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Rahman SR, Lozier JD. Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes. Sci Rep 2023; 13:14901. [PMID: 37689750 PMCID: PMC10492822 DOI: 10.1038/s41598-023-41896-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.
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Affiliation(s)
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
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2
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van Oers K, van den Heuvel K, Sepers B. The Epigenetics of Animal Personality. Neurosci Biobehav Rev 2023; 150:105194. [PMID: 37094740 DOI: 10.1016/j.neubiorev.2023.105194] [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: 10/29/2022] [Revised: 04/12/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
Animal personality, consistent individual differences in behaviour, is an important concept for understanding how individuals vary in how they cope with environmental challenges. In order to understand the evolutionary significance of animal personality, it is crucial to understand the underlying regulatory mechanisms. Epigenetic marks such as DNA methylation are hypothesised to play a major role in explaining variation in phenotypic changes in response to environmental alterations. Several characteristics of DNA methylation also align well with the concept of animal personality. In this review paper, we summarise the current literature on the role that molecular epigenetic mechanisms may have in explaining personality variation. We elaborate on the potential for epigenetic mechanisms to explain behavioural variation, behavioural development and temporal consistency in behaviour. We then suggest future routes for this emerging field and point to potential pitfalls that may be encountered. We conclude that a more inclusive approach is needed for studying the epigenetics of animal personality and that epigenetic mechanisms cannot be studied without considering the genetic background.
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Affiliation(s)
- Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands.
| | - Krista van den Heuvel
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands; Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, the Netherlands
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3
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Ghavami S, Zamani M, Ahmadi M, Erfani M, Dastghaib S, Darbandi M, Darbandi S, Vakili O, Siri M, Grabarek BO, Boroń D, Zarghooni M, Wiechec E, Mokarram P. Epigenetic regulation of autophagy in gastrointestinal cancers. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166512. [PMID: 35931405 DOI: 10.1016/j.bbadis.2022.166512] [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: 03/17/2022] [Revised: 07/11/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
The development of novel therapeutic approaches is necessary to manage gastrointestinal cancers (GICs). Considering the effective molecular mechanisms involved in tumor growth, the therapeutic response is pivotal in this process. Autophagy is a highly conserved catabolic process that acts as a double-edged sword in tumorigenesis and tumor inhibition in a context-dependent manner. Depending on the stage of malignancy and cellular origin of the tumor, autophagy might result in cancer cell survival or death during the GICs' progression. Moreover, autophagy can prevent the progression of GIC in the early stages but leads to chemoresistance in advanced stages. Therefore, targeting specific arms of autophagy could be a promising strategy in the prevention of chemoresistance and treatment of GIC. It has been revealed that autophagy is a cytoplasmic event that is subject to transcriptional and epigenetic regulation inside the nucleus. The effect of epigenetic regulation (including DNA methylation, histone modification, and expression of non-coding RNAs (ncRNAs) in cellular fate is still not completely understood. Recent findings have indicated that epigenetic alterations can modify several genes and modulators, eventually leading to inhibition or promotion of autophagy in different cancer stages, and mediating chemoresistance or chemosensitivity. The current review focuses on the links between autophagy and epigenetics in GICs and discusses: 1) How autophagy and epigenetics are linked in GICs, by considering different epigenetic mechanisms; 2) how epigenetics may be involved in the alteration of cancer-related phenotypes, including cell proliferation, invasion, and migration; and 3) how epidrugs modulate autophagy in GICs to overcome chemoresistance.
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Affiliation(s)
- Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada; Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Research Institute of Hematology and Oncology, Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada; Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland.
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazaher Ahmadi
- Department of Analytical Chemistry, Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran
| | - Mehran Erfani
- Department of Biochemistry, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Sanaz Dastghaib
- Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahsa Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran; Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Sara Darbandi
- Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran; Gene Therapy and Regenerative Medicine Research Center, Hope Generation Foundation, Tehran, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Beniamin Oskar Grabarek
- Department of Histology, Cytophysiology, and Embryology in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland; Department of Gynecology and Obstetrics in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
| | - Dariusz Boroń
- Department of Histology, Cytophysiology, and Embryology in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland; Department of Gynecology and Obstetrics in Zabrze, Faculty of Medicine in Zabrze, University of Technology in Katowice, Academia of Silesia, 41-800 Zabrze, Poland
| | - Maryam Zarghooni
- Department of Laboratory Medicine and Pathobiology, University of Toronto Alumni, Toronto, Canada
| | - Emilia Wiechec
- Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linköping University, 58185 Linköping, Sweden
| | - Pooneh Mokarram
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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4
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Next-Generation Bisulfite Sequencing for Targeted DNA Methylation Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2458:47-62. [PMID: 35103961 DOI: 10.1007/978-1-0716-2140-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Bisulfite sequencing is the "gold-standard" technique for DNA methylation analysis. By combining bisulfite sequencing with high-throughput, next-generation sequencing technology, we can document methylation from many thousands of individual reads (equivalent to alleles or "cells"), for multiple target regions and from many samples simultaneously. Here, we describe a next-generation bisulfite-sequencing assay for targeted DNA methylation analysis which offers scope for the simultaneous interrogation of multiple genomic loci across numerous samples.
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5
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Ying H, Hayward DC, Klimovich A, Bosch TCG, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE, Miller DJ. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Mol Biol Evol 2022; 39:6516040. [PMID: 35084499 PMCID: PMC8857917 DOI: 10.1093/molbev/msac018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.
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Affiliation(s)
- Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University, Kiel, Germany.,Collaborative Research Center for the Origin and Function of Metaorganisms, Christian Albrechts University, Kiel, Germany
| | - Laura Baldassarre
- Department of Zoology and Organismal Interactions, Heinrich-Heine-University Düsseldorf, Germany
| | - Teresa Neeman
- Biological Data Institute, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, USA
| | - Sebastian Fraune
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology, Japan
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6
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Uysal F, Cinar O, Can A. Knockdown of Dnmt1 and Dnmt3a gene expression disrupts preimplantation embryo development through global DNA methylation. J Assist Reprod Genet 2021; 38:3135-3144. [PMID: 34533678 DOI: 10.1007/s10815-021-02316-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/08/2021] [Indexed: 11/24/2022] Open
Abstract
PURPOSE DNA methylation is one of the epigenetic mechanisms that plays critical roles in preimplantation embryo development executed by DNA methyltransferase (Dnmt) enzymes. Dnmt1, responsible for the maintenance of methylation, and Dnmt3a, for de novo methylation, are gradually erased from the zygote in succeeding stages and then reestablished in the blastocyst. This study was designed to address the vital role of Dnmt1 and Dnmt3a enzymes by silencing their gene expressions in embryonic development in mice. METHODS Groups were (i) control, (ii) Dnmt1-siRNA, (iii) Dnmt3a-siRNA, and (iv) non-targeted (NT) siRNA. Knockdown of Dnmt genes using siRNAs was confirmed by measuring the targeted proteins using Western blot and immunofluorescence. Following knockdown of Dnmt1 and Dnmt3a in zygotes, the developmental competence and global DNA methylation levels were analyzed after 96 h in embryo cultures. RESULTS A significant number of embryos arrested at the 2-cell stage or had undergone degeneration in the Dnmt1 and Dnmt3a knocked-down groups. By 3D observations in super-resolution microscopy, we noted that Dnmt1 was exclusively found in juxtanuclear cytoplasm, while the Dnmt3a signal was preferentially localized in the nucleus, both in trophoblasts (TBs) and embryoblasts (EBs). Interestingly, the global DNA methylation level decreased in the Dnmt1 knockdown group, while it increased in the Dnmt3a knockdown group. CONCLUSION Precisely aligned expression of Dnmt genes is highly essential for the fate of an embryo in the early developmental period. Our data indicates that further analysis is mandatory to designate the specific targets of these methylation/demethylation processes in mouse and human preimplantation embryos.
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Affiliation(s)
- Fatma Uysal
- Laboratory for Stem Cells and Reproductive Cell Biology, Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Ozgur Cinar
- Laboratory for Stem Cells and Reproductive Cell Biology, Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey
| | - Alp Can
- Laboratory for Stem Cells and Reproductive Cell Biology, Department of Histology and Embryology, Ankara University School of Medicine, Ankara, Turkey.
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7
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Liu X, Weikum ER, Tilo D, Vinson C, Ortlund EA. Structural basis for glucocorticoid receptor recognition of both unmodified and methylated binding sites, precursors of a modern recognition element. Nucleic Acids Res 2021; 49:8923-8933. [PMID: 34289059 PMCID: PMC8421226 DOI: 10.1093/nar/gkab605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/24/2021] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
The most common form of DNA methylation involves the addition of a methyl group to a cytosine base in the context of a cytosine–phosphate–guanine (CpG) dinucleotide. Genomes from more primitive organisms are more abundant in CpG sites that, through the process of methylation, deamination and subsequent mutation to thymine–phosphate–guanine (TpG) sites, can produce new transcription factor binding sites. Here, we examined the evolutionary history of the over 36 000 glucocorticoid receptor (GR) consensus binding motifs in the human genome and identified a subset of them in regulatory regions that arose via a deamination and subsequent mutation event. GR can bind to both unmodified and methylated pre-GR binding sequences (GBSs) that contain a CpG site. Our structural analyses show that CpG methylation in a pre-GBS generates a favorable interaction with Arg447 mimicking that made with a TpG in a GBS. This methyl-specific recognition arose 420 million years ago and was conserved during the evolution of GR and likely helps fix the methylation on the relevant cytosines. Our study provides the first genetic, biochemical and structural evidence of high-affinity binding for the likely evolutionary precursor of extant TpG-containing GBS.
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Affiliation(s)
- Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Desiree Tilo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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8
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Gerdol M, La Vecchia C, Strazzullo M, De Luca P, Gorbi S, Regoli F, Pallavicini A, D’Aniello E. Evolutionary History of DNA Methylation Related Genes in Bivalvia: New Insights From Mytilus galloprovincialis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an essential epigenetic mechanism influencing gene expression in all organisms. In metazoans, the pattern of DNA methylation changes during embryogenesis and adult life. Consequently, differentiated cells develop a stable and unique DNA methylation pattern that finely regulates mRNA transcription during development and determines tissue-specific gene expression. Currently, DNA methylation remains poorly investigated in mollusks and completely unexplored in Mytilus galloprovincialis. To shed light on this process in this ecologically and economically important bivalve, we screened its genome, detecting sequences homologous to DNA methyltransferases (DNMTs), methyl-CpG-binding domain (MBD) proteins and Ten-eleven translocation methylcytosine dioxygenase (TET) previously described in other organisms. We characterized the gene architecture and protein domains of the mussel sequences and studied their phylogenetic relationships with the ortholog sequences from other bivalve species. We then comparatively investigated their expression levels across different adult tissues in mussel and other bivalves, using previously published transcriptome datasets. This study provides the first insights on DNA methylation regulators in M. galloprovincialis, which may provide fundamental information to better understand the complex role played by this mechanism in regulating genome activity in bivalves.
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Uysal F, Ozturk S. The loss of global DNA methylation due to decreased DNMT expression in the postnatal mouse ovaries may associate with infertility emerging during ovarian aging. Histochem Cell Biol 2020; 154:301-314. [PMID: 32514790 DOI: 10.1007/s00418-020-01890-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/15/2022]
Abstract
Ovarian aging is one of the main causes of female infertility, and its molecular background is still largely unknown. As DNA methylation regulates many oogenesis/folliculogenesis-related genes, the expression levels and cellular localizations of DNA methyltransferases (DNMTs) playing key roles in this process is important in the ovaries from early to aged terms. In the present study, we aimed to evaluate the spatial and temporal expression of the Dnmt1, Dnmt3a, Dnmt3b, and Dnmt3l genes as well as global DNA methylation levels in the mouse ovaries during aging. For this purpose, the following groups were created: young (1- and 2-week old; n = 3 from each week), prepubertal (3- and 4-week-old; n = 3 from each week), pubertal (5- and 6-week-old; n = 3 from each week), postpubertal (16- and 18-week-old; n = 3 from each week), and aged (52-, 60- and 72-week-old; n = 3 from each week). We found here that Dnmt1, Dnmt3a, and Dnmt3l genes' expression at mRNA and protein levels as well as global DNA methylation profiles were gradually and significantly decreased in the postnatal ovaries from young to aged groups (P < 0.05). In contrast, there was a remarkable increase of Dnmt3b expression in the pubertal, postpubertal and aged groups (P < 0.05). Our findings suggest that the significantly altered DNMT expression and global DNA methylation levels during ovarian aging may contribute to female infertility development at the later terms of lifespan. Also, new researches are required to determine the molecular biological mechanism(s) that how altered DNMT expression and decreased DNA methylation lead to ovarian aging.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University School of Medicine, 07070, Antalya, Turkey
- Department of Histology and Embryology, Ankara University School of Medicine, 06100, Ankara, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, 07070, Antalya, Turkey.
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10
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Abstract
Multicellular eukaryotic genomes show enormous differences in size. A substantial part of this variation is due to the presence of transposable elements (TEs). They contribute significantly to a cell's mass of DNA and have the potential to become involved in host gene control. We argue that the suppression of their activities by methylation of the C-phosphate-G (CpG) dinucleotide in DNA is essential for their long-term accommodation in the host genome and, therefore, to its expansion. An inevitable consequence of cytosine methylation is an increase in C-to-T transition mutations via deamination, which causes CpG loss. Cytosine deamination is often needed for TEs to take on regulatory functions in the host genome. Our study of the whole-genome sequences of 53 organisms showed a positive correlation between the size of a genome and the percentage of TEs it contains, as well as a negative correlation between size and the CpG observed/expected (O/E) ratio in both TEs and the host DNA. TEs are seldom found at promoters and transcription start sites, but they are found more at enhancers, particularly after they have accumulated C-to-T and other mutations. Therefore, the methylation of TE DNA allows for genome expansion and also leads to new opportunities for gene control by TE-based regulatory sites.
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11
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Jin J, He X, Silva E. Stable intronic sequence RNAs (sisRNAs) are selected regions in introns with distinct properties. BMC Genomics 2020; 21:287. [PMID: 32264855 PMCID: PMC7137253 DOI: 10.1186/s12864-020-6687-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/18/2020] [Indexed: 12/31/2022] Open
Abstract
Background Stable introns and intronic fragments make up the largest population of RNA in the oocyte nucleus of the frog Xenopus tropicalis. These stable intronic sequence RNAs (sisRNAs) persist through the onset of zygotic transcription when synchronous cell division has ended, and the developing embryo consists of approximately 8000 cells. Despite their abundance, the sequence properties and biological function of sisRNAs are just beginning to be understood. Results To characterize this population of non-coding RNA, we identified all of the sisRNAs in the X. tropicalis oocyte nucleus using published high-throughput RNA sequencing data. Our analysis revealed that sisRNAs, have an average length of ~ 360 nt, are widely expressed from genes with multiple introns, and are derived from specific regions of introns that are GC and TG rich, while CpG poor. They are enriched in introns at both ends of transcripts but preferentially at the 3′ end. The consensus binding sites of specific transcription factors such as Stat3 are enriched in sisRNAs, suggesting an association between sisRNAs and transcription factors involved in early development. Evolutionary conservation analysis of sisRNA sequences in seven vertebrate genomes indicates that sisRNAs are as conserved as other parts of introns, but much less conserved than exons. Conclusion In total, our results indicate sisRNAs are selected intron regions with distinct properties and may play a role in gene expression regulation.
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Affiliation(s)
- Jing Jin
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Department of Biology, Georgetown University, 37th and O Sts, NW, Washington DC, 20057, USA
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Elena Silva
- Department of Biology, Georgetown University, 37th and O Sts, NW, Washington DC, 20057, USA.
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12
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El Sherbini MA, Mansour AA, Sallam MM, Shaban EA, Shehab ElDin ZA, El-Shalakany AH. KLK10 exon 3 unmethylated PCR product concentration: a new potential early diagnostic marker in ovarian cancer? - A pilot study. J Ovarian Res 2018; 11:32. [PMID: 29690914 PMCID: PMC5913797 DOI: 10.1186/s13048-018-0407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND KLK10 exon 3 hypermethylation correlated to tumor-specific lack of KLK10 expression in cancer cell lines and primary tumors. In the present study we investigate the possible role of KLK10 exon 3 methylation in ovarian tumor diagnosis and prognosis. RESULTS Qualitative methylation-specific PCR (MSP) results did not show statistically significant differences in patient group samples (normal and tumor) where all samples were positive only for the unmethylated-specific PCR except for two malignant samples that were either doubly positive (serous carcinoma) or doubly negative (Sertoli-Leydig cell tumor) for the two MSP tests. However, KLK10 exon 3 unmethylated PCR product concentration (ng/μl) showed statistically significant differences in benign and malignant patient group samples; mean ± SD (n): tumor: 0.077 ± 0.035 (14) and 0.047 ± 0.021 (15), respectively, p-value = 0.011; and normal: 0.094 ± 0.039 (7) and 0.046 ± 0.027 (6), respectively, p-value = 0.031. Moreover, ROC curve analysis of KLK10 exon 3 unmethylated PCR product concentration in overall patient group samples showed good diagnostic ability (AUC = 0.778; p-value = 0.002). Patient survival (living and died) showed statistically significant difference according to preoperative serum CA125 concentration (U/ml); median (n): 101.25 (10) and 1252 (5), respectively, p-value = 0.037, but not KLK10 exon 3 unmethylated PCR product concentration (ng/μl) in overall malignant patient samples; mean ± SD (n): 0.042 ± 0.015 (14) and 0.055 ± 0.032 (7), p-value = 0.228. CONCLUSION To the best of our knowledge, this is the first report on KLK10 exon 3 unmethylated PCR product concentration as potential early epigenetic diagnostic marker in primary ovarian tumors. Taken into account the limitations in our study (small sample size and semi-quantitative PCR product analysis) further studies are strongly recommended.
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Affiliation(s)
- Mustafa A El Sherbini
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Amal A Mansour
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Maha M Sallam
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Emtiaz A Shaban
- Medical Biochemistry Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | | | - Amr H El-Shalakany
- Gynecologic Oncology Unit, Ain Shams University Maternity Hospital, Cairo, Egypt
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13
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Abstract
Since every cell of a multicellular organism contains the same genome, it is intriguing to understand why genetically homogenous cells are different from each other and what controls this. Several observations indicate that DNA methylation has an essential regulatory function in mammalian development, which is to establish the correct pattern of gene expression, and that DNA methylation pattern is tightly correlated with chromatin structure. Various physiological processes are controlled by specific DNA methylation patterns including genomic imprinting, inactivation of the X chromosome, regulation of tissue-specific gene expression and repression of transposons. Moreover, aberrant methylation could confer a selective advantage to cells, leading to cancerous growth. In this review we focus on the epigenetic molecular mechanisms during normal development and discuss how DNA methylation could affect the expression of genes leading to cancer transformation.
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Affiliation(s)
- Marcella Macaluso
- Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA, USA
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14
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Epigenetic drivers of tumourigenesis and cancer metastasis. Semin Cancer Biol 2017; 51:149-159. [PMID: 28807546 DOI: 10.1016/j.semcancer.2017.08.004] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/13/2017] [Accepted: 08/02/2017] [Indexed: 02/07/2023]
Abstract
Since the completion of the first human genome sequence and the advent of next generation sequencing technologies, remarkable progress has been made in understanding the genetic basis of cancer. These studies have mainly defined genetic changes as either causal, providing a selective advantage to the cancer cell (a driver mutation) or consequential with no selective advantage (not directly causal, a passenger mutation). A vast unresolved question is how a primary cancer cell becomes metastatic and what are the molecular events that underpin this process. However, extensive sequencing efforts indicate that mutation may not be a causal factor for primary to metastatic transition. On the other hand, epigenetic changes are dynamic in nature and therefore potentially play an important role in determining metastatic phenotypes and this area of research is just starting to be appreciated. Unlike genetic studies, current limitations in studying epigenetic events in cancer metastasis include a lack of conceptual understanding and an analytical framework for identifying putative driver and passenger epigenetic changes. In this review, we discuss the key concepts involved in understanding the role of epigenetic alterations in the metastatic cascade. We particularly focus on driver epigenetic events, and we describe analytical approaches and biological frameworks for distinguishing between "epi-driver" and "epi-passenger" events in metastasis. Finally, we suggest potential directions for future research in this important area of cancer research.
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15
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Progress in Rett Syndrome: from discovery to clinical trials. Wien Med Wochenschr 2016; 166:325-32. [PMID: 27491553 PMCID: PMC5005392 DOI: 10.1007/s10354-016-0491-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 07/04/2016] [Indexed: 12/27/2022]
Abstract
Fifty years ago, Andreas Rett described a disorder in 22 females featuring prominent regression of fine motor and communication skills, cognitive impairment, stereotypic movements, periodic breathing, and gait abnormalities. This disorder became known as Rett syndrome (RTT) following the report of Hagberg et al. in 1983. Although RTT was scarcely recognized at that time in the United States, here the efforts of Rett and Hagberg led to rapid progress in recognition and diagnosis, a clearer understanding of its clinical and pathological underpinnings, and, ultimately, identification of mutations in the methyl-CpG-binding protein 2 (MECP2) gene as the primary cause of this unique and challenging neurodevelopmental disorder. Thereafter, a natural history study and critical translational research in animal models paved the way for potential disease-modifying agents to be assessed in human clinical trials. To be successful, the energies of the international community at all levels, including researchers in clinical and basic science, funding agencies, pharmaceutical companies, patient advocates, and, above all, parents and their children are essential. Otherwise, hopes for effective treatment, if not, a cure, will remain unfulfilled.
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Keller TE, Han P, Yi SV. Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary. Mol Biol Evol 2015; 33:1019-28. [PMID: 26715626 PMCID: PMC4776710 DOI: 10.1093/molbev/msv345] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate–vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate–vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression.
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Affiliation(s)
| | | | - Soojin V Yi
- School of Biology, Georgia Institute of Technology
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17
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Dabe EC, Sanford RS, Kohn AB, Bobkova Y, Moroz LL. DNA Methylation in Basal Metazoans: Insights from Ctenophores. Integr Comp Biol 2015; 55:1096-110. [PMID: 26173712 PMCID: PMC4817592 DOI: 10.1093/icb/icv086] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Epigenetic modifications control gene expression without altering the primary DNA sequence. However, little is known about DNA methylation in invertebrates and its evolution. Here, we characterize two types of genomic DNA methylation in ctenophores, 5-methyl cytosine (5-mC) and the unconventional form of methylation 6-methyl adenine (6-mA). Using both bisulfite sequencing and an ELISA-based colorimetric assay, we experimentally confirmed the presence of 5-mC DNA methylation in ctenophores. In contrast to other invertebrates studied, Mnemiopsis leidyi has lower levels of genome-wide 5-mC methylation, but higher levels of 5-mC methylation in promoters when compared with gene bodies. Phylogenetic analysis showed that ctenophores have distinct forms of DNA methyltransferase 1 (DNMT1); the zf-CXXC domain type, which localized DNMT1 to CpG sites, and is a metazoan specific innovation. We also show that ctenophores encode the full repertoire of putative enzymes for 6-mA DNA methylation, and these genes are expressed in the aboral organ of Mnemiopsis. Using an ELISA-based colorimetric assay, we experimentally confirmed the presence of 6-mA methylation in the genomes of three different species of ctenophores, M. leidyi, Beroe abyssicola, and Pleurobrachia bachei. The functional role of this novel epigenomic mark is currently unknown. In summary, despite their compact genomes, there is a wide variety of epigenomic mechanisms employed by basal metazoans that provide novel insights into the evolutionary origins of biological novelties.
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Affiliation(s)
- Emily C Dabe
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rachel S Sanford
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrea B Kohn
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
| | - Yelena Bobkova
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
| | - Leonid L Moroz
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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18
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He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray GJ, Stamatoyannopoulos J, FitzGerald PC, Vinson C. Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution. Genome Biol Evol 2015; 7:3155-69. [PMID: 26507798 PMCID: PMC4994754 DOI: 10.1093/gbe/evv205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In mammals, the cytosine in CG dinucleotides is typically methylated producing
5-methylcytosine (5mC), a chemically less stable form of cytosine that can spontaneously
deaminate to thymidine resulting in a T•G mismatched base pair. Unlike other eukaryotes
that efficiently repair this mismatched base pair back to C•G, in mammals, 5mCG
deamination is mutagenic, sometimes producing TG dinucleotides, explaining the depletion
of CG dinucleotides in mammalian genomes. It was suggested that new TG dinucleotides
generate genetic diversity that may be critical for evolutionary change. We tested this
conjecture by examining the DNA sequence properties of regulatory sequences identified by
DNase I hypersensitive sites (DHSs) in human and mouse genomes. We hypothesized that the
new TG dinucleotides generate transcription factor binding sites (TFBS) that become
tissue-specific DHSs (TS-DHSs). We find that 8-mers containing the CG dinucleotide are
enriched in DHSs in both species. However, 8-mers containing a TG and no CG dinucleotide
are preferentially enriched in TS-DHSs when compared with 8-mers with neither a TG nor a
CG dinucleotide. The most enriched 8-mer with a TG and no CG dinucleotide in
tissue-specific regulatory regions in both genomes is the AP-1 motif
(TGAC/GTCAN), and we find evidence that
TG dinucleotides in the AP-1 motif arose from CG dinucleotides. Additional TS-DHS-enriched
TFBS containing the TG/CA dinucleotide are the E-Box motif
(GCAGCTGC), the NF-1 motif (GGCA—TGCC), and the
GR (glucocorticoid receptor) motif (G-ACA—TGT-C). Our results support the
suggestion that cytosine methylation is mutagenic in tetrapods producing TG dinucleotides
that create TFBS that drive evolution.
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Affiliation(s)
- Ximiao He
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington
| | - Khund-Sayeed Syed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Callie Deng
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - G Jordan Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Peter C FitzGerald
- Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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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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20
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Chatterjee A, Ozaki Y, Stockwell PA, Horsfield JA, Morison IM, Nakagawa S. Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing. Epigenetics 2013; 8:979-89. [PMID: 23975027 PMCID: PMC3883775 DOI: 10.4161/epi.25797] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish.
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Affiliation(s)
- Aniruddha Chatterjee
- Department of Pathology; Dunedin School of Medicine; University of Otago; Dunedin, New Zealand; Gravida: National Centre for Growth and Development; Auckland, New Zealand
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21
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Effects of early-life environment and epigenetics on cardiovascular disease risk in children: highlighting the role of twin studies. Pediatr Res 2013; 73:523-30. [PMID: 23314296 DOI: 10.1038/pr.2013.6] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide and originates in early life. The exact mechanisms of this early-life origin are unclear, but a likely mediator at the molecular level is epigenetic dysregulation of gene expression. Epigenetic factors have thus been posited as the likely drivers of early-life programming of adult-onset diseases. This review summarizes recent advances in epidemiology and epigenetic research of CVD risk in children, with a particular focus on twin studies. Classic twin studies enable partitioning of phenotypic variance within a population into additive genetic, shared, and nonshared environmental variances, and are invaluable in research in this area. Longitudinal cohort twin studies, in particular, may provide important insights into the role of epigenetics in the pathogenesis of CVD. We describe candidate gene and epigenome-wide association studies (EWASs) and transgenerational epigenetic inheritance of CVD, and discuss the potential for evidence-based interventions. Identifying epigenetic changes associated with CVD-risk biomarkers in children will provide new opportunities to unravel the underlying biological mechanism of the origins of CVD and enable identification of those at risk for early-life interventions to alter the risk trajectory and potentially reduce CVD incidence later in life.
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22
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MeCP2 dependent heterochromatin reorganization during neural differentiation of a novel Mecp2-deficient embryonic stem cell reporter line. PLoS One 2012; 7:e47848. [PMID: 23112857 PMCID: PMC3480415 DOI: 10.1371/journal.pone.0047848] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/21/2012] [Indexed: 01/17/2023] Open
Abstract
The X-linked Mecp2 is a known interpreter of epigenetic information and mutated in Rett syndrome, a complex neurological disease. MeCP2 recruits HDAC complexes to chromatin thereby modulating gene expression and, importantly regulates higher order heterochromatin structure. To address the effects of MeCP2 deficiency on heterochromatin organization during neural differentiation, we developed a versatile model for stem cell in vitro differentiation. Therefore, we modified murine Mecp2 deficient (Mecp2−/y) embryonic stem cells to generate cells exhibiting green fluorescent protein expression upon neural differentiation. Subsequently, we quantitatively analyzed heterochromatin organization during neural differentiation in wild type and in Mecp2 deficient cells. We found that MeCP2 protein levels increase significantly during neural differentiation and accumulate at constitutive heterochromatin. Statistical analysis of Mecp2 wild type neurons revealed a significant clustering of heterochromatin per nuclei with progressing differentiation. In contrast we found Mecp2 deficient neurons and astroglia cells to be significantly impaired in heterochromatin reorganization. Our results (i) introduce a new and manageable cellular model to study the molecular effects of Mecp2 deficiency, and (ii) support the view of MeCP2 as a central protein in heterochromatin architecture in maturating cells, possibly involved in stabilizing their differentiated state.
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23
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Jjingo D, Conley AB, Yi SV, Lunyak VV, Jordan IK. On the presence and role of human gene-body DNA methylation. Oncotarget 2012; 3:462-74. [PMID: 22577155 PMCID: PMC3380580 DOI: 10.18632/oncotarget.497] [Citation(s) in RCA: 347] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/28/2012] [Indexed: 01/23/2023] Open
Abstract
DNA methylation of promoter sequences is a repressive epigenetic mark that down-regulates gene expression. However, DNA methylation is more prevalent within gene-bodies than seen for promoters, and gene-body methylation has been observed to be positively correlated with gene expression levels. This paradox remains unexplained, and accordingly the role of DNA methylation in gene-bodies is poorly understood. We addressed the presence and role of human gene-body DNA methylation using a meta-analysis of human genome-wide methylation, expression and chromatin data sets. Methylation is associated with transcribed regions as genic sequences have higher levels of methylation than intergenic or promoter sequences. We also find that the relationship between gene-body DNA methylation and expression levels is non-monotonic and bell-shaped. Mid-level expressed genes have the highest levels of gene-body methylation, whereas the most lowly and highly expressed sets of genes both have low levels of methylation. While gene-body methylation can be seen to efficiently repress the initiation of intragenic transcription, the vast majority of methylated sites within genes are not associated with intragenic promoters. In fact, highly expressed genes initiate the most intragenic transcription inconsistent with the previously held notion that gene-body methylation serves to repress spurious intragenic transcription to allow for efficient transcriptional elongation. These observations lead us to propose a model to explain the presence of human gene-body methylation. This model holds that the repression of intragenic transcription by gene-body methylation is largely epiphenomenal, and suggests that gene-body methylation levels are predominantly shaped via the accessibility of the DNA to methylating enzyme complexes.
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Affiliation(s)
- Daudi Jjingo
- School of Biology, Georgia Institute of Technology, Atlanta GA, 30332 USA
| | - Andrew B. Conley
- School of Biology, Georgia Institute of Technology, Atlanta GA, 30332 USA
| | - Soojin V. Yi
- School of Biology, Georgia Institute of Technology, Atlanta GA, 30332 USA
| | | | - I. King Jordan
- School of Biology, Georgia Institute of Technology, Atlanta GA, 30332 USA
- PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia
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24
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Rajender S, Avery K, Agarwal A. Epigenetics, spermatogenesis and male infertility. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2011; 727:62-71. [DOI: 10.1016/j.mrrev.2011.04.002] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 04/07/2011] [Accepted: 04/08/2011] [Indexed: 12/31/2022]
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25
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Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR. DNA methylation profiling in zebrafish. Methods Cell Biol 2011; 104:327-39. [PMID: 21924171 DOI: 10.1016/b978-0-12-374814-0.00018-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation on cytosine in vertebrates such as zebrafish serves to silence gene expression by interfering with the binding of certain transcription factors and through the recruitment of repressive chromatin machinery. Cytosine DNA methylation is chemically stable and heritable through the germline - but also reversible through many modes, making it a useful and dynamic epigenetic modification. Virtually all of the enzymes and factors involved in the deposition, binding, and removal of cytosine methylation are conserved in zebrafish, and therefore the organism an excellent model for understanding the use of DNA methylation in the control of gene regulation and other processes. Here, we discuss the main approaches to quantifying DNA methylation levels genome-wide in zebrafish: one is an established method for revealing regional methylation (methylated DNA immunoprecipitation (MeDIP)), and the other is an emerging method that reveals DNA methylation at base-pair resolution (shotgun bisulphite sequencing). We also introduce some of the analytical methods that are useful for identifying regions of hypo- or hyper-methylation, and ways to identify differentially methylated regions.
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Affiliation(s)
- Shan-Fu Wu
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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26
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Epigenetics and chemical safety assessment. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2010; 705:83-95. [DOI: 10.1016/j.mrrev.2010.04.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 03/29/2010] [Accepted: 04/08/2010] [Indexed: 01/01/2023]
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27
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Nicholas CR, Chavez SL, Baker VL, Reijo Pera RA. Instructing an embryonic stem cell-derived oocyte fate: lessons from endogenous oogenesis. Endocr Rev 2009; 30:264-83. [PMID: 19366753 PMCID: PMC2726843 DOI: 10.1210/er.2008-0034] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Female reproductive potential is limited in the majority of species due to oocyte depletion. Because functional human oocytes are restricted in number and accessibility, a robust system to differentiate oocytes from stem cells would enable a thorough investigation of the genetic, epigenetic, and environmental factors affecting human oocyte development. Also, the differentiation of functional oocytes from stem cells may permit the success of human somatic cell nuclear transfer for reprogramming studies and for the production of patient-specific embryonic stem cells (ESCs). Thus, ESC-derived oocytes could ultimately help to restore fertility in women. Here, we review endogenous and ESC-derived oocyte development, and we discuss the potential and challenges for differentiating functional oocytes from ESCs.
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Affiliation(s)
- Cory R Nicholas
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Palo Alto, California 94304, USA.
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28
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Ho SM, Tang WY. Techniques used in studies of epigenome dysregulation due to aberrant DNA methylation: an emphasis on fetal-based adult diseases. Reprod Toxicol 2007; 23:267-82. [PMID: 17317097 PMCID: PMC2055548 DOI: 10.1016/j.reprotox.2007.01.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2006] [Revised: 01/04/2007] [Accepted: 01/08/2007] [Indexed: 12/31/2022]
Abstract
Epigenetic changes are heritable modifications that do not involve alterations in the primary DNA sequence. They regulate crucial cellular functions such as genome stability, X-chromosome inactivation, and gene imprinting. Epidemiological and experimental observations now suggest that such changes may also explain the fetal basis of adult diseases such as cancer, obesity, diabetes, cardiovascular disorders, neurological diseases, and behavioral modifications. The main molecular events known to initiate and sustain epigenetic modifications are histone modification and DNA methylation. This review specifically focuses on existing and emerging technologies used in studying DNA methylation, which occurs primarily at CpG dinucleotides in the genome. These include standard exploratory tools used for global profiling of DNA methylation and targeted gene investigation: methylation sensitive restriction fingerprinting (MSRF), restriction landmark genomic scanning (RLGS), methylation CpG island amplification-representational difference analysis (MCA-RDA), differential methylation hybridization (DMH), and cDNA microarrays combined with treatment with demethylating agents and inhibitors of histone deacetylase. The basic operating principals, resource requirements, applications, and benefits and limitations of each methodology are discussed. Validation methodologies and functional assays needed to establish the role of a CpG-rich sequence in regulating the expression of a target or candidate gene are outlined. These include in silico database searches, methylation status studies (bisulfite genomic sequencing, COBRA, MS-PCR, MS-SSCP), gene expression studies, and promoter activity analyses. Our intention is to give readers a starting point for choosing methodologies and to suggest a workflow to follow during their investigations. We believe studies of epigenetic changes such as DNA methylation hold great promise in understanding the early origins of adult diseases and in advancing their diagnosis, prevention, and treatment.
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Affiliation(s)
- Shuk-mei Ho
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
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29
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Kremenskoy M, Kremenska Y, Suzuki M, Imai K, Takahashi S, Hashizume K, Yagi S, Shiota K. Epigenetic characterization of the CpG islands of bovine Leptin and POU5F1 genes in cloned bovine fetuses. J Reprod Dev 2006; 52:277-85. [PMID: 16474211 DOI: 10.1262/jrd.17100] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abnormal development and fetal loss during postimplantation period are concerns for production of nuclear transferred animals. Aberrant DNA methylation is one of the reasons for poor survival of cloned animals. In mammalian genome DNA, CpG islands are preferentially located at the start of transcription of housekeeping genes and are associated with tissue-specific genes. The correct and consecutive mechanisms of DNA methylation in the CpG islands are necessary for selective gene expressions that determine the properties of individual cells, tissues, and organs. In this study, we investigated the methylation status of the CpG islands of the bovine Leptin and POU5F1 genes in fetal and placental tissues from fetuses produced by artificial insemination (AI) and nuclear transfer (NT) at days 48 and 59 of pregnancy. Altered DNA methylation was observed in the normal and cloned fetal, placental, and endometrial tissues using bisulfite sequencing and pyrosequencing. Different tissue-specific methylated regions in the bovine Leptin and POU5F1 genes show a variable methylation status in NT fetuses compared to AI control.
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Affiliation(s)
- Maksym Kremenskoy
- Laboratory of Cellular Biochemistry, Animal Resource Science/Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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30
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Zaina S, Døssing KBV, Lindholm MW, Lund G. Chromatin modification by lipids and lipoprotein components: an initiating event in atherogenesis? Curr Opin Lipidol 2005; 16:549-53. [PMID: 16148540 DOI: 10.1097/01.mol.0000180165.70077.ee] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This review examines recent evidence proposing that lipids and lipoproteins can act as nuclear factors regulating chromatin structure. These novel data broaden our understanding of the mechanisms by which lipoproteins can affect basic biological phenomena such as transcription, genome stability, and cell differentiation. Furthermore, they provide novel insights into the mechanisms of diseases associated with abnormal lipid levels, such as atherosclerosis and diabetes. RECENT FINDINGS Data consistent with a role for lipids and lipoprotein components as nuclear factors, as well as initiators of cytoplasmic signalling events resulting in chromatin modification, have been published in the past year. In particular, new insights into the mechanisms of interaction between chromatin and small lipid molecules such as short-chain fatty acids and cholesterol, and endogenous lipid peroxidation products have been obtained. Furthermore, it has been shown that hyperlipidaemic lipoprotein profiles are associated with aberrant DNA methylation patterns at early stages of atherosclerosis in mice and in cultured human macrophages, suggesting that a rearrangement of DNA methylation patterns is among early molecular changes associated with atherogenesis. SUMMARY The findings described here are prompting efforts to understand further how lipids and lipoprotein components can affect gene expression in normal and pathological cell behaviour through regulation of the chromatin structure. It is possible that novel candidate therapeutic tools will emerge from these studies.
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Affiliation(s)
- Silvio Zaina
- Institute of Medical Research, University of Guanajuato, Leon, Gto., Mexico.
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31
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Abstract
The plant life cycle involves a series of developmental phase transitions. These transitions require the regulation and highly co-ordinated expression of many genes. Epigenetic controls have now been shown to be a key element of this mechanism of regulation. In the model plant Arabidopsis, recent genetic and molecular studies on chromatin have begun to dissect the molecular basis of these epigenetic controls. Chromatin dynamics represent the emerging and exciting field of gene regulation notably involved in plant developmental transitions. By comparing plant and animal systems, new insights into the molecular complexes and mechanisms governing development can be delineated. We are now beginning to identify the components of chromatin complexes and their functions.
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Affiliation(s)
- Frédéric Berger
- Laboratoire RDP, UMR 5667, ENS-Lyon, 46 allée d'Italie, F-69364 Lyon cedex 07, France
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32
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Affiliation(s)
- Gabriela Gebrin Cezar
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, Wisconsin 06340, USA.
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Edwards YJK, Carver TJ, Vavouri T, Frith M, Bishop MJ, Elgar G. Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence. Nucleic Acids Res 2003; 31:3510-7. [PMID: 12824356 PMCID: PMC168908 DOI: 10.1093/nar/gkg501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Revised: 01/17/2003] [Accepted: 01/27/2003] [Indexed: 01/12/2023] Open
Abstract
Theatre is a web-based computing system designed for the comparative analysis of genomic sequences, especially with respect to motifs likely to be involved in the regulation of gene expression. Theatre is an interface to commonly used sequence analysis tools and biological sequence databases to determine or predict the positions of coding regions, repetitive sequences and transcription factor binding sites in families of DNA sequences. The information is displayed in a manner that can be easily understood and can reveal patterns that might not otherwise have been noticed. In addition to web-based output, Theatre can produce publication quality colour hardcopies showing predicted features in aligned genomic sequences. A case study using the p53 promoter region of four mammalian species and two fish species is described. Unlike the mammalian sequences the promoter regions in fish have not been previously predicted or characterized and we report the differences in the p53 promoter region of four mammals and that predicted for two fish species. Theatre can be accessed at http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/.
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Affiliation(s)
- Yvonne J K Edwards
- Comparative Genomics Group, Research Division, MRC UK Human Genome Mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK.
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Guilleret I, Yan P, Grange F, Braunschweig R, Bosman FT, Benhattar J. Hypermethylation of the human telomerase catalytic subunit (hTERT) gene correlates with telomerase activity. Int J Cancer 2002; 101:335-41. [PMID: 12209957 DOI: 10.1002/ijc.10593] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is an epigenetic process involved in embryonic development, differentiation and aging. It is 1 of the mechanisms resulting in gene silencing in carcinogenesis, especially in tumor suppressor genes (e.g., p16, Rb). Telomerase, the DNA polymerase adding TTAGGG repeats to the chromosome end, is involved in the regulation of the replicative life span by maintaining telomere length. This enzyme is activated in germ and stem cells, repressed in normal somatic cells and reactivated in a large majority of tumor cells. The promoter region of the hTERT gene, encoding for the catalytic subunit of human telomerase, has been located in a CpG island and may therefore be regulated at least in part by DNA methylation. We analyzed the methylation status of 27 CpG sites within the hTERT promoter core region by methylation-sensitive single-strand conformation analysis (MS-SSCA) and direct sequencing using bisulfite-modified DNA in 56 human tumor cell lines, as well as tumor and normal tissues from different organs. A positive correlation was observed among hypermethylation of the hTERT promoter, hTERT mRNA expression and telomerase activity (p < 0.00001). Furthermore, this correlation was confirmed in normal tissues where hypermethylation of the hTERT promoter was found exclusively in hTERT-expressing telomerase-positive samples and was absent in telomerase-negative samples (p < 0.00002). Since tumor tissues contain also nonneoplastic stromal elements, we performed microdissection to allow confirmation that the hTERT promoter methylation truly occurred in tumor cells. Our results suggest that methylation may be involved in the regulation of hTERT gene expression. To our knowledge, this is the first gene in which methylation of its promoter sequence has been found to be positively correlated with gene expression.
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Affiliation(s)
- Isabelle Guilleret
- Institut de Pathologie and Institut de Médecine Légale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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35
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Carty SM, Greenleaf AL. Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing. Mol Cell Proteomics 2002; 1:598-610. [PMID: 12376575 DOI: 10.1074/mcp.m200029-mcp200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using an interaction blot approach to search in the human nuclear proteome, we identified eight novel proteins that bind the hyperphosphorylated C-terminal repeat domain (phosphoCTD) of RNA polymerase II. Unexpectedly, five of the new phosphoCTD-associating proteins (PCAPs) represent either enzymes that act on DNA and chromatin (topoisomerase I, DNA (cytosine-5) methyltransferase 1, poly(ADP-ribose) polymerase-1) or proteins known to bind DNA (heterogeneous nuclear ribonucleoprotein (hnRNP) U/SAF-A, hnRNP D). The other three PCAPs represent factors involved in pre-mRNA metabolism as anticipated (CA150, NSAP1/hnRNP Q, hnRNP R) (note that hnRNP U/SAF-A and hnRNP D are also implicated in pre-mRNA metabolism). Identifying as PCAPs proteins involved in diverse DNA transactions suggests that the range of phosphoCTD functions extends far beyond just transcription and RNA processing. In view of the activities possessed by the DNA-directed PCAPs, it is likely that the phosphoCTD plays important roles in genome integrity, epigenetic regulation, and potentially nuclear structure. We present a model in which the phosphoCTD association of the PCAPs poises them to act either on the nascent transcript or on the DNA/chromatin template. We propose that the phosphoCTD of elongating RNA polymerase II is a major organizer of nuclear functions.
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Affiliation(s)
- Sherry M Carty
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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36
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Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet 1999; 23:62-6. [PMID: 10471500 DOI: 10.1038/12664] [Citation(s) in RCA: 599] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Methylation of DNA at the dinucleotide CpG is essential for mammalian development and is correlated with stable transcriptional silencing. This transcriptional silencing has recently been linked at a molecular level to histone deacetylation through the demonstration of a physical association between histone deacetylases and the methyl CpG-binding protein MeCP2 (refs 4,5). We previously purified a histone deacetylase complex from Xenopus laevis egg extracts that consists of six subunits, including an Rpd3-like deacetylase, the RbA p48/p46 histone-binding protein and the nucleosome-stimulated ATPase Mi-2 (ref. 6). Similar species were subsequently isolated from human cell lines, implying functional conservation across evolution. This complex represents the most abundant form of deacetylase in amphibian eggs and cultured mammalian cells. Here we identify the remaining three subunits of this enzyme complex. One of them binds specifically to methylated DNA in vitro and molecular cloning reveals a similarity to a known methyl CpG-binding protein. Our data substantiate the mechanistic link between DNA methylation, histone deacetylation and transcriptional silencing.
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Affiliation(s)
- P A Wade
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Building 18T Room 106, Bethesda, Maryland 20892, USA
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Pedersen AG, Baldi P, Chauvin Y, Brunak S. The biology of eukaryotic promoter prediction--a review. COMPUTERS & CHEMISTRY 1999; 23:191-207. [PMID: 10404615 DOI: 10.1016/s0097-8485(99)00015-7] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational prediction of eukaryotic promoters from the nucleotide sequence is one of the most attractive problems in sequence analysis today, but it is also a very difficult one. Thus, current methods predict in the order of one promoter per kilobase in human DNA, while the average distance between functional promoters has been estimated to be in the range of 30-40 kilobases. Although it is conceivable that some of these predicted promoters correspond to cryptic initiation sites that are used in vivo, it is likely that most are false positives. This suggests that it is important to carefully reconsider the biological data that forms the basis of current algorithms, and we here present a review of data that may be useful in this regard. The review covers the following topics: (1) basal transcription and core promoters, (2) activated transcription and transcription factor binding sites, (3) CpG islands and DNA methylation, (4) chromosomal structure and nucleosome modification, and (5) chromosomal domains and domain boundaries. We discuss the possible lessons that may be learned, especially with respect to the wealth of information about epigenetic regulation of transcription that has been appearing in recent years.
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Affiliation(s)
- A G Pedersen
- Department of Biotechnology, Technical University of Denmark, Lyngby, Denmark.
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38
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Huber R, Hansen RS, Strazzullo M, Pengue G, Mazzarella R, D'Urso M, Schlessinger D, Pilia G, Gartler SM, D'Esposito M. DNA methylation in transcriptional repression of two differentially expressed X-linked genes, GPC3 and SYBL1. Proc Natl Acad Sci U S A 1999; 96:616-21. [PMID: 9892682 PMCID: PMC15185 DOI: 10.1073/pnas.96.2.616] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/1998] [Indexed: 12/22/2022] Open
Abstract
Methylation of CpG islands is an established transcriptional repressive mechanism and is a feature of silencing in X chromosome inactivation. Housekeeping genes that are subject to X inactivation exhibit differential methylation of their CpG islands such that the inactive alleles are hypermethylated. In this report, we examine two contrasting X-linked genes with CpG islands for regulation by DNA methylation: SYBL1, a housekeeping gene in the Xq pseudoautosomal region, and GPC3, a tissue-specific gene in Xq26 that is implicated in the etiology of the Simpson-Golabi-Behmel overgrowth syndrome. We observed that in vitro methylation of either the SYBL1 or the GPC3 promoter resulted in repression of reporter constructs. In normal contexts, we found that both the Y and inactive X alleles of SYBL1 are repressed and hypermethylated, whereas the active X allele is expressed and unmethylated. Furthermore, the Y and inactive X alleles of SYBL1 were derepressed by treatment with the demethylating agent azadeoxycytidine. GPC3 is also subject to X inactivation, and the active X allele is unmethylated in nonexpressing leukocytes as well as in an expressing cell line, suggesting that methylation is not involved in the tissue-specific repression of this allele. The inactive X allele, however, is hypermethylated in leukocytes, presumably reflecting early X inactivation events that become important for gene dosage in expressing lineages. These and other data suggest that all CpG islands on Xq, including the pseudoautosomal region, are subject to X inactivation-induced methylation. Additionally, methylation of SYBL1 on Yq may derive from a process related to X inactivation that targets large chromatin domains for transcriptional repression.
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Affiliation(s)
- R Huber
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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39
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Abstract
Apoptosis seems characterized by a cascade of megabase to 200-bp fragmentations and by a commitment to perish at the initial level. How that could be achieved seems unclear. Preferential cleavage of transcriptionally active chromatin by apoptotic nuclease activity has long been suggested. We show here the manifestation of self-inflicted G-banding patterns in mitotic chromosomes, or G-band expression, occurring concurrently with a pattern of megabase fragmentations in two apoptotic systems that we have established in human Chang liver cells using (a) staurosporine and (b) vanadyl(4) prepulsing. We further show that rare-cutting NotI and MluI restriction endonucleases with C-G dinucleotide sequence specificity had produced similar G-bandings and megabase fragmentations cascading down to the 200-bp ladder fragmentation that were also associated with the expression of characteristic apoptotic morphologies by the digested cells. CpG-specific methylation using the methylase SssI abolished the DNA fragmentation cascade, G-banding, and apoptotic expressions induced by NotI and MluI, implicating endonuclease cleavage of active chromatin, where CpG islands are concentrated, as the initiating event. Reproducing the G-bandings and megabase fragmentations by directly applying NotI and MluI endonucleases to fixed chromosomes and extracted genomic DNA, respectively, further confirmed the notion of endonucleolytic cleavage of active chromatin as the causation. Nuclease-digested light G-band regions of chromosomes appeared to be the chromosome sites providing the megabase fragments. Transcriptionally active genes of the genome are known to be preferentially cleaved by nuclease activity and are established as being concentrated in the light G-bandings that correspond to R-bandings, which are also known to be the sites of more frequent cytogenetic breakpoints. Manifestation of self-inflicted G-banding patterns (G-banding expression) in apoptosis would then imply cleavage of the transcriptionally active genes in every light G-band site of every chromosome in the genome. This must be suicidal.
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Affiliation(s)
- D L Chen
- Department of Anatomy, Faculty of Medicine, National University of Singapore, Kent Ridge, Singapore
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40
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Singal R, Ferris R, Little JA, Wang SZ, Ginder GD. Methylation of the minimal promoter of an embryonic globin gene silences transcription in primary erythroid cells. Proc Natl Acad Sci U S A 1997; 94:13724-9. [PMID: 9391093 PMCID: PMC28373 DOI: 10.1073/pnas.94.25.13724] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/1997] [Indexed: 02/05/2023] Open
Abstract
Methylation of cytosines in the dinucleotide CpG has been shown to suppress transcription of a number of tissue-specific genes, yet the precise mechanism is not fully understood. The vertebrate globin genes were among the first examples in which an inverse correlation was shown between CpG methylation and transcription. We studied the methylation pattern of the 235-bp rho-globin gene promoter in genomic DNA from primary chicken erythroid cells using the sodium bisulfite conversion technique and found all CpGs in the promoter to be methylated in erythroid cells from adult chickens in which the rho-globin gene is silent but unmethylated in 5-day (primitive) embryonic red cells in which the gene is transcribed. To elucidate further the mechanism of methylation-induced silencing, an expression construct consisting of 235 bp of 5' promoter sequence of the rho-globin gene along with a strong 5' erythroid enhancer driving a chloramphenicol acetyltransferase reporter gene, rho-CAT, was transfected into primary avian erythroid cells derived from 5-day embryos. Methylation of just the 235-bp rho-globin gene promoter fragment at every CpG resulted in a 20- to 30-fold inhibition of transcription, and this effect was not overridden by the presence of potent erythroid-specific enhancers. The ability of the 235-bp rho-globin gene promoter to bind to a DNA Methyl Cytosine binding Protein Complex (MeCPC) was tested in electrophoretic mobility shift assays utilizing primary avian erythroid cell nuclear extract. The results were that fully methylated but not unmethylated 235-bp rho-globin gene promoter fragment could compete efficiently for MeCPC binding. These results are a direct demonstration that site-specific methylation of a globin gene promoter at the exact CpGs that are methylated in vivo can silence transcription in homologous primary erythroid cells. Further, these data implicate binding of MeCPC to the promoter in the mechanism of silencing.
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Affiliation(s)
- R Singal
- Department of Medicine, Division of Medical Oncology, University of Minnesota, Minneapolis, MN 55455-0362, USA
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41
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Kass SU, Landsberger N, Wolffe AP. DNA methylation directs a time-dependent repression of transcription initiation. Curr Biol 1997; 7:157-65. [PMID: 9395433 DOI: 10.1016/s0960-9822(97)70086-1] [Citation(s) in RCA: 305] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND The regulation of DNA methylation is required for differential expression of imprinted genes during vertebrate development. Earlier studies that monitored the activity of the Herpes simplex virus (HSV) thymidine kinase (tk) gene after injection into rodent cells have suggested that assembly of chromatin influences the methylation-dependent repression of gene activity. Here, we examine the mechanism of methylation-dependent HSV tk gene regulation by direct determination of nucleoprotein organization during the establishment of a transcriptionally silenced state after microinjection of templates with defined methylation states into Xenopus oocyte nuclei. RESULTS The transcriptional silencing conferred by a methylated DNA segment was not immediate, as methylated templates were initially assembled into active transcription complexes. The eventual loss of DNase I hypersenitive sites and inhibition of transcription at the HSV tk promoter only occurred after several hours. Flanking methylated vector DNA silenced the adjacent unmethylated HSV tk promoter, indicative of a dominant transmissible repression originating from a center of methylation. The resulting repressive nucleoprotein structure silenced transcription in the presence of activators that are able to overcome repression of transcription by nucleosomes. CONCLUSIONS Silencing of transcription by DNA methylation is achieved at the level of transcription initiation and involves the removal of transcriptional machinery from active templates. This transcriptional repression can occur by indirect mechanisms involving the time-dependent assembly of repressive nucleoprotein complexes, which are able to inhibit transcription more effectively than nucleosomes alone.
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Affiliation(s)
- S U Kass
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892-5431, USA
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42
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Abstract
MeCP2 is an abundant mammalian protein that binds to methylated CpG. We have found that native and recombinant MeCP2 repress transcription in vitro from methylated promoters but do not repress nonmethylated promoters. Repression is nonlinearly dependent on the local density of methylation, becoming significant at the density found in bulk vertebrate genomic DNA. Transient transfection using fusions with the GAL4 DNA binding domain identified a region of MeCP2 that is capable of long-range repression in vivo. Moreover, MeCP2 is able to displace histone H1 from preassembled chromatin that contains methyl-CpG. These properties, together with the abundance of MeCP2 and the high frequency of its 2 bp binding site, suggest a role as a global transcriptional repressor in vertebrate genomes.
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Affiliation(s)
- X Nan
- Institute of Cell and Molecular Biology, University of Edinburgh, United Kingdom
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