstract
The discovery of an increasing number of alternative splicing events in the human genome highlighted that ∼94% of genes generate alternatively spliced transcripts that may produce different protein isoforms with diverse functions. It is now well known that several diseases are a direct and indirect consequence of aberrant splicing events in humans. In addition to the conventional mode of alternative splicing regulation by 'cis' RNA-binding sites and 'trans' RNA-binding proteins, recent literature provides enormous evidence for epigenetic regulation of alternative splicing. The epigenetic modifications may regulate alternative splicing by either influencing the transcription elongation rate of RNA polymerase II or by recruiting a specific splicing regulator via different chromatin adaptors. The epigenetic alterations and aberrant alternative splicing are known to be associated with various diseases individually, but this review discusses/highlights the latest literature on the role of epigenetic alterations in the regulation of alternative splicing and thereby cancer progression. This review also points out the need for further studies to understand the interplay between epigenetic modifications and aberrant alternative splicing in cancer progression.
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Pang APS, Sugai C, Maunakea AK. High-throughput sequencing offers new insights into 5-hydroxymethylcytosine. Biomol Concepts 2017; 7:169-78. [PMID: 27356236 DOI: 10.1515/bmc-2016-0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/01/2016] [Indexed: 01/15/2023] Open
Abstract
Chemical modifications of DNA comprise epigenetic mechanisms that contribute to the maintenance of cellular activities and memory. Although the function of 5-methylcytosine (5-mC) has been extensively studied, little is known about the function(s) of relatively rarer and underappreciated cytosine modifications including 5-hydroxymethylcytosine (5-hmC). The discovery that ten-eleven translocation (Tet) proteins mediate conversion of 5-mC to 5-hmC, and other oxidation derivatives, sparked renewed interest to understand the biological role of 5-hmC. Studies examining total 5-hmC levels revealed the highly dynamic yet tissue-specific nature of this modification, implicating a role in epigenetic regulation and development. Intriguingly, 5-hmC levels are highest during early development and in the brain where abnormal patterns of 5-hmC have been observed in disease conditions. Thus, 5-hmC adds to the growing list of epigenetic modifications with potential utility in clinical applications and warrants further investigation. This review discusses the emerging functional roles of 5-hmC in normal and disease states, focusing primarily on insights provided by recent studies exploring the genome-wide distribution of this modification in mammals.
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Karambataki M, Malousi A, Tzimagiorgis G, Haitoglou C, Fragou A, Georgiou E, Papadopoulou F, Krassas GE, Kouidou S. Association of two synonymous splicing-associated CpG single nucleotide polymorphisms in calpain 10 and solute carrier family 2 member 2 with type 2 diabetes. Biomed Rep 2016; 6:146-158. [PMID: 28357066 PMCID: PMC5351308 DOI: 10.3892/br.2016.833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/11/2016] [Indexed: 01/01/2023] Open
Abstract
Coding synonymous single nucleotide polymorphisms (SNPs) have attracted little attention until recently. However, such SNPs located in epigenetic, CpG sites modifying exonic splicing enhancers (ESEs) can be informative with regards to the recently verified association of intragenic methylation and splicing. The present study describes the association of type 2 diabetes (T2D) with the exonic, synonymous, epigenetic SNPs, rs3749166 in calpain 10 (CAPN10) glucose transporter (GLUT4) translocator and rs5404 in solute carrier family 2, member 2 (SLC2A2), also termed GLUT2, which, according to prior bioinformatic analysis, strongly modify the splicing potential of glucose transport-associated genes. Previous association studies reveal that only rs5404 exhibits a strong negative T2D association, while data on the CAPN10 polymorphism are contradictory. In the present study DNA from blood samples of 99 Greek non-diabetic control subjects and 71 T2D patients was analyzed. In addition, relevant publicly available cases (40) resulting from examination of 110 Personal Genome Project data files were analyzed. The frequency of the rs3749166 A allele, was similar in the patients and non-diabetic control subjects. However, AG heterozygotes were more frequent among patients (73.24% for Greek patients and 54.55% for corresponding non-diabetic control subjects; P=0.0262; total cases, 52.99 and 75.00%, respectively; P=0.0039). The rs5404 T allele was only observed in CT heterozygotes (Greek non-diabetic control subjects, 39.39% and Greek patients, 22.54%; P=0.0205; total cases, 34.69 and 21.28%, respectively; P=0.0258). Notably, only one genotype, heterozygous AG/CC, was T2D-associated (Greek non-diabetic control subjects, 29.29% and Greek patients, 56.33%; P=0.004; total cases, 32.84 and 56.58%, respectively; P=0.0008). Furthermore, AG/CC was strongly associated with very high (≥8.5%) glycosylated plasma hemoglobin levels among patients (P=0.0002 for all cases). These results reveal the complex heterozygotic SNP association with T2D, and indicate possible synergies of these epigenetic, splicing-regulatory, synonymous SNPs, which modify the splicing potential of two alternative glucose transport-associated genes.
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Affiliation(s)
- Maria Karambataki
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece; Department of Endocrinology, Diabetes and Metabolism, Panagia General Hospital, Thessaloniki 55132, Greece
| | - Andigoni Malousi
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Georgios Tzimagiorgis
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Constantinos Haitoglou
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Aikaterini Fragou
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Elisavet Georgiou
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Foteini Papadopoulou
- Department of Endocrinology, Diabetes and Metabolism, Panagia General Hospital, Thessaloniki 55132, Greece
| | - Gerasimos E Krassas
- Department of Endocrinology, Diabetes and Metabolism, Panagia General Hospital, Thessaloniki 55132, Greece
| | - Sofia Kouidou
- Laboratory of Biological Chemistry, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
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28
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The integration of epigenetics and genetics in nutrition research for CVD risk factors. Proc Nutr Soc 2016; 76:333-346. [DOI: 10.1017/s0029665116000823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is increasing evidence documenting gene-by-environment (G × E) interactions for CVD related traits. However, the underlying mechanisms are still unclear. DNA methylation may represent one of such potential mechanisms. The objective of this review paper is to summarise the current evidence supporting the interplay among DNA methylation, genetic variants, and environmental factors, specifically (1) the association between SNP and DNA methylation; (2) the role that DNA methylation plays in G × E interactions. The current evidence supports the notion that genotype-dependent methylation may account, in part, for the mechanisms underlying observed G × E interactions in loci such asAPOE, IL6and ATP-binding cassette A1. However, these findings should be validated using intervention studies with high level of scientific evidence. The ultimate goal is to apply the knowledge and the technology generated by this research towards genetically based strategies for the development of personalised nutrition and medicine.
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Mamrut S, Avidan N, Staun-Ram E, Ginzburg E, Truffault F, Berrih-Aknin S, Miller A. Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions. Epigenetics 2016; 10:943-57. [PMID: 26291385 DOI: 10.1080/15592294.2015.1084462] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The relationship between DNA methylation and gene expression is complex and elusive. To further elucidate these relations, we performed an integrative analysis of the methylome and transcriptome of 4 circulating immune cell subsets (B cells, monocytes, CD4(+), and CD8(+) T cells) from healthy females. Additionally, in light of the known sex bias in the prevalence of several immune-mediated diseases, the female datasets were compared with similar public available male data sets. Immune cell-specific differentially methylated regions (DMRs) were found to be highly similar between sexes, with an average correlation coefficient of 0.82; however, numerous sex-specific DMRs, shared by the cell subsets, were identified, mainly on autosomal chromosomes. This provides a list of highly interesting candidate genes to be studied in disorders with sexual dimorphism, such as autoimmune diseases. Immune cell-specific DMRs were mainly located in the gene body and intergenic region, distant from CpG islands but overlapping with enhancer elements, indicating that distal regulatory elements are important in immune cell specificity. In contrast, sex-specific DMRs were overrepresented in CpG islands, suggesting that the epigenetic regulatory mechanisms of sex and immune cell specificity may differ. Both positive and, more frequently, negative correlations between subset-specific expression and methylation were observed, and cell-specific DMRs of both interactions were associated with similar biological pathways, while sex-specific DMRs were linked to networks of early development or estrogen receptor and immune-related molecules. Our findings of immune cell- and sex-specific methylome and transcriptome profiles provide novel insight on their complex regulatory interactions and may particularly contribute to research of immune-mediated diseases.
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Affiliation(s)
- Shimrat Mamrut
- a Rappaport Faculty of Medicine; Technion-Israel Institute of Technology ; Haifa , Israel
| | - Nili Avidan
- a Rappaport Faculty of Medicine; Technion-Israel Institute of Technology ; Haifa , Israel
| | - Elsebeth Staun-Ram
- a Rappaport Faculty of Medicine; Technion-Israel Institute of Technology ; Haifa , Israel
| | - Elizabeta Ginzburg
- a Rappaport Faculty of Medicine; Technion-Israel Institute of Technology ; Haifa , Israel
| | - Frederique Truffault
- b INSERM - U974/CNRS UMR7215//UPMC UM76/AIM; Institute of Myology Pitie-Salpetriere ; Paris , France
| | - Sonia Berrih-Aknin
- b INSERM - U974/CNRS UMR7215//UPMC UM76/AIM; Institute of Myology Pitie-Salpetriere ; Paris , France
| | - Ariel Miller
- a Rappaport Faculty of Medicine; Technion-Israel Institute of Technology ; Haifa , Israel.,c Division of Neuroimmunology; Lady Davis Carmel Medical Center ; Haifa , Israel
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Shojaei Saadi HA, Gagné D, Fournier É, Baldoceda Baldeon LM, Sirard MA, Robert C. Responses of bovine early embryos to S-adenosyl methionine supplementation in culture. Epigenomics 2016; 8:1039-60. [PMID: 27419740 DOI: 10.2217/epi-2016-0022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM There is a growing concern about the potential adverse effects of high dose folic acid (FA) supplementation before and during pregnancy. FA metabolism generates S-adenosyl methionine (SAM) which is an important cofactor of epigenetic programming. We sought to assess the impact of a large dose of SAM on early embryo development. MATERIALS & METHODS In vitro cultured bovine embryos were treated with SAM from the eight-cell stage to the blastocyst stage. In addition to the phenotype, the genome-wide epigenetic and transcription profiles were analyzed. RESULTS Treatment significantly improved embryo hatching and caused a shift in sex ratio in favor of males. SAM caused genome-wide hypermethylation mainly in exonic regions and in CpG islands. Although differentially expressed genes were associated with response to nutrients and developmental processes, no correspondence was found with the differentially methylated regions, suggesting that cellular responses to SAM treatment during early embryo development may not require DNA methylation-driven changes. CONCLUSION Since bovine embryos were not indifferent to SAM, effects of large-dose FA supplements on early embryonic development in humans cannot be ruled out.
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Affiliation(s)
- Habib A Shojaei Saadi
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Dominic Gagné
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Éric Fournier
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Luis Manuel Baldoceda Baldeon
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Marc-André Sirard
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Claude Robert
- Centre de recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des sciences animales, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, G1V 0A6, Canada
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31
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González C, Salces-Ortiz J, Calvo JH, Serrano MM. In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene. Cell Stress Chaperones 2016; 21:415-27. [PMID: 26810179 PMCID: PMC4837184 DOI: 10.1007/s12192-016-0668-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/02/2016] [Accepted: 01/06/2016] [Indexed: 01/21/2023] Open
Abstract
Gene promoters are essential regions of DNA where the transcriptional molecular machinery to produce RNA molecules is recruited. In this process, DNA epigenetic modifications can acquire a fundamental role in the regulation of gene expression. Recently, in a previous work of our group, functional features and DNA methylation involved in the ovine HSP90AA1 gene expression regulation have been observed. In this work, we report a combination of methylation analysis by bisulfite sequencing in several tissues and at different developmental stages together with in silico bioinformatic analysis of putative regulating factors in order to identify regulative mechanisms both at the promoter and gene body. Our results show a "hybrid structure" (TATA box + CpG island) of the ovine HSP90AA1 gene promoter both in somatic and non-differentiated germ tissues, revealing the ability of the HSP90AA1 gene to be regulated both in an inducible and constitutive fashion. In addition, in silico analysis showed that several putative alternative spliced regulatory motifs, exonic splicing enhancers (ESEs), and G-quadruplex secondary structures were somehow related to the DNA methylation pattern found. The results obtained here could help explain the differences in cell-type transcripts, tissue expression rate, and transcription silencing mechanisms found in this gene.
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Affiliation(s)
| | | | - Jorge H Calvo
- Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain
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32
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Habano W, Kawamura K, Iizuka N, Terashima J, Sugai T, Ozawa S. Analysis of DNA methylation landscape reveals the roles of DNA methylation in the regulation of drug metabolizing enzymes. Clin Epigenetics 2015; 7:105. [PMID: 26421064 PMCID: PMC4587720 DOI: 10.1186/s13148-015-0136-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/15/2015] [Indexed: 12/24/2022] Open
Abstract
Background Drug metabolizing enzymes (DMEs) exhibit dramatic inter- and intra-individual variability in expression and activity. However, the mechanisms determining this variability have not been fully elucidated. The aim of this study was to evaluate the biological significance of DNA methylation in the regulation of DME genes by genome-wide integrative analysis. Results DNA methylation and mRNA expression profiles of human tissues and hepatoma cells were examined by microarrays. The data were combined with GEO datasets of liver tissues, and integrative analysis was performed on selected DME genes. Detailed DNA methylation statuses at individual CpG sites were evaluated by DNA methylation mapping. From analysis of 20 liver tissues, highly variable DNA methylation was observed in 37 DME genes, 7 of which showed significant inverse correlations between DNA methylation and mRNA expression. In hepatoma cells, treatment with a demethylating agent resulted in upregulation of 5 DME genes, which could be explained by DNA methylation status. Interestingly, some DMEs were suggested to act as tumor-suppressor or housekeeper based on their unique DNA methylation features. Moreover, tissue-specific and age-dependent expression of UDP-glucuronosyltransferase 1A splicing variants was associated with DNA methylation status of individual first exons. Conclusions Some DME genes were regulated by DNA methylation, potentially resulting in inter- and intra-individual differences in drug metabolism. Analysis of DNA methylation landscape facilitated elucidation of the role of DNA methylation in the regulation of DME genes, such as mediator of inter-individual variability, guide for correct alternative splicing, and potential tumor-suppressor or housekeeper. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0136-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wataru Habano
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Kohei Kawamura
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Natsuki Iizuka
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Jun Terashima
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Tamotsu Sugai
- Department of Diagnostic Pathology, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Shogo Ozawa
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
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Salami F, Qiao S, Homayouni R. Expression of mouse Dab2ip transcript variants and gene methylation during brain development. Gene 2015; 568:19-24. [PMID: 25958345 DOI: 10.1016/j.gene.2015.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/15/2015] [Accepted: 05/05/2015] [Indexed: 11/24/2022]
Abstract
Dab2ip (DOC-2/DAB2 interacting protein) is a RasGAP protein which shows a growth-inhibitory effect in human prostate cancer cell lines. Recent studies have shown that Dab2ip also plays an important role in regulating dendrite development and neuronal migration during brain development. In this study, we provide a more complete description of the mouse Dab2ip (mDab2ip) gene locus and examined DNA methylation and expression of Dab2ip during cerebellar development. Analysis of cDNA sequences in public databases revealed a total of 20 possible exons for mDab2ip gene, spanning over 172kb. Using Cap Analysis of Gene Expression (CAGE) data available through FANTOM5 project, we deduced five different transcription start sites for mDab2ip. Here, we characterized three different mDab2ip transcript variants beginning with exon 1. These transcripts varied by the presence or absence of exons 3 and 5, which encode a putative nuclear localization signal and the N-terminal region of a PH-domain, respectively. The 5' region of the mDab2ip gene contains three putative CpG islands (CpG131, CpG54, and CpG85). Interestingly, CpG54 and CpG85 are localized on exons 3 and 5. Bisulfate DNA sequencing showed that methylation level of CpG54 remained constant whereas methylation of CpG85 increased during cerebellar development. Real-time PCR analysis showed that the proportion of PH-domain containing mDab2ip transcripts increased during cerebellar development, in correlation with the increase in CpG85 methylation. These data suggest that site-specific methylation of mDab2ip gene during cerebellar development may play a role in inclusion of exon 5, resulting in a Dab2ip transcript variant that encodes a full pleckstrin homology (PH) domain.
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Affiliation(s)
- Farimah Salami
- Department of Biological Sciences, University of Memphis, Memphis, TN, United States
| | - Shuhong Qiao
- Department of Biological Sciences, University of Memphis, Memphis, TN, United States
| | - Ramin Homayouni
- Department of Biological Sciences, University of Memphis, Memphis, TN, United States.
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34
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Hassan MA, Saeij JP. Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits. Bioessays 2014; 36:1032-40. [PMID: 25171292 PMCID: PMC4280019 DOI: 10.1002/bies.201400079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing can also generate proteomic diversity and impact genetic traits. Indeed, it is known that splicing and RNA editing modulate several traits in humans and model organisms. Using high-throughput RNA sequencing (RNA-seq) analysis, it is now possible to integrate the genetics of transcript abundance, alternative splicing (AS) and editing with the analysis of complex traits. We recently demonstrated that both AS and mRNA editing are modulated by genetic and environmental factors, and potentially engender phenotypic diversity in a genetically segregating mouse population. Therefore, the analysis of splicing and RNA editing can expand not only the regulatory landscape of transcriptome and proteome complexity, but also the repertoire of candidate genes for complex traits.
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Affiliation(s)
- Musa A. Hassan
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
| | - Jeroen P.J. Saeij
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
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35
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Jiang N, Wang L, Chen J, Wang L, Leach L, Luo Z. Conserved and divergent patterns of DNA methylation in higher vertebrates. Genome Biol Evol 2014; 6:2998-3014. [PMID: 25355807 PMCID: PMC4255770 DOI: 10.1093/gbe/evu238] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2014] [Indexed: 02/07/2023] Open
Abstract
DNA methylation in the genome plays a fundamental role in the regulation of gene expression and is widespread in the genome of eukaryotic species. For example, in higher vertebrates, there is a "global" methylation pattern involving complete methylation of CpG sites genome-wide, except in promoter regions that are typically enriched for CpG dinucleotides, or so called "CpG islands." Here, we comprehensively examined and compared the distribution of CpG sites within ten model eukaryotic species and linked the observed patterns to the role of DNA methylation in controlling gene transcription. The analysis revealed two distinct but conserved methylation patterns for gene promoters in human and mouse genomes, involving genes with distinct distributions of promoter CpGs and gene expression patterns. Comparative analysis with four other higher vertebrates revealed that the primary regulatory role of the DNA methylation system is highly conserved in higher vertebrates.
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Affiliation(s)
- Ning Jiang
- Department of Biostatistics & Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China School of Biosciences, The University of Birmingham, Birmingham B15 2TT United Kingdom
| | - Lin Wang
- Department of Biostatistics & Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Chen
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT United Kingdom
| | - Luwen Wang
- Department of Biostatistics & Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Lindsey Leach
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT United Kingdom
| | - Zewei Luo
- Department of Biostatistics & Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China School of Biosciences, The University of Birmingham, Birmingham B15 2TT United Kingdom
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Liyanage VRB, Jarmasz JS, Murugeshan N, Del Bigio MR, Rastegar M, Davie JR. DNA modifications: function and applications in normal and disease States. BIOLOGY 2014; 3:670-723. [PMID: 25340699 PMCID: PMC4280507 DOI: 10.3390/biology3040670] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/12/2022]
Abstract
Epigenetics refers to a variety of processes that have heritable effects on gene expression programs without changes in DNA sequence. Key players in epigenetic control are chemical modifications to DNA, histone, and non-histone chromosomal proteins, which establish a complex regulatory network that controls genome function. Methylation of DNA at the fifth position of cytosine in CpG dinucleotides (5-methylcytosine, 5mC), which is carried out by DNA methyltransferases, is commonly associated with gene silencing. However, high resolution mapping of DNA methylation has revealed that 5mC is enriched in exonic nucleosomes and at intron-exon junctions, suggesting a role of DNA methylation in the relationship between elongation and RNA splicing. Recent studies have increased our knowledge of another modification of DNA, 5-hydroxymethylcytosine (5hmC), which is a product of the ten-eleven translocation (TET) proteins converting 5mC to 5hmC. In this review, we will highlight current studies on the role of 5mC and 5hmC in regulating gene expression (using some aspects of brain development as examples). Further the roles of these modifications in detection of pathological states (type 2 diabetes, Rett syndrome, fetal alcohol spectrum disorders and teratogen exposure) will be discussed.
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Affiliation(s)
- Vichithra R B Liyanage
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Jessica S Jarmasz
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Nanditha Murugeshan
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Marc R Del Bigio
- Department of Human Anatomy and Cell Science, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - Mojgan Rastegar
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
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Song Y, Zuo Y. Occurrence of HHIP gene CpG island methylation in gastric cancer. Oncol Lett 2014; 8:2340-2344. [PMID: 25295121 PMCID: PMC4186611 DOI: 10.3892/ol.2014.2518] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 08/07/2014] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to observe the methylation status of the CpG islands at the human hedgehog interacting protein (HHIP) gene in gastric cancer tissues, peritumoral tissues and the AGS cell line, to analyze the association between the methylation status of the CpG islands and the tumorigenesis of gastric cancer. The HHIP mRNA expression in 60 human gastric carcinnoma tissues, peritumoral tissues and the gastric carcinoma AGS cell line were detected by reverse transcription polymerase chain reaction (RT-PCR). The HHIP methylation status of the promoter region in the gastric carcinnoma tissues and peritumoral tissues was detected by methylation-specific PCR (MSP). Prior to and following treatment with methyl transferase inhibitor 5-aza-2'-deoxycitydine (5-aza-dc), the HHIP mRNA expression level, the methylation status of the promoter region and the methylation site loci on the CpG islands in the AGS cells were detected by RT-PCR, MSP and bisulfite sequencing PCR (BSP), respectively. The correlation between the methylation status of the CpG islands at the HHIP promoter region and the HHIP mRNA expression level were analyzed. It was found that the expression level of the HHIP mRNA in the gastric carcinoma tissues was significantly lower than that in the adjacent tissues (0.82±0.38 vs. 1.60±0.26, respectively; P<0.001). No significant correlations were observed between the expression of HHIP mRNA and age, gender, tumor-node-metastasis stage, differentiation degree and presence of lymph node metastasis (P>0.05). The degree of methylation of the HHIP gene promotor in the peritumoral tissues (17.7±3.59%) was significantly lower than that in the gastric cancer tissues (62.9±6.14%) and in the AGS cells (99.7±0.67%) (P<0.05). Compared with prior to 5-aza-dc intervention, the HHIP mRNA expression level in the AGS cells was significantly increased subsequent to intervention (0.21±0.12 vs. 4.68±0.22; P<0.01), while the degree of methylation in the AGS cells was significantly decreased (90.2±0.67 vs. 10.1±0.21%; P<0.01), and the methylation sites in CpG islands were significantly reduced. The degree of HHIP methylation showed a negative correlation with the level of mRNA expression (r=-0.693; P<0.01). It can be hypothesized that a high degree of methylation of the HHIP gene promoter CpG islands in gastric cancer tissues and cells causes a decrease in HHIP mRNA expression, which may be involved in the carcinogenesis of gastric cancer.
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Affiliation(s)
- Yu Song
- Department of Oncology, Zhangjiagang First People's Hospital, Suzhou, Jiangsu 215600, P.R. China
| | - Yun Zuo
- Department of Oncology, Zhangjiagang First People's Hospital, Suzhou, Jiangsu 215600, P.R. China
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Jeong M, Goodell MA. New answers to old questions from genome-wide maps of DNA methylation in hematopoietic cells. Exp Hematol 2014; 42:609-17. [PMID: 24993071 PMCID: PMC4137036 DOI: 10.1016/j.exphem.2014.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 01/10/2023]
Abstract
DNA methylation is a well-studied epigenetic modification essential for efficient cellular differentiation. Aberrant DNA methylation patterns are a characteristic feature of cancer, including myeloid malignancies such as acute myeloid leukemia. Recurrent mutations in DNA-modifying enzymes were identified in acute myeloid leukemia and linked to distinct DNA methylation signatures. In addition, discovery of Tet enzymes provided new mechanisms for the reversal of DNA methylation. Advances in base-resolution profiling of DNA methylation have enabled a more comprehensive understanding of the methylome landscape in the genome. This review will summarize and discuss the key questions in the function of DNA methylation in the hematopoietic system, including where and how DNA methylation regulates diverse biological processes in the genome as elucidated by recent studies.
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Affiliation(s)
- Mira Jeong
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Margaret A. Goodell
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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Messerschmidt DM, Knowles BB, Solter D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev 2014; 28:812-28. [PMID: 24736841 PMCID: PMC4003274 DOI: 10.1101/gad.234294.113] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Methylation of DNA is an essential epigenetic control mechanism in mammals. Messerschmidt et al. review the current understanding of epigenetic dynamics regulating the molecular processes that prepare the mammalian embryo for normal development. Methylation of DNA is an essential epigenetic control mechanism in mammals. During embryonic development, cells are directed toward their future lineages, and DNA methylation poses a fundamental epigenetic barrier that guides and restricts differentiation and prevents regression into an undifferentiated state. DNA methylation also plays an important role in sex chromosome dosage compensation, the repression of retrotransposons that threaten genome integrity, the maintenance of genome stability, and the coordinated expression of imprinted genes. However, DNA methylation marks must be globally removed to allow for sexual reproduction and the adoption of the specialized, hypomethylated epigenome of the primordial germ cell and the preimplantation embryo. Recent technological advances in genome-wide DNA methylation analysis and the functional description of novel enzymatic DNA demethylation pathways have provided significant insights into the molecular processes that prepare the mammalian embryo for normal development.
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Affiliation(s)
- Daniel M Messerschmidt
- Developmental Epigenetics and Disease, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), 138673 Singapore,
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40
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Schneider E, El Hajj N, Richter S, Roche-Santiago J, Nanda I, Schempp W, Riederer P, Navarro B, Bontrop RE, Kondova I, Scholz CJ, Haaf T. Widespread differences in cortex DNA methylation of the "language gene" CNTNAP2 between humans and chimpanzees. Epigenetics 2014; 9:533-45. [PMID: 24434791 PMCID: PMC4121364 DOI: 10.4161/epi.27689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CNTNAP2, one of the largest genes in the human genome, has been linked to human-specific language abilities and neurodevelopmental disorders. Our hypothesis is that epigenetic rather than genetic changes have accelerated the evolution of the human brain. To compare the cortex DNA methylation patterns of human and chimpanzee CNTNAP2 at ultra-high resolution, we combined methylated DNA immunoprecipitation (MeDIP) with NimbleGen tiling arrays for the orthologous gene and flanking sequences. Approximately 1.59 Mb of the 2.51 Mb target region could be aligned and analyzed with a customized algorithm in both species. More than one fifth (0.34 Mb) of the analyzed sequence throughout the entire gene displayed significant methylation differences between six human and five chimpanzee cortices. One of the most striking interspecies differences with 28% methylation in human and 59% in chimpanzee cortex (by bisulfite pyrosequencing) lies in a region 300 bp upstream of human SNP rs7794745 which has been associated with autism and parent-of-origin effects. Quantitative real-time RT PCR revealed that the protein-coding splice variant CNTNAP2-201 is 1.6-fold upregulated in human cortex, compared with the chimpanzee. Transcripts CNTNAP2-001, -002, and -003 did not show skewed allelic expression, which argues against CNTNAP2 imprinting, at least in adult human brain. Collectively, our results suggest widespread cortex DNA methylation changes in CNTNAP2 since the human-chimpanzee split, supporting a role for CNTNAP2 fine-regulation in human-specific language and communication traits.
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Affiliation(s)
- Eberhard Schneider
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | - Nady El Hajj
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | - Steven Richter
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | | | - Indrajit Nanda
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
| | - Werner Schempp
- Institute for Human Genetics; University of Freiburg; Freiburg, Germany
| | - Peter Riederer
- Clinical Neurochemistry Laboratory; Department of Psychiatry; University Hospital; Würzburg, Germany
| | - Bianca Navarro
- Institute of Legal Medicine; University Medical Center; Mainz, Germany
| | | | - Ivanela Kondova
- Biomedical Primate Research Center; Rijswijk, The Netherlands
| | - Claus Jürgen Scholz
- Laboratory for Microarray Applications; IZKF; Julius Maximilians University; Würzburg, Germany
| | - Thomas Haaf
- Institute for Human Genetics; Julius Maximilian University; Würzburg, Germany
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41
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Tatarinova T, Elhaik E, Pellegrini M. Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol 2013; 5:1443-56. [PMID: 23833164 PMCID: PMC3762193 DOI: 10.1093/gbe/evt103] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The GC content in the third codon position (GC3) exhibits a unimodal distribution in many plant and animal genomes. Interestingly, grasses and homeotherm vertebrates exhibit a unique bimodal distribution. High GC3 was previously found to be associated with variable expression, higher frequency of upstream TATA boxes, and an increase of GC3 from 5′ to 3′. Moreover, GC3-rich genes are predominant in certain gene classes and are enriched in CpG dinucleotides that are potential targets for methylation. Based on the GC3 bimodal distribution we hypothesize that GC3 has a regulatory role involving methylation and gene expression. To test that hypothesis, we selected diverse taxa (rice, thale cress, bee, and human) that varied in the modality of their GC3 distribution and tested the association between GC3, DNA methylation, and gene expression. We examine the relationship between cytosine methylation levels and GC3, gene expression, genome signature, gene length, and other gene compositional features. We find a strong negative correlation (Pearson’s correlation coefficient r = −0.67, P value < 0.0001) between GC3 and genic CpG methylation. The comparison between 5′-3′ gradients of CG3-skew and genic methylation for the taxa in the study suggests interplay between gene-body methylation and transcription-coupled cytosine deamination effect. Compositional features are correlated with methylation levels of genes in rice, thale cress, human, bee, and fruit fly (which acts as an unmethylated control). These patterns allow us to generate evolutionary hypotheses about the relationships between GC3 and methylation and how these affect expression patterns. Specifically, we propose that the opposite effects of methylation and compositional gradients along coding regions of GC3-poor and GC3-rich genes are the products of several competing processes.
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Affiliation(s)
- Tatiana Tatarinova
- Laboratory of Applied Pharmacokinetics and Bioinformatics, University of Southern California.
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42
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Chuang TJ, Chen FC. DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals. Mol Biol Evol 2013; 31:387-96. [PMID: 24157417 PMCID: PMC3907051 DOI: 10.1093/molbev/mst208] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA methylation at CpG dinucleotides can significantly increase the rate of cytosine-to-thymine mutations and the level of sequence divergence. Although the correlations between DNA methylation and genomic sequence evolution have been widely studied, an unaddressed yet fundamental question is how DNA methylation is associated with the conservation of individual nucleotides in different sequence contexts. Here, we demonstrate that in mammalian exons, the correlations between DNA methylation and the conservation of individual nucleotides are dependent on the type of exonic sequence (coding or untranslated), the degeneracy of coding nucleotides, background selection pressure, and the relative position (first or nonfirst exon in the transcript) where the nucleotides are located. For untranslated and nonzero-fold degenerate nucleotides, methylated sites are less conserved than unmethylated sites regardless of background selection pressure and the relative position of the exon. For zero-fold degenerate (or nondegenerate) nucleotides, however, the reverse trend is observed in nonfirst coding exons and first coding exons that are under stringent background selection pressure. Furthermore, cytosine-to-thymine mutations at methylated zero-fold degenerate nucleotides are predicted to be more detrimental than those that occur at unmethylated nucleotides. As zero-fold and nonzero-fold degenerate nucleotides are very close to each other, our results suggest that the "functional resolution" of DNA methylation may be finer than previously recognized. In addition, the positive correlation between CpG methylation and the level of conservation at zero-fold degenerate nucleotides implies that CpG methylation may serve as an "indicator" of functional importance of these nucleotides.
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Affiliation(s)
- Trees-Juen Chuang
- Physical and Computational Genomics Division, Genomics Research Center, Academia Sinica, Taipei, Taiwan
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Abstract
Epigenetics is a key mechanism regulating the expression of genes. There are three main and interrelated mechanisms: DNA methylation, post-translational modification of histone proteins and non-coding RNA. Gene activation is generally associated with lower levels of DNA methylation in promoters and with distinct histone marks such as acetylation of amino acids in histones. Unlike the genetic code, the epigenome is altered by endogenous (e.g. hormonal) and environmental (e.g. diet, exercise) factors and changes with age. Recent evidence implicates epigenetic mechanisms in the pathogenesis of common rheumatic disease, including RA, OA, SLE and scleroderma. Epigenetic drift has been implicated in age-related changes in the immune system that result in the development of a pro-inflammatory status termed inflammageing, potentially increasing the risk of age-related conditions such as polymyalgia rheumatica. Therapeutic targeting of the epigenome has shown promise in animal models of rheumatic diseases. Rapid advances in computational biology and DNA sequencing technology will lead to a more comprehensive understanding of the roles of epigenetics in the pathogenesis of common rheumatic diseases.
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Affiliation(s)
- Steffen Gay
- Department of Infection and Immunity, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, UK.
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Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res 2013; 23:1256-69. [PMID: 23938295 PMCID: PMC3817542 DOI: 10.1038/cr.2013.110] [Citation(s) in RCA: 405] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/22/2013] [Accepted: 05/17/2013] [Indexed: 12/16/2022] Open
Abstract
Although the function of DNA methylation in gene promoter regions is well established in transcriptional repression, the function of the evolutionarily conserved widespread distribution of DNA methylation in gene body regions remains incompletely understood. Here, we show that DNA methylation is enriched in included alternatively spliced exons (ASEs), and that inhibition of DNA methylation results in aberrant splicing of ASEs. The methyl-CpG-binding protein MeCP2 is enriched in included ASEs, particularly those that are also highly methylated, and inhibition of DNA methylation disrupts specific targeting of MeCP2 to exons. Interestingly, ablation of MeCP2 results in increased histone acetylation and aberrant ASE-skipping events. We further show that inhibition of histone deacetylase (HDAC) activity leads to exon skipping that shows a highly significant degree of overlap with that caused by MeCP2 knockdown. Together, our data indicate that intragenic DNA methylation operates in exon definition to modulate alternative RNA splicing and can enhance exon recognition via recruitment of the multifunctional protein MeCP2, which thereby maintains local histone hypoacetylation through the subsequent recruitment of HDACs.
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Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:1161-74. [PMID: 23938249 DOI: 10.1016/j.bbagrm.2013.08.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 08/02/2013] [Accepted: 08/05/2013] [Indexed: 02/06/2023]
Abstract
Ever since the discovery of DNA methylation at cytosine residues, the role of this so called fifth base has been extensively studied and debated. Until recently, the majority of DNA methylation studies focused on the analysis of CpG islands associated to promoter regions. However, with the upcoming possibilities to study DNA methylation in a genome-wide context, this epigenetic mark can now be studied in an unbiased manner. As a result, recent studies have shown that not only promoters but also intragenic and intergenic regions are widely modulated during physiological processes and disease. In particular, it is becoming increasingly clear that DNA methylation in the gene body is not just a passive witness of gene transcription but it seems to be actively involved in multiple gene regulation processes. In this review we discuss the potential role of intragenic DNA methylation in alternative promoter usage, regulation of short and long non-coding RNAs, alternative RNA processing, as well as enhancer activity. Furthermore, we summarize how the intragenic DNA methylome is modified both during normal cell differentiation and neoplastic transformation.
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Wan J, Oliver VF, Zhu H, Zack DJ, Qian J, Merbs SL. Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs. Nucleic Acids Res 2013; 41:8503-14. [PMID: 23887936 PMCID: PMC3794605 DOI: 10.1093/nar/gkt652] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The exact role of intragenic DNA methylation in regulating tissue-specific gene regulation is unclear. Recently, the DNA-binding protein CTCF has been shown to participate in the regulation of alternative splicing in a DNA methylation-dependent manner. To globally evaluate the relationship between DNA methylation and tissue-specific alternative splicing, we performed genome-wide DNA methylation profiling of mouse retina and brain. In protein-coding genes, tissue-specific differentially methylated regions (T-DMRs) were preferentially located in exons and introns. Gene ontology and evolutionary conservation analysis suggest that these T-DMRs are likely to be biologically relevant. More than 14% of alternatively spliced genes were associated with a T-DMR. T-DMR-associated genes were enriched for developmental genes, suggesting that a specific set of alternatively spliced genes may be regulated through DNA methylation. Novel DNA sequences motifs overrepresented in T-DMRs were identified as being associated with positive and/or negative regulation of alternative splicing in a position-dependent context. The majority of these evolutionarily conserved motifs contain a CpG dinucleotide. Some transcription factors, which recognize these motifs, are known to be involved in splicing. Our results suggest that DNA methylation-dependent alternative splicing is widespread and lay the foundation for further mechanistic studies of the role of DNA methylation in tissue-specific splicing regulation.
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Affiliation(s)
- Jun Wan
- Department of Ophthalmology, Wilmer Institute, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Pharmacology and Molecular Science, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Department of Neuroscience, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA, Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, 21287 Baltimore, MD, USA and Institut de la Vision, 17 rue Moreau, 75012 Paris, France
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Deng N, Sanchez CG, Lasky JA, Zhu D. Detecting splicing variants in idiopathic pulmonary fibrosis from non-differentially expressed genes. PLoS One 2013; 8:e68352. [PMID: 23844188 PMCID: PMC3699530 DOI: 10.1371/journal.pone.0068352] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/01/2013] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease of unknown cause that lacks a proven therapy for altering its high mortality rate. Microarrays have been employed to investigate the pathogenesis of IPF, but are presented mostly at the gene-expression level due to technologic limitations. In as much as, alternative RNA splicing isoforms are increasingly identified as potential regulators of human diseases, including IPF, we propose a new approach with the capacity to detect splicing variants using RNA-seq data. We conducted a joint analysis of differential expression and differential splicing on annotated human genes and isoforms, and identified 122 non-differentially expressed genes with a high degree of "switch" between major and minor isoforms. Three cases with variant mechanisms for alternative splicing were validated using qRT-PCR, among the group of genes in which expression was not significantly changed at the gene level. We also identified 35 novel transcripts that were unique to the fibrotic lungs using exon-exon junction evidence, and selected a representative for qRT-PCR validation. The results of our study are likely to provide new insight into the pathogenesis of pulmonary fibrosis and may eventuate in new treatment targets.
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Affiliation(s)
- Nan Deng
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
| | - Cecilia G. Sanchez
- Tulane Cancer Center, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Joseph A. Lasky
- Tulane Cancer Center, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (DZ); (JAL)
| | - Dongxiao Zhu
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
- * E-mail: (DZ); (JAL)
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48
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Eadon MT, Wheeler HE, Stark AL, Zhang X, Moen EL, Delaney SM, Im HK, Cunningham PN, Zhang W, Dolan ME. Genetic and epigenetic variants contributing to clofarabine cytotoxicity. Hum Mol Genet 2013; 22:4007-20. [PMID: 23720496 DOI: 10.1093/hmg/ddt240] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10(-6). Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
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Chen GL, Miller GM. Extensive alternative splicing of the repressor element silencing transcription factor linked to cancer. PLoS One 2013; 8:e62217. [PMID: 23614038 PMCID: PMC3628349 DOI: 10.1371/journal.pone.0062217] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/18/2013] [Indexed: 12/15/2022] Open
Abstract
The repressor element silencing transcription factor (REST) is a coordinate transcriptional and epigenetic regulator which functions as a tumor suppressor or an oncogene depending on cellular context, and a truncated splice variant REST4 has been linked to various types of cancer. We performed a comprehensive analysis of alternative splicing (AS) of REST by rapid amplification of cDNA ends and PCR amplification of cDNAs from various tissues and cell lines with specific primers. We identified 8 novel alternative exons including an alternate last exon which doubles the REST gene boundary, along with numerous 5'/3' splice sites and ends in the constitutive exons. With the combination of various splicing patterns (e.g. exon skipping and alternative usage of the first and last exons) that are predictive of altered REST activity, at least 45 alternatively spliced variants of coding and non-coding mRNA were expressed in a species- and cell-type/tissue-specific manner with individual differences. By examining the repertoire of REST pre-mRNA splicing in 27 patients with kidney, liver and lung cancer, we found that all patients without exception showed differential expression of various REST splice variants between paired tumor and adjacent normal tissues, with striking cell-type/tissue and individual differences. Moreover, we revealed that exon 3 skipping, which causes no frame shift but loss of a domain essential for nuclear translocation, was affected by pioglitazone, a highly selective activator of the peroxisome proliferator-activated receptor gamma (PPARγ) which contributes to cell differentiation and tumorigenesis besides its metabolic actions. Accordingly, this study demonstrates an extensive AS of REST pre-mRNA which redefines REST gene boundary and structure, along with a general but differential link between REST pre-mRNA splicing and various types of cancer. These findings advance our understanding of the complex, context-dependent regulation of REST gene expression and function, and provide potential biomarkers and therapeutic targets for cancer.
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Affiliation(s)
- Guo-Lin Chen
- Division of Neuroscience, New England Primate Research Center, Harvard Medical School, Southborough, Massachusetts, United States of America.
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DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res 2013; 23:789-99. [PMID: 23502848 PMCID: PMC3638135 DOI: 10.1101/gr.143503.112] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon–intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking introns, and the other with similar GC content in exons and introns. The first group has higher nucleosome occupancy on exons than introns, whereas the second group exhibits weak nucleosome marking of exons, suggesting another type of epigenetic marker distinguishes exons from introns when GC content is similar. We find different and specific patterns of DNA methylation in each of the GC architectures; yet in both groups, DNA methylation clearly marks the exons. Exons of the leveled GC architecture exhibit a significantly stronger DNA methylation signal in relation to their flanking introns compared to exons of the differential GC architecture. This is accentuated by a reduction of the DNA methylation level in the intronic sequences in proximity to the splice sites and shows that different epigenetic modifications mark the location of exons already at the DNA level. Also, lower levels of methylated CpGs on alternative exons can successfully distinguish alternative exons from constitutive ones. Three positions at the splice sites show high CpG abundance and accompany elevated nucleosome occupancy in a leveled GC architecture. Overall, these results suggest that DNA methylation affects exon recognition and is influenced by the GC architecture of the exon and flanking introns.
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