151
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Ware CB. Concise Review: Lessons from Naïve Human Pluripotent Cells. Stem Cells 2016; 35:35-41. [PMID: 27663171 DOI: 10.1002/stem.2507] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/06/2016] [Indexed: 12/19/2022]
Abstract
The naïve state of pluripotency is actively being explored by a number of labs. There is some controversy in the field as to the true identity of naïve human pluripotent cells as they are not exact mirrors of the mouse. The various reports published, although in basic agreement, present discrepancies in the characterization of the various lines, which likely reflect the etiology of these lines. The primary lesson learned from these contributions is that a human naïve state reflecting the preimplantation human is likely to exist. The essential factors that will universally maintain the naïve state in human cells in vitro are not yet fully understood. These first need to be identified in order to describe the definitive characteristics of this state. Comparisons of naïve and primed human pluripotent cells have also highlighted consistencies between states and broadened our understanding of embryonic metabolism, epigenetic change required for development, embryonic DNA repair strategies and embryonic expression dynamics. Stem Cells 2017;35:35-41.
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Affiliation(s)
- Carol B Ware
- Department of Comparative Medicine, University of Washington, Seattle, Washington, USA
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152
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DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells. Cell Res 2016; 27:165-183. [PMID: 27824029 PMCID: PMC5339845 DOI: 10.1038/cr.2016.128] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 12/24/2022] Open
Abstract
Chromatin remodeling is important for the epigenetic reprogramming of human primordial germ cells. However, the comprehensive chromatin state has not yet been analyzed for human fetal germ cells (FGCs). Here we use nucleosome occupancy and methylation sequencing method to analyze both the genome-wide chromatin accessibility and DNA methylome at a series of crucial time points during fetal germ cell development in both human and mouse. We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. Moreover, we find that the distal NDRs are enriched specifically for binding motifs of the pluripotency and germ cell master regulators such as NANOG, SOX17, AP2γ and OCT4 in human FGCs, indicating the existence of a delicate regulatory balance between pluripotency-related genes and germ cell-specific genes in human FGCs, and the functional significance of these genes for germ cell development in vivo. Our work offers a comprehensive and high-resolution roadmap for dissecting chromatin state transition dynamics during the epigenomic reprogramming of human and mouse FGCs.
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153
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Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T. Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. Am J Hum Genet 2016; 99:1045-1058. [PMID: 27843122 DOI: 10.1016/j.ajhg.2016.08.021] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022] Open
Abstract
DNA methylation is globally reprogrammed after fertilization, and as a result, the parental genomes have similar DNA-methylation profiles after implantation except at the germline differentially methylated regions (gDMRs). We and others have previously shown that human blastocysts might contain thousands of transient maternally methylated gDMRs (transient mDMRs), whose maternal methylation is lost in embryonic tissues after implantation. In this study, we performed genome-wide allelic DNA methylation analyses of purified trophoblast cells from human placentas and, surprisingly, found that more than one-quarter of the transient-in-embryo mDMRs maintained their maternally biased DNA methylation. RNA-sequencing-based allelic expression analyses revealed that some of the placenta-specific mDMRs were associated with expression of imprinted genes (e.g., TIGAR, SLC4A7, PROSER2-AS1, and KLHDC10), and three imprinted gene clusters were identified. This approach also identified some X-linked gDMRs. Comparisons of the data with those from other mammals revealed that genomic imprinting in the placenta is highly variable. These findings highlight the incomplete erasure of germline DNA methylation in the human placenta; understanding this erasure is important for understanding normal placental development and the pathogenesis of developmental disorders with imprinting effects.
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154
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Killian JK, Dorssers LCJ, Trabert B, Gillis AJM, Cook MB, Wang Y, Waterfall JJ, Stevenson H, Smith WI, Noyes N, Retnakumar P, Stoop JH, Oosterhuis JW, Meltzer PS, McGlynn KA, Looijenga LHJ. Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors. Genome Res 2016; 26:1490-1504. [PMID: 27803193 PMCID: PMC5088592 DOI: 10.1101/gr.201293.115] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 09/14/2016] [Indexed: 12/12/2022]
Abstract
Testicular germ cell tumors (TGCTs) share germline ancestry but diverge phenotypically and clinically as seminoma (SE) and nonseminoma (NSE), the latter including the pluripotent embryonal carcinoma (EC) and its differentiated derivatives, teratoma (TE), yolk sac tumor (YST), and choriocarcinoma. Epigenomes from TGCTs may illuminate reprogramming in both normal development and testicular tumorigenesis. Herein we investigate pure-histological forms of 130 TGCTs for conserved and subtype-specific DNA methylation, including analysis of relatedness to pluripotent stem cell (ESC, iPSC), primordial germ cell (PGC), and differentiated somatic references. Most generally, TGCTs conserve PGC-lineage erasure of maternal and paternal genomic imprints and DPPA3 (also known as STELLA); however, like ESCs, TGCTs show focal recurrent imprinted domain hypermethylation. In this setting of shared physiologic erasure, NSEs harbor a malignancy-associated hypermethylation core, akin to that of a diverse cancer compendium. Beyond these concordances, we found subtype epigenetic homology with pluripotent versus differentiated states. ECs demonstrate a striking convergence of both CpG and CpH (non-CpG) methylation with pluripotent states; the pluripotential methyl-CpH signature crosses species boundaries and is distinct from neuronal methyl-CpH. EC differentiation to TE and YST entails reprogramming toward the somatic state, with loss of methyl-CpH but de novo methylation of pluripotency loci such as NANOG. Extreme methyl-depletion among SE reflects the PGC methylation nadir. Adjacent to TGCTs, benign testis methylation profiles are determined by spermatogenetic proficiency measured by Johnsen score. In sum, TGCTs share collective entrapment in a PGC-like state of genomic-imprint and DPPA3 erasure, recurrent hypermethylation of cancer-associated targets, and subtype-dependent pluripotent, germline, or somatic methylation.
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Affiliation(s)
- J Keith Killian
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Lambert C J Dorssers
- Department of Pathology, Erasmus MC-University Medical Center, Rotterdam, 3015, The Netherlands
| | - Britton Trabert
- Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ad J M Gillis
- Department of Pathology, Erasmus MC-University Medical Center, Rotterdam, 3015, The Netherlands
| | - Michael B Cook
- Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yonghong Wang
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Joshua J Waterfall
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Holly Stevenson
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William I Smith
- Suburban Hospital Department of Pathology, Bethesda, Maryland 20814, USA
| | - Natalia Noyes
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Parvathy Retnakumar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - J Hans Stoop
- Department of Pathology, Erasmus MC-University Medical Center, Rotterdam, 3015, The Netherlands
| | - J Wolter Oosterhuis
- Department of Pathology, Erasmus MC-University Medical Center, Rotterdam, 3015, The Netherlands
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Katherine A McGlynn
- Hormonal and Reproductive Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Leendert H J Looijenga
- Department of Pathology, Erasmus MC-University Medical Center, Rotterdam, 3015, The Netherlands
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Abstract
Epigenetic modifications established during gametogenesis regulate transcription and other nuclear processes in gametes, but also have influences in the zygote, embryo and postnatal life. This is best understood for DNA methylation which, established at discrete regions of the oocyte and sperm genomes, governs genomic imprinting. In this review, we describe how imprinting has informed our understanding of de novo DNA methylation mechanisms, highlight how recent genome-wide profiling studies have provided unprecedented insights into establishment of the sperm and oocyte methylomes and consider the fate and function of gametic methylation and other epigenetic modifications after fertilization.
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Affiliation(s)
- Kathleen R Stewart
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK2200 Copenhagen, Denmark
| | - Lenka Veselovska
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Developmental Biology & Genetics, Department of Molecular Biology, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
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157
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Epigenetic studies in Developmental Origins of Health and Disease: pitfalls and key considerations for study design and interpretation. J Dev Orig Health Dis 2016; 8:30-43. [DOI: 10.1017/s2040174416000507] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The field of Developmental Origins of Health and Disease (DOHaD) seeks to understand the relationships between early-life environmental exposures and long-term health and disease. Until recently, the molecular mechanisms underlying these phenomena were poorly understood; however, epigenetics has been proposed to bridge the gap between the environment and phenotype. Epigenetics involves the study of heritable changes in gene expression, which occur without changes to the underlying DNA sequence. Different types of epigenetic modifications include DNA methylation, post-translational histone modifications and non-coding RNAs. Increasingly, changes to the epigenome have been associated with early-life exposures in both humans and animal models, offering both an explanation for how the environment may programme long-term health, as well as molecular changes that could be developed as biomarkers of exposure and/or future disease. As such, epigenetic studies in DOHaD hold much promise; however, there are a number of factors which should be considered when designing and interpreting such studies. These include the impact of the genome on the epigenome, the tissue-specificity of epigenetic marks, the stability (or lack thereof) of epigenetic changes over time and the importance of associating epigenetic changes with changes in transcription or translation to demonstrate functional consequences. In this review, we discuss each of these key concepts and provide practical strategies to mitigate some common pitfalls with the aim of providing a useful guide for future epigenetic studies in DOHaD.
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158
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Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Sci Rep 2016; 6:32207. [PMID: 27573482 PMCID: PMC5004121 DOI: 10.1038/srep32207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/03/2016] [Indexed: 12/04/2022] Open
Abstract
Although non-CG methylations are abundant in several mammalian cell types, their biological significance is sparsely characterized. We gathered 51 human and mouse DNA methylomes from brain neurons, embryonic stem cells and induced pluripotent stem cells, primordial germ cells and oocytes. We utilized an unbiased sub-motif prediction method and reported CW as the representative non-CG methylation context, which is distinct from CC methylation in terms of sequence context and genomic distribution. A two-dimensional comparison of non-CG methylations across cell types and species was performed. Unambiguous studies of sequence preferences and genomic region enrichment showed that CW methylation is cell-type specific and is also conserved between humans and mice. In brain neurons, it was found that active long interspersed nuclear element-1 (LINE-1) lacked CW methylations but not CG methylations. Coincidentally, both human Alu and mouse B1 elements preferred high CW methylations at specific loci during their respective evolutionary development. Last, the strand-specific distributions of CW methylations in introns and long interspersed nuclear elements are also cell-type specific and conserved. In summary, our results illustrate that CW methylations are highly conserved among species, are dynamically regulated in each cell type, and are potentially involved in the evolution of transposon elements.
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159
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Abstract
PURPOSE OF REVIEW The purpose of this review is to highlight the recent advances in epigenetic regulation and chromatin biology for a better understanding of gene regulation related to human disease. RECENT FINDINGS Alterations to chromatin influence genomic function, including gene transcription. At its most simple level, this involves DNA methylation and posttranscriptional histone modifications. However, recent developments in biochemical and molecular techniques have revealed that transcriptional regulation is far more complex, involving combinations of histone modifications and discriminating transcription factor binding, and long-range chromatin loops with enhancers, to generate a multifaceted code. Here, we describe the most recent advances, culminating in the example of genomic imprinting, the parent-of-origin monoallelic expression that utilizes the majority of these mechanisms to attain one active and one repressed allele. SUMMARY It is becoming increasingly evident that epigenetic mechanisms work in unison to maintain tight control of gene expression and genome function. With the wealth of knowledge gained from recent molecular studies, future goals should focus on the application of this information in deciphering their role in developmental diseases.
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160
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Derakhshan-Horeh M, Abolhassani F, Jafarpour F, Moini A, Karbalaie K, Hosseini SM, Ostadhosseini S, Nasr-Esfahani MH. Methylation Status of H19/IGF2 Differentially Methylated Region in in vitro Human Blastocysts Donated by Healthy Couples. IRANIAN BIOMEDICAL JOURNAL 2016; 21:16-23. [PMID: 27432596 PMCID: PMC5141249 DOI: 10.6091/.21.1.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Imprinted genes are a unique subset of few genes that have been differentially methylated region (DMR) in a parental origin-dependent manner during gametogenesis, and these genes are highly protected during pre-implantation epigenetic reprogramming. Several studies have shown that the particular vulnerability of imprinting genes during suboptimal pre- and peri-conception micro-environments often is occurred by assisted reproduction techniques (ART). This study investigated the methylation status of H19/IGF2 DMR at high-quality expanding/expanded human blastocysts donated by healthy individuals to evaluate the risks linked to ART. METHODS Methylation levels of H19/IGF2 DMR were analyzed by bisulfite conversion and sequencing at 18 CpG sites (CpGs) located in this region. RESULTS The overall percentage of methylated CpGs and the proportion of hyper-methylated clones of H19/IGF2 DMR in analyzed blastocysts were 37.85±4.87% and 43.75±5.1%, respectively. For validation of our technique, the corresponding methylation levels of peripheral human lymphocytes were defined (49.52±1.86% and 50%, respectively). CONCLUSIONS Considering the absence of in vivo- produced human embryos, it is not possible to conclude that the methylation found in H19/IGF2 DMR is actually normal or abnormal. Regarding the possible risks associated with ART, the procedures should be optimized in order to at least reduce some of the epigenetic risks.
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Affiliation(s)
| | - Farid Abolhassani
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Ashraf Moini
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Obstetrics and Gynecology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Karbalaie
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; 6Isfahan Fertility and Infertility Center, Isfahan, Iran
| | - Sayyed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Somayyeh Ostadhosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; 6Isfahan Fertility and Infertility Center, Isfahan, Iran.,Isfahan Fertility and Infertility Center, Isfahan, Iran
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161
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Madissoon E, Jouhilahti EM, Vesterlund L, Töhönen V, Krjutškov K, Petropoulous S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J. Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. Sci Rep 2016; 6:28995. [PMID: 27412763 PMCID: PMC4944136 DOI: 10.1038/srep28995] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 01/07/2023] Open
Abstract
PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes, ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB, NOBOX, TPRX1 and TPRX2, were expressed in human preimplantation embryos. In the current study we characterized these PRD-like homeobox genes in depth and studied their functions as transcription factors. We cloned multiple transcript variants from human embryos and showed that the expression of these genes is specific to embryos and pluripotent stem cells. Overexpression of the genes in human embryonic stem cells confirmed their roles as transcription factors as either activators (CPHX1, CPHX2, ARGFX) or repressors (DPRX, DUXA, TPRX2) with distinct targets that could be explained by the amino acid sequence in homeodomain. Some PRD-like homeodomain transcription factors had high concordance of target genes and showed enrichment for both developmentally important gene sets and a 36 bp DNA recognition motif implicated in Embryo Genome Activation (EGA). Our data implicate a role for these previously uncharacterized PRD-like homeodomain proteins in the regulation of human embryo genome activation and preimplantation embryo development.
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Affiliation(s)
- Elo Madissoon
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | | | - Virpi Töhönen
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kaarel Krjutškov
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Sophie Petropoulous
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Robert Månsson
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | - Shintaro Katayama
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Juha Kere
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
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162
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Chavatte-Palmer P, Robles M, Tarrade A, Duranthon V. Gametes, Embryos, and Their Epigenome: Considerations for Equine Embryo Technologies. J Equine Vet Sci 2016. [DOI: 10.1016/j.jevs.2016.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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163
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Niemann H. Epigenetic reprogramming in mammalian species after SCNT-based cloning. Theriogenology 2016; 86:80-90. [PMID: 27160443 DOI: 10.1016/j.theriogenology.2016.04.021] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/23/2016] [Accepted: 03/14/2016] [Indexed: 12/16/2022]
Abstract
The birth of "Dolly," the first mammal cloned from an adult mammary epithelial cell, abolished the decades-old scientific dogma implying that a terminally differentiated cell cannot be reprogrammed into a pluripotent embryonic state. The most dramatic epigenetic reprogramming occurs in SCNT when the expression profile of a differentiated cell is abolished and a new embryo-specific expression profile, involving 10,000 to 12,000 genes, and thus, most genes of the entire genome is established, which drives embryonic and fetal development. The initial release from somatic cell epigenetic constraints is followed by establishment of post-zygotic expression patterns, X-chromosome inactivation, and adjustment of telomere length. Somatic cell nuclear transfer may be associated with a variety of pathologic changes of the fetal and placental phenotype in a proportion of cloned offspring, specifically in ruminants, that are thought to be caused by aberrant epigenetic reprogramming. Improvements in our understanding of this dramatic epigenetic reprogramming event will be instrumental in realizing the great potential of SCNT for basic research and for important agricultural and biomedical applications. Here, current knowledge on epigenetic reprogramming after use of SCNT in livestock is reviewed, with emphasis on gene-specific and global DNA methylation, imprinting, X-chromosome inactivation, and telomere length restoration in early development.
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Affiliation(s)
- Heiner Niemann
- Institute of Farm Animal Genetics (FLI), Mariensee, Neustadt, Germany.
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164
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Alves da Silva AF, Machado FB, Pavarino ÉC, Biselli-Périco JM, Zampieri BL, da Silva Francisco Junior R, Mozer Rodrigues PT, Terra Machado D, Santos-Rebouças CB, Gomes Fernandes M, Chuva de Sousa Lopes SM, Lopes Rios ÁF, Medina-Acosta E. Trisomy 21 Alters DNA Methylation in Parent-of-Origin-Dependent and -Independent Manners. PLoS One 2016; 11:e0154108. [PMID: 27100087 PMCID: PMC4839675 DOI: 10.1371/journal.pone.0154108] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 04/09/2016] [Indexed: 12/31/2022] Open
Abstract
The supernumerary chromosome 21 in Down syndrome differentially affects the methylation statuses at CpG dinucleotide sites and creates genome-wide transcriptional dysregulation of parental alleles, ultimately causing diverse pathologies. At present, it is unknown whether those effects are dependent or independent of the parental origin of the nondisjoined chromosome 21. Linkage analysis is a standard method for the determination of the parental origin of this aneuploidy, although it is inadequate in cases with deficiency of samples from the progenitors. Here, we assessed the reliability of the epigenetic 5mCpG imprints resulting in the maternally (oocyte)-derived allele methylation at a differentially methylated region (DMR) of the candidate imprinted WRB gene for asserting the parental origin of chromosome 21. We developed a methylation-sensitive restriction enzyme-specific PCR assay, based on the WRB DMR, across single nucleotide polymorphisms (SNPs) to examine the methylation statuses in the parental alleles. In genomic DNA from blood cells of either disomic or trisomic subjects, the maternal alleles were consistently methylated, while the paternal alleles were unmethylated. However, the supernumerary chromosome 21 did alter the methylation patterns at the RUNX1 (chromosome 21) and TMEM131 (chromosome 2) CpG sites in a parent-of-origin-independent manner. To evaluate the 5mCpG imprints, we conducted a computational comparative epigenomic analysis of transcriptome RNA sequencing (RNA-Seq) and histone modification expression patterns. We found allele fractions consistent with the transcriptional biallelic expression of WRB and ten neighboring genes, despite the similarities in the confluence of both a 17-histone modification activation backbone module and a 5-histone modification repressive module between the WRB DMR and the DMRs of six imprinted genes. We concluded that the maternally inherited 5mCpG imprints at the WRB DMR are uncoupled from the parental allele expression of WRB and ten neighboring genes in several tissues and that trisomy 21 alters DNA methylation in parent-of-origin-dependent and -independent manners.
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Affiliation(s)
- Antônio Francisco Alves da Silva
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Graduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (AFAS); (FBM); (EM-A)
| | - Filipe Brum Machado
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Postgraduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (AFAS); (FBM); (EM-A)
| | | | | | | | - Ronaldo da Silva Francisco Junior
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Douglas Terra Machado
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | | | - Maria Gomes Fernandes
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | | | - Álvaro Fabricio Lopes Rios
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Laboratory of Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, Rio de Janeiro, Brazil
- Molecular Identification and Diagnostics Unit, Hospital Escola Álvaro Alvim, Campos dos Goytacazes, Rio de Janeiro, Brazil
- Graduate Program in Biosciences and Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil
- * E-mail: (AFAS); (FBM); (EM-A)
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165
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Canovas S, Ross PJ. Epigenetics in preimplantation mammalian development. Theriogenology 2016; 86:69-79. [PMID: 27165992 DOI: 10.1016/j.theriogenology.2016.04.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 02/27/2016] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
Abstract
Fertilization is a very dynamic period of comprehensive chromatin remodeling, from which two specialized cells result in a totipotent zygote. The formation of a totipotent cell requires extensive epigenetic remodeling that, although independent of modifications in the DNA sequence, still entails a profound cell-fate change, supported by transcriptional profile modifications. As a result of finely tuned interactions between numerous mechanisms, the goal of fertilization is to form a full healthy new individual. To avoid the persistence of alterations in epigenetic marks, the epigenetic information contained in each gamete is reset during early embryogenesis. Covalent modification of DNA by methylation, as well as posttranslational modifications of histone proteins and noncoding RNAs, appears to be the main epigenetic mechanisms that control gene expression. These allow different cells in an organism to express different transcription profiles, despite each cell containing the same DNA sequence. In the context of replacement of spermatic protamine with histones from the oocyte, active cell division, and specification of different lineages, active and passive mechanisms of epigenetic remodeling have been revealed as critical for editing the epigenetic profile of the early embryo. Importantly, redundant factors and mechanisms are likely in place, and only a few have been reported as critical for fertilization or embryo survival by the use of knockout models. The aim of this review is to highlight the main mechanisms of epigenetic remodeling that ensue after fertilization in mammals.
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Affiliation(s)
- Sebastian Canovas
- LARCEL (Laboratorio Andaluz de Reprogramacion Celular), BIONAND, Centro Andaluz de Nanomedicina y Biotecnologia Campanillas, Malaga, Spain.
| | - Pablo Juan Ross
- Department of Animal Science, University of California, Davis, California, USA.
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166
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Bak M, Boonen SE, Dahl C, Hahnemann JMD, Mackay DJDG, Tümer Z, Grønskov K, Temple IK, Guldberg P, Tommerup N. Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57. BMC MEDICAL GENETICS 2016; 17:29. [PMID: 27075368 PMCID: PMC4831126 DOI: 10.1186/s12881-016-0292-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 04/08/2016] [Indexed: 12/21/2022]
Abstract
Background Transient neonatal diabetes mellitus 1 (TNDM1) is a rare imprinting disorder characterized by intrautering growth retardation and diabetes mellitus usually presenting within the first six weeks of life and resolves by the age of 18 months. However, patients have an increased risk of developing diabetes mellitus type 2 later in life. Transient neonatal diabetes mellitus 1 is caused by overexpression of the maternally imprinted genes PLAGL1 and HYMAI on chromosome 6q24. One of the mechanisms leading to overexpression of the locus is hypomethylation of the maternal allele of PLAGL1 and HYMAI. A subset of patients with maternal hypomethylation at PLAGL1 have hypomethylation at additional imprinted loci throughout the genome, including GRB10, ZIM2 (PEG3), MEST (PEG1), KCNQ1OT1 and NESPAS (GNAS-AS1). About half of the TNDM1 patients carry mutations in ZFP57, a transcription factor involved in establishment and maintenance of methylation of imprinted loci. Our objective was to investigate whether additional regions are aberrantly methylated in ZFP57 mutation carriers. Methods Genome-wide DNA methylation analysis was performed on four individuals with homozygous or compound heterozygous ZFP57 mutations, three relatives with heterozygous ZFP57 mutations and five controls. Methylation status of selected regions showing aberrant methylation in the patients was verified using bisulfite-sequencing. Results We found large variability among the patients concerning the number and identity of the differentially methylated regions, but more than 60 regions were aberrantly methylated in two or more patients and a novel region within PPP1R13L was found to be hypomethylated in all the patients. The hypomethylated regions in common between the patients are enriched for the ZFP57 DNA binding motif. Conclusions We have expanded the epimutational spectrum of TNDM1 associated with ZFP57 mutations and found one novel region within PPP1R13L which is hypomethylated in all TNDM1 patients included in this study. Functional studies of the locus might provide further insight into the etiology of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0292-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.
| | - Susanne E Boonen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.,Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - Christina Dahl
- Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark
| | - Johanne M D Hahnemann
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - Deborah J D G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.,Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury NHS Foundation Trust, SP2 8BJ, Salisbury, UK
| | - Zeynep Tümer
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.,Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200N, Copenhagen, Denmark
| | - Karen Grønskov
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.,Wessex Clinical Genetics Service, Southampton University Hospitals Trust, Southampton, SO16 5YA, UK
| | - Per Guldberg
- Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark
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167
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van Otterdijk SD, Michels KB. Transgenerational epigenetic inheritance in mammals: how good is the evidence? FASEB J 2016; 30:2457-65. [PMID: 27037350 DOI: 10.1096/fj.201500083] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/21/2016] [Indexed: 01/02/2023]
Abstract
Epigenetics plays an important role in orchestrating key biologic processes. Epigenetic marks, including DNA methylation, histones, chromatin structure, and noncoding RNAs, are modified throughout life in response to environmental and behavioral influences. With each new generation, DNA methylation patterns are erased in gametes and reset after fertilization, probably to prevent these epigenetic marks from being transferred from parents to their offspring. However, some recent animal studies suggest an apparent resistance to complete erasure of epigenetic marks during early development, enabling transgenerational epigenetic inheritance. Whether there are similar mechanisms in humans remains unclear, with the exception of epigenetic imprinting. Nevertheless, a distinctly different mechanism-namely, intrauterine exposure to environmental stressors that may affect establishment of the newly composing epigenetic patterns after fertilization-is often confused with transgenerational epigenetic inheritance. In this review, we delineate the definition of and requirement for transgenerational epigenetic inheritance, differentiate it from the consequences of intrauterine exposure, and discuss the available evidence in both animal models and humans.-Van Otterdijk, S. D., Michels, K. B. Transgenerational epigenetic inheritance in mammals: how good is the evidence?
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Affiliation(s)
- Sanne D van Otterdijk
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany
| | - Karin B Michels
- Institute for Prevention and Cancer Epidemiology, University Medical Center Freiburg, Freiburg, Germany; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; and Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
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168
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Tan Y, Wu L, Li D, Liu X, Ding J, Chen S. Methylation status of DJ-1 in leukocyte DNA of Parkinson's disease patients. Transl Neurodegener 2016; 5:5. [PMID: 27034775 PMCID: PMC4815061 DOI: 10.1186/s40035-016-0052-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/11/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND DJ-1 has been thought as a candidate biomarker for Parkinson's disease (PD). It was found reduced in PD brains, CSF and saliva, although there were conflicting results. How DJ-1 expression may be regulated is not clear. Recently, blood-based DNA methylation represents a highly promising biomarker for PD by regulating the causative gene expression. Thus, in this study, we try to explore whether blood-based DNA methylation of DJ-1 could be used as a biomarker to differentiate PD patients from normal control (NC), and whether DNA methylation could regulate DJ-1 expression in a SH-SY5Y cell model. METHODS Forty PD patients and 40 NC were recruited in this study. DNA was extracted from peripheral blood leukocytes (PBLs). Methylation status of two CpG islands (CpG1 and CpG2) in promoter region of DJ-1 was explored by bisulfite specific PCR-based sequencing method. Methylation inhibitor 5-Aza-dC was used to treat SH-SY5Y cell line, DJ-1 level was detected in both mRNA and protein level. RESULTS CpG sites in these two CpG islands (CpG1 and CpG2) of DJ-1 were unmethylated in both PD and NC group. In SH-SY5Y cell model treated by methylation inhibitor, there was no significant change of DJ-1 expression in either mRNA level or protein level. CONCLUSIONS Our results indicated that DNA methylation inhibitor didn't alter DJ-1 gene expression in SH-SY5Y cell model, and DNA methylation of DJ-1 promoter region in PBLs level might not be an efficient biomarker for PD patients.
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Affiliation(s)
- Yuyan Tan
- Department of Neurology, and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Li Wu
- Department of Neurology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200011 China
| | - Dunhui Li
- Department of Neurology, and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Xiaoli Liu
- Department of Neurology, and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Jianqing Ding
- Department of Neurology, and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Shengdi Chen
- Department of Neurology, and Institute of Neurology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China.,Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing, 100069 China
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169
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Grothaus K, Kanber D, Gellhaus A, Mikat B, Kolarova J, Siebert R, Wieczorek D, Horsthemke B. Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment. Epigenetics 2016; 11:216-26. [PMID: 26890210 DOI: 10.1080/15592294.2016.1145330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Gene duplication by retrotransposition, i.e., the reverse transcription of an mRNA and integration of the cDNA into the genome, is an important mechanism in evolution. Based on whole-genome bisulfite sequencing of monocyte DNA, we have investigated the methylation state of all CpG islands (CGIs) associated with a retrocopy (n = 1,319), their genomic environment, as well as the CGIs associated with the ancestral genes. Approximately 10% of retrocopies are associated with a CGI. Whereas almost all CGIs of the human genome are unmethylated, 68% of the CGIs associated with a retrocopy are methylated. In retrocopies resulting from multiple retrotranspositions of the same ancestral gene, the methylation state of the CGI often differs. There is a strong positive correlation between the methylation state of the CGI/retrocopy and their genomic environment, suggesting that the methylation state of the integration site determined the methylation state of the CGI/retrocopy, or that methylation of the retrocopy by a host defense mechanism has spread into the adjacent regions. Only a minor fraction of CGI/retrocopies (n = 195) has intermediate methylation levels. Among these, the previously reported CGI/retrocopy in intron 2 of the RB1 gene (PPP1R26P1) as well as the CGI associated with the retrocopy RPS2P32 identified in this study carry a maternal methylation imprint. In conclusion, these findings shed light on the evolutionary dynamics and constraints of DNA methylation.
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Affiliation(s)
- Katrin Grothaus
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Deniz Kanber
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Alexandra Gellhaus
- b Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Essen , Essen , Germany
| | - Barbara Mikat
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Julia Kolarova
- c Institut für Humangenetik, Christian-Albrechts-Universität Kiel & Universitätsklinikum Schleswig-Holstein , Campus Kiel, Kiel , Germany
| | - Reiner Siebert
- c Institut für Humangenetik, Christian-Albrechts-Universität Kiel & Universitätsklinikum Schleswig-Holstein , Campus Kiel, Kiel , Germany
| | - Dagmar Wieczorek
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Bernhard Horsthemke
- a Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
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170
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An expanded sequence context model broadly explains variability in polymorphism levels across the human genome. Nat Genet 2016; 48:349-55. [PMID: 26878723 PMCID: PMC4811712 DOI: 10.1038/ng.3511] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 01/22/2016] [Indexed: 12/15/2022]
Abstract
The rate of single nucleotide polymorphism varies substantially across the human genome and fundamentally influences evolution and incidence of genetic disease. Previous studies have only considered the immediate flanking nucleotides around a polymorphic site –the site’s trinucleotide sequence context– to study polymorph levels across the genome. Moreover, the impact of larger sequence contexts has not been fully clarified, even though context substantially influences rates of polymorphism. Using a new statistical framework and data from the 1000 Genomes Project, we demonstrate that a heptanucleotide context explains >81% of variability in substitution probabilities, revealing new mutation-promoting motifs at ApT dinucleotide, CAAT, and TACG sequences. Our approach also identifies previously undocumented variability in C-to-T substitutions at CpG sites, which is not immediately explained by differential methylation intensity. Using our model, we present informative substitution intolerance scores for genes and a new intolerance score for amino acids, and we demonstrate clinical use of the model in neuropsychiatric diseases.
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171
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Chavatte-Palmer P, Vialard F, Tarrade A, Dupont C, Duranthon V, Lévy R. [DOHaD and pre- or peri-conceptional programming]. Med Sci (Paris) 2016; 32:57-65. [PMID: 26850608 DOI: 10.1051/medsci/20163201010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The pre- and peri-conceptional periods (before and just after fertilization, until the blastocyst stage) are critical in the context of the Developmental Origins of Health and Disease (DOHaD). Maternal in vivo environment, in particular nutrition, can disturb the apposition of epigenetic marks throughout gametogenesis, fertilization and the first steps of embryonic development, which are times during which major epigenetic changes take place. The in vitro environment, in the case of assisted reproduction techniques, also affects epigenetic marks. Whilst the embryo is a target of these changes, female and male gametes are both target and vector of these epigenetic changes, thus leading to multigenerational effects. Long term consequences on the phenotype of offspring vary according to the sex of the vector parent, the sex of the individual and the generation.
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Affiliation(s)
- Pascale Chavatte-Palmer
- UMR BDR, INRA, ENVA, Université Paris Saclay, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - François Vialard
- Unité Gamète-Implantation-Gestation, EA7404 Université de Versailles Saint-Quentin-en-Yvelines et Centre hospitalier intercommunal de Poissy St-Germain, laboratoire assistance médicale à la procréation-cytogénétique, France
| | - Anne Tarrade
- UMR BDR, INRA, ENVA, Université Paris Saclay, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - Charlotte Dupont
- UMR BDR, INRA, ENVA, Université Paris Saclay, Domaine de Vilvert, 78350 Jouy-en-Josas, France - APHP, hôpital Jean Verdier, 93140, Bondy, France
| | - Véronique Duranthon
- UMR BDR, INRA, ENVA, Université Paris Saclay, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - Rachel Lévy
- APHP, hôpital Jean Verdier, 93140, Bondy, France
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172
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Pastor WA, Chen D, Liu W, Kim R, Sahakyan A, Lukianchikov A, Plath K, Jacobsen SE, Clark AT. Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell Stem Cell 2016; 18:323-329. [PMID: 26853856 DOI: 10.1016/j.stem.2016.01.019] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 10/02/2015] [Accepted: 01/15/2016] [Indexed: 10/22/2022]
Abstract
Human embryonic stem cells (hESCs) typically exhibit "primed" pluripotency, analogous to stem cells derived from the mouse post-implantation epiblast. This has led to a search for growth conditions that support self-renewal of hESCs akin to hypomethylated naive epiblast cells in human pre-implantation embryos. We have discovered that reverting primed hESCs to a hypomethylated naive state or deriving a new hESC line under naive conditions results in the establishment of Stage Specific Embryonic Antigen 4 (SSEA4)-negative hESC lines with a transcriptional program resembling the human pre-implantation epiblast. In contrast, we discovered that the methylome of naive hESCs in vitro is distinct from that of the human epiblast in vivo with loss of DNA methylation at primary imprints and a lost "memory" of the methylation state of the human oocyte. This failure to recover the naive epiblast methylation landscape appears to be a consistent feature of self-renewing hypomethylated naive hESCs in vitro.
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Affiliation(s)
- William A Pastor
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles CA 90095
| | - Di Chen
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles CA 90095
| | - Wanlu Liu
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles CA 90095
| | - Rachel Kim
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research University of California Los Angeles, Los Angeles CA 90095
| | - Anna Sahakyan
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles CA 90095
| | - Anastasia Lukianchikov
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles CA 90095
| | - Kathrin Plath
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research University of California Los Angeles, Los Angeles CA 90095
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles CA 90095.,Department of Biological Chemistry, University of California Los Angeles, Los Angeles CA 90095.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research University of California Los Angeles, Los Angeles CA 90095.,Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles CA 90095
| | - Amander T Clark
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles CA 90095.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research University of California Los Angeles, Los Angeles CA 90095
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173
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Hanna CW, Peñaherrera MS, Saadeh H, Andrews S, McFadden DE, Kelsey G, Robinson WP. Pervasive polymorphic imprinted methylation in the human placenta. Genome Res 2016; 26:756-67. [PMID: 26769960 PMCID: PMC4889973 DOI: 10.1101/gr.196139.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/07/2016] [Indexed: 01/19/2023]
Abstract
The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilization. There are a large number of germline DMRs that have not yet been associated with imprinting, and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation between diandric and digynic triploid conceptions in addition to female and male gametes. Seventy-two novel DMRs showed a pattern consistent with placental-specific imprinting, and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation between placental samples. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Maria S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Deborah E McFadden
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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174
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Demura M, Saijoh K. The Role of DNA Methylation in Hypertension. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 956:583-598. [PMID: 27888489 DOI: 10.1007/5584_2016_80] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation is the covalent modification of DNA that affects its function, without altering DNA sequences. Three important roles of DNA methylation include intrauterine programming, acquired predisposition, and transgenerational inheritance. A wide variety of factors can affect DNA methylation. Intrauterine programming involves drastic changes in DNA methylation patterns during cellular development and differentiation, which have a long-lasting effect on the predisposition of offspring. Influences from the mother, including maternal nutritional status, modify intrauterine epigenetic programming. In contrast to the rapid and drastic changes in utero, postnatal factors in daily life can also continue to slowly and dynamically change DNA methylation patterns in both somatic and germ cells. Epigenetic changes occurring in germ cell DNA exert a transgenerational impact on the phenotype of future generations, thus providing a means for ancestral transmission of environmental experiences. Despite adaptive ability, mismatch effect of transgenerational inheritance could be potentially harmful to health if environment has changed, and the acquired acclimatization is no longer beneficial. Increasing evidence from both human and animal studies indicates that DNA methylation exerts a causal impact on the development of hypertension. Therefore, an adverse outcome of maternal malnutrition could be the development of hypertension in offspring, whereby nutritional factors or disease conditions could induce phenotypes susceptible to hypertension through alteration of DNA methylation patterns. These factors are likely to alter DNA methylation patterns in all tissues including germ cells, and despite no direct evidence of an association between transgenerational epigenetic inheritance and hypertension, it is likely to play a role.
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Affiliation(s)
- Masashi Demura
- Department of Hygiene, Graduate School of Medical Science, Kanazawa University, Kanazawa, 920-8640, Japan.
| | - Kiyofumi Saijoh
- Department of Hygiene, Graduate School of Medical Science, Kanazawa University, Kanazawa, 920-8640, Japan
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175
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Sanchez-Delgado M, Martin-Trujillo A, Tayama C, Vidal E, Esteller M, Iglesias-Platas I, Deo N, Barney O, Maclean K, Hata K, Nakabayashi K, Fisher R, Monk D. Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-Effect Mutations Reveals Widespread Placenta-Specific Imprinting. PLoS Genet 2015; 11:e1005644. [PMID: 26544189 PMCID: PMC4636177 DOI: 10.1371/journal.pgen.1005644] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/12/2015] [Indexed: 11/18/2022] Open
Abstract
Familial recurrent hydatidiform mole (RHM) is a maternal-effect autosomal recessive disorder usually associated with mutations of the NLRP7 gene. It is characterized by HM with excessive trophoblastic proliferation, which mimics the appearance of androgenetic molar conceptuses despite their diploid biparental constitution. It has been proposed that the phenotypes of both types of mole are associated with aberrant genomic imprinting. However no systematic analyses for imprinting defects have been reported. Here, we present the genome-wide methylation profiles of both spontaneous androgenetic and biparental NLRP7 defective molar tissues. We observe total paternalization of all ubiquitous and placenta-specific differentially methylated regions (DMRs) in four androgenetic moles; namely gain of methylation at paternally methylated loci and absence of methylation at maternally methylated regions. The methylation defects observed in five RHM biopsies from NLRP7 defective patients are restricted to lack-of-methylation at maternal DMRs. Surprisingly RHMs from two sisters with the same missense mutations, as well as consecutive RHMs from one affected female show subtle allelic methylation differences, suggesting inter-RHM variation. These epigenotypes are consistent with NLRP7 being a maternal-effect gene and involved in imprint acquisition in the oocyte. In addition, bioinformatic screening of the resulting methylation datasets identified over sixty loci with methylation profiles consistent with imprinting in the placenta, of which we confirm 22 as novel maternally methylated loci. These observations strongly suggest that the molar phenotypes are due to defective placenta-specific imprinting and over-expression of paternally expressed transcripts, highlighting that maternal-effect mutations of NLRP7 are associated with the most severe form of multi-locus imprinting defects in humans.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alejandro Martin-Trujillo
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Enrique Vidal
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona, Spain
| | - Nandita Deo
- Whipps Cross University Hospital, Barts Health NHS Trust, Leytonstone, London, United Kingdom
| | - Olivia Barney
- Leicester Royal Infirmary, Leicester, United Kingdom
| | | | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Rosemary Fisher
- Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
- Trophoblastic Tumour Screening and Treatment Centre, Department of Oncology, Imperial College London, London, United Kingdom
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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176
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Monk D. Genomic imprinting in the human placenta. Am J Obstet Gynecol 2015; 213:S152-62. [PMID: 26428495 DOI: 10.1016/j.ajog.2015.06.032] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 12/22/2022]
Abstract
With the launch of the National Institute of Child Health and Human Development/National Institutes of Health Human Placenta Project, the anticipation is that this often-overlooked organ will be the subject of much intense research. Compared with somatic tissues, the cells of the placenta have a unique epigenetic profile that dictates its transcription patterns, which when disturbed may be associated with adverse pregnancy outcomes. One major class of genes that is dependent on strict epigenetic regulation in the placenta is subject to genomic imprinting, the parent-of-origin-dependent monoallelic gene expression. This review discusses the differences in allelic expression and epigenetic profiles of imprinted genes that are identified between different species, which reflect the continuous evolutionary adaption of this form of epigenetic regulation. These observations divulge that placenta-specific imprinted gene that is reliant on repressive histone signatures in mice are unlikely to be imprinted in humans, whereas intense methylation profiling in humans has uncovered numerous maternally methylated regions that are restricted to the placenta that are not conserved in mice. Imprinting has been proposed to be a mechanism that regulates parental resource allocation and ultimately can influence fetal growth, with the placenta being the key in this process. Furthermore, I discuss the developmental dynamics of both classic and transient placenta-specific imprinting and examine the evidence for an involvement of these genes in intrauterine growth restriction and placenta-associated complications. Finally, I focus on examples of genes that are regulated aberrantly in complicated pregnancies, emphasizing their application as pregnancy-related disease biomarkers to aid the diagnosis of at-risk pregnancies early in gestation.
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Affiliation(s)
- David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain.
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177
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Slieker RC, Roost MS, van Iperen L, Suchiman HED, Tobi EW, Carlotti F, de Koning EJP, Slagboom PE, Heijmans BT, Chuva de Sousa Lopes SM. DNA Methylation Landscapes of Human Fetal Development. PLoS Genet 2015; 11:e1005583. [PMID: 26492326 PMCID: PMC4619663 DOI: 10.1371/journal.pgen.1005583] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/16/2015] [Indexed: 12/14/2022] Open
Abstract
Remodelling the methylome is a hallmark of mammalian development and cell differentiation. However, current knowledge of DNA methylation dynamics in human tissue specification and organ development largely stems from the extrapolation of studies in vitro and animal models. Here, we report on the DNA methylation landscape using the 450k array of four human tissues (amnion, muscle, adrenal and pancreas) during the first and second trimester of gestation (9,18 and 22 weeks). We show that a tissue-specific signature, constituted by tissue-specific hypomethylated CpG sites, was already present at 9 weeks of gestation (W9). Furthermore, we report large-scale remodelling of DNA methylation from W9 to W22. Gain of DNA methylation preferentially occurred near genes involved in general developmental processes, whereas loss of DNA methylation mapped to genes with tissue-specific functions. Dynamic DNA methylation was associated with enhancers, but not promoters. Comparison of our data with external fetal adrenal, brain and liver revealed striking similarities in the trajectory of DNA methylation during fetal development. The analysis of gene expression data indicated that dynamic DNA methylation was associated with the progressive repression of developmental programs and the activation of genes involved in tissue-specific processes. The DNA methylation landscape of human fetal development provides insight into regulatory elements that guide tissue specification and lead to organ functionality.
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Affiliation(s)
- Roderick C. Slieker
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias S. Roost
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Liesbeth van Iperen
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - H. Eka D. Suchiman
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Elmar W. Tobi
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Françoise Carlotti
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eelco J. P. de Koning
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
| | - P. Eline Slagboom
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology Section, Leiden University Medical Center, Leiden, The Netherlands
| | - Susana M. Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
- Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
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178
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Trost B, Moir CA, Gillespie ZE, Kusalik A, Mitchell JA, Eskiw CH. Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150402. [PMID: 26473061 PMCID: PMC4593695 DOI: 10.1098/rsos.150402] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/02/2015] [Indexed: 06/05/2023]
Abstract
DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth to quiescence using both DNA microarrays and RNA-seq. The internal reproducibility of the RNA-seq data was greater than that of the microarray data. Correlations between the RNA-seq data and the individual microarrays were low, but correlations between the RNA-seq values and the geometric mean of the microarray values were moderate. The two technologies had good agreement when considering probes with the largest (both positive and negative) fold change (FC) values. An independent technique, quantitative reverse-transcription PCR (qRT-PCR), was used to measure the FC of 76 genes between proliferative and quiescent samples, and a higher correlation was observed between the qRT-PCR data and the RNA-seq data than between the qRT-PCR data and the microarray data.
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Affiliation(s)
- Brett Trost
- Department of Computer Science, University of Saskatchewan, Saskatoon Canada S7N 5C9
| | - Catherine A. Moir
- Department of Life Sciences, Brunel University, Uxbridge UB8 3PH, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Zoe E. Gillespie
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon Canada S7N 5A8
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon Canada S7N 5C9
| | - Jennifer A. Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto Canada M5S 3G5
| | - Christopher H. Eskiw
- Department of Life Sciences, Brunel University, Uxbridge UB8 3PH, UK
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon Canada S7N 5A8
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179
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Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas. PLoS Genet 2015; 11:e1005442. [PMID: 26241857 PMCID: PMC4524645 DOI: 10.1371/journal.pgen.1005442] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/14/2015] [Indexed: 12/11/2022] Open
Abstract
Over the last 20-80 million years the mammalian placenta has taken on a variety of morphologies through both divergent and convergent evolution. Recently we have shown that the human placenta genome has a unique epigenetic pattern of large partially methylated domains (PMDs) and highly methylated domains (HMDs) with gene body DNA methylation positively correlating with level of gene expression. In order to determine the evolutionary conservation of DNA methylation patterns and transcriptional regulatory programs in the placenta, we performed a genome-wide methylome (MethylC-seq) analysis of human, rhesus macaque, squirrel monkey, mouse, dog, horse, and cow placentas as well as opossum extraembryonic membrane. We found that, similar to human placenta, mammalian placentas and opossum extraembryonic membrane have globally lower levels of methylation compared to somatic tissues. Higher relative gene body methylation was the conserved feature across all mammalian placentas, despite differences in PMD/HMDs and absolute methylation levels. Specifically, higher methylation over the bodies of genes involved in mitosis, vesicle-mediated transport, protein phosphorylation, and chromatin modification was observed compared with the rest of the genome. As in human placenta, higher methylation is associated with higher gene expression and is predictive of genic location across species. Analysis of DNA methylation in oocytes and preimplantation embryos shows a conserved pattern of gene body methylation similar to the placenta. Intriguingly, mouse and cow oocytes and mouse early embryos have PMD/HMDs but their placentas do not, suggesting that PMD/HMDs are a feature of early preimplantation methylation patterns that become lost during placental development in some species and following implantation of the embryo.
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180
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Wang K, Li X, Dong S, Liang J, Mao F, Zeng C, Wu H, Wu J, Cai W, Sun ZS. Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses. Epigenetics 2015. [PMID: 26213102 DOI: 10.1080/15592294.2015.1075690] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Reduced representation bisulfite sequencing (RRBS) is a powerful method of DNA methylome profiling that can be applied to single cells. However, no previous report has described how PCR-based duplication-induced artifacts affect the accuracy of this method when measuring DNA methylation levels. For quantifying the effects of duplication-induced artifacts on methylome profiling when using ultra-trace amounts of starting material, we developed a novel method, namely quantitative RRBS (Q-RRBS), in which PCR-induced duplication is excluded through the use of unique molecular identifiers (UMIs). By performing Q-RRBS on varying amounts of starting material, we determined that duplication-induced artifacts were more severe when small quantities of the starting material were used. However, through using the UMIs, we successfully eliminated these artifacts. In addition, Q-RRBS could accurately detect allele-specific methylation in absence of allele-specific genetic variants. Our results demonstrate that Q-RRBS is an optimal strategy for DNA methylation profiling of single cells or samples containing ultra-trace amounts of cells.
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Affiliation(s)
- Kangli Wang
- a Institute of Genomic Medicine; Wenzhou Medical University ; Wenzhou , China
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181
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Tang WWC, Dietmann S, Irie N, Leitch HG, Floros VI, Bradshaw CR, Hackett JA, Chinnery PF, Surani MA. A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development. Cell 2015; 161:1453-67. [PMID: 26046444 PMCID: PMC4459712 DOI: 10.1016/j.cell.2015.04.053] [Citation(s) in RCA: 459] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 01/24/2023]
Abstract
Resetting of the epigenome in human primordial germ cells (hPGCs) is critical for development. We show that the transcriptional program of hPGCs is distinct from that in mice, with co-expression of somatic specifiers and naive pluripotency genes TFCP2L1 and KLF4. This unique gene regulatory network, established by SOX17 and BLIMP1, drives comprehensive germline DNA demethylation by repressing DNA methylation pathways and activating TET-mediated hydroxymethylation. Base-resolution methylome analysis reveals progressive DNA demethylation to basal levels in week 5-7 in vivo hPGCs. Concurrently, hPGCs undergo chromatin reorganization, X reactivation, and imprint erasure. Despite global hypomethylation, evolutionarily young and potentially hazardous retroelements, like SVA, remain methylated. Remarkably, some loci associated with metabolic and neurological disorders are also resistant to DNA demethylation, revealing potential for transgenerational epigenetic inheritance that may have phenotypic consequences. We provide comprehensive insight on early human germline transcriptional network and epigenetic reprogramming that subsequently impacts human development and disease.
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Affiliation(s)
- Walfred W C Tang
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 3EG, UK
| | - Sabine Dietmann
- Wellcome Trust-Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 3EG, UK
| | - Naoko Irie
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 3EG, UK
| | - Harry G Leitch
- Wellcome Trust-Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 3EG, UK
| | - Vasileios I Floros
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Charles R Bradshaw
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, UK
| | - Jamie A Hackett
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 3EG, UK
| | - Patrick F Chinnery
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, Downing Street, University of Cambridge, Cambridge CB2 3EG, UK; Wellcome Trust-Medical Research Council Stem Cell Institute, Tennis Court Road, University of Cambridge, Cambridge CB2 3EG, UK.
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182
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The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 2015; 161:1437-52. [DOI: 10.1016/j.cell.2015.05.015] [Citation(s) in RCA: 397] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/26/2015] [Accepted: 04/24/2015] [Indexed: 12/18/2022]
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183
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Monk D. Germline-derived DNA methylation and early embryo epigenetic reprogramming: The selected survival of imprints. Int J Biochem Cell Biol 2015; 67:128-38. [PMID: 25966912 DOI: 10.1016/j.biocel.2015.04.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/27/2015] [Indexed: 12/27/2022]
Abstract
DNA methylation is an essential epigenetic mechanism involved in many essential cellular processes. During development epigenetic reprograming takes place during gametogenesis and then again in the pre-implantation embryo. These two reprograming windows ensure genome-wide removal of methylation in the primordial germ cells so that sex-specific signatures can be acquired in the sperm and oocyte. Following fertilization the majority of this epigenetic information is erased to give the developing embryo an epigenetic profile coherent with pluripotency. It is estimated that ∼65% of the genome is differentially methylated between the gametes, however following embryonic reprogramming only parent-of-origin methylation at known imprinted loci remains. This suggests that trans-acting factors such as Zfp57 can discriminate imprinted differentially methylated regions (DMRs) from the thousands of CpG rich regions that are differentially marked in the gametes. Recently transient imprinted DMRs have been identified suggesting that these loci are also protected from pre-implantation reprograming but succumb to de novo remethylation at the implantation stage. This highlights that "ubiquitous" imprinted loci are also resilient to gaining methylation by protecting their unmethylated alleles. In this review I examine the processes involved in epigenetic reprograming and the mechanisms that ensure allelic methylation at imprinted loci is retained throughout the life of the organism, discussing the critical differences between mouse and humans. This article is part of a Directed Issue entitled: Epigenetics Dynamics in development and disease.
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Affiliation(s)
- David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08908, Spain.
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184
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Cheong CY, Chng K, Ng S, Chew SB, Chan L, Ferguson-Smith AC. Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. Genome Res 2015; 25:611-23. [PMID: 25862382 PMCID: PMC4417110 DOI: 10.1101/gr.183301.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
Genomic imprinting is an epigenetic mechanism resulting in parental allele-specific gene expression. Defects in normal imprinting are found in cancer, assisted reproductive technologies, and several human syndromes. In mouse models, germline-derived DNA methylation is shown to regulate imprinting. Though imprinting is largely conserved between mammals, species- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque (Macaca fascicularis) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse and unlike human, macaque IGF2R is consistently imprinted, and the PLAGL1, INPP5F transcript variant 2, and PEG3 imprinting control regions are not methylated in the macaque germline but acquire this post-fertilization. Methylome data from human early embryos appear to support this finding. These suggest fundamental differences in imprinting control mechanisms between primate species and rodents at some imprinted domains, with implications for our understanding of the epigenetic programming process in humans and its influence on disease.
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Affiliation(s)
- Clara Y Cheong
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Keefe Chng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Shilen Ng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Siew Boom Chew
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Louiza Chan
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Anne C Ferguson-Smith
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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