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Abstract
The epigenetic mark 5-methylcytosine confers heritable regulation of gene expression that can be dynamically modulated during transitions in cell fate. With the development of high-throughput sequencing technologies, it is now possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape, but the application of these techniques to limited material remains challenging. Here, we present an optimized protocol to perform whole-genome bisulfite sequencing on low inputs (100-5000 somatic cells) using a post-bisulfite adapter tagging approach. In this strategy, bisulfite treatment is performed prior to library generation in order to both convert unmethylated cytosines and fragment DNA to an appropriate size. Then sequencing adapters are added by complementary strand synthesis using random tetramer priming, and libraries are subsequently amplified by PCR.
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Affiliation(s)
- Julian R Peat
- Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Sébastien A Smallwood
- Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Friedrich Miescher Institute for Biomedical Research, PO Box 3775, Maulbeerstrasse 66, CH-4058, Basel, Switzerland.
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2
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Abstract
BACKGROUND Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. METHODS We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results: Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. CONCLUSIONS Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
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Affiliation(s)
- Julian R Peat
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | | | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
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Arand J, Wossidlo M, Lepikhov K, Peat JR, Reik W, Walter J. Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo. Epigenetics Chromatin 2015; 8:1. [PMID: 25621012 PMCID: PMC4304184 DOI: 10.1186/1756-8935-8-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/26/2014] [Indexed: 11/28/2022] Open
Abstract
Background DNA methylomes are extensively reprogrammed during mouse pre-implantation and early germ cell development. The main feature of this reprogramming is a genome-wide decrease in 5-methylcytosine (5mC). Standard high-resolution single-stranded bisulfite sequencing techniques do not allow discrimination of the underlying passive (replication-dependent) or active enzymatic mechanisms of 5mC loss. We approached this problem by generating high-resolution deep hairpin bisulfite sequencing (DHBS) maps, allowing us to follow the patterns of symmetric DNA methylation at CpGs dyads on both DNA strands over single replications. Results We compared DHBS maps of repetitive elements in the developing zygote, the early embryo, and primordial germ cells (PGCs) at defined stages of development. In the zygote, we observed distinct effects in paternal and maternal chromosomes. A significant loss of paternal DNA methylation was linked to replication and to an increase in continuous and dispersed hemimethylated CpG dyad patterns. Overall methylation levels at maternal copies remained largely unchanged, but showed an increased level of dispersed hemi-methylated CpG dyads. After the first cell cycle, the combined DHBS patterns of paternal and maternal chromosomes remained unchanged over the next three cell divisions. By contrast, in PGCs the DNA demethylation process was continuous, as seen by a consistent decrease in fully methylated CpG dyads over consecutive cell divisions. Conclusions The main driver of DNA demethylation in germ cells and in the zygote is partial impairment of maintenance of symmetric DNA methylation at CpG dyads. In the embryo, this passive demethylation is restricted to the first cell division, whereas it continues over several cell divisions in germ cells. The dispersed patterns of CpG dyads in the early-cleavage embryo suggest a continuous partial (and to a low extent active) loss of methylation apparently compensated for by selective de novo methylation. We conclude that a combination of passive and active demethylation events counteracted by de novo methylation are involved in the distinct reprogramming dynamics of DNA methylomes in the zygote, the early embryo, and PGCs. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia Arand
- University of Saarland, FR 8.3, Biological Sciences, Genetics/Epigenetics, Campus A2.4, 66123 Saarbrücken, Germany ; Departments of Pediatrics and Genetics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA 94305 USA
| | - Mark Wossidlo
- University of Saarland, FR 8.3, Biological Sciences, Genetics/Epigenetics, Campus A2.4, 66123 Saarbrücken, Germany ; Departments of Genetics and Obstetrics & Gynaecology, Stanford University School of Medicine, Institute for Stem Cell Biology & Regenerative Medicine, 265 Campus Drive, Stanford, CA 94305 USA
| | - Konstantin Lepikhov
- University of Saarland, FR 8.3, Biological Sciences, Genetics/Epigenetics, Campus A2.4, 66123 Saarbrücken, Germany
| | - Julian R Peat
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT UK ; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA UK
| | - Jörn Walter
- University of Saarland, FR 8.3, Biological Sciences, Genetics/Epigenetics, Campus A2.4, 66123 Saarbrücken, Germany
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Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W. Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation. Cell Rep 2014; 9:1990-2000. [PMID: 25497087 PMCID: PMC4542306 DOI: 10.1016/j.celrep.2014.11.034] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 11/18/2014] [Accepted: 11/20/2014] [Indexed: 12/26/2022] Open
Abstract
Fertilization triggers global erasure of paternal 5-methylcytosine as part of epigenetic reprogramming during the transition from gametic specialization to totipotency. This involves oxidation by TET3, but our understanding of its targets and the wider context of demethylation is limited to a small fraction of the genome. We employed an optimized bisulfite strategy to generate genome-wide methylation profiles of control and TET3-deficient zygotes, using SNPs to access paternal alleles. This revealed that in addition to pervasive removal from intergenic sequences and most retrotransposons, gene bodies constitute a major target of zygotic demethylation. Methylation loss is associated with zygotic genome activation and at gene bodies is also linked to increased transcriptional noise in early development. Our data map the primary contribution of oxidative demethylation to a subset of gene bodies and intergenic sequences and implicate redundant pathways at many loci. Unexpectedly, we demonstrate that TET3 activity also protects certain CpG islands against methylation buildup. An enhanced bisulfite strategy allows genome-wide methylation profiling of zygotes Gene bodies constitute a major target of zygotic demethylation and TET3 oxidation The impact of TET3 loss is moderate and implicates redundant demethylation pathways Protective TET3 activity shields certain CpG islands against methylation buildup
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Affiliation(s)
- Julian R Peat
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK.
| | - Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Stephen J Clark
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Gabriella Ficz
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Jong Kyoung Kim
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - John C Marioni
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Timothy A Hore
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK.
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Seisenberger S, Peat JR, Hore TA, Santos F, Dean W, Reik W. Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110330. [PMID: 23166394 PMCID: PMC3539359 DOI: 10.1098/rstb.2011.0330] [Citation(s) in RCA: 301] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In mammalian development, epigenetic modifications, including DNA methylation patterns, play a crucial role in defining cell fate but also represent epigenetic barriers that restrict developmental potential. At two points in the life cycle, DNA methylation marks are reprogrammed on a global scale, concomitant with restoration of developmental potency. DNA methylation patterns are subsequently re-established with the commitment towards a distinct cell fate. This reprogramming of DNA methylation takes place firstly on fertilization in the zygote, and secondly in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. In each reprogramming window, a unique set of mechanisms regulates DNA methylation erasure and re-establishment. Recent advances have uncovered roles for the TET3 hydroxylase and passive demethylation, together with base excision repair (BER) and the elongator complex, in methylation erasure from the zygote. Deamination by AID, BER and passive demethylation have been implicated in reprogramming in PGCs, but the process in its entirety is still poorly understood. In this review, we discuss the dynamics of DNA methylation reprogramming in PGCs and the zygote, the mechanisms involved and the biological significance of these events. Advances in our understanding of such natural epigenetic reprogramming are beginning to aid enhancement of experimental reprogramming in which the role of potential mechanisms can be investigated in vitro. Conversely, insights into in vitro reprogramming techniques may aid our understanding of epigenetic reprogramming in the germline and supply important clues in reprogramming for therapies in regenerative medicine.
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Seisenberger S, Peat JR, Reik W. Conceptual links between DNA methylation reprogramming in the early embryo and primordial germ cells. Curr Opin Cell Biol 2013; 25:281-8. [PMID: 23510682 DOI: 10.1016/j.ceb.2013.02.013] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/12/2013] [Accepted: 02/19/2013] [Indexed: 01/09/2023]
Abstract
DNA methylation is a carrier of important regulatory information that undergoes global reprogramming in the mammalian germ line, including pre-implantation embryos and primordial germ cells (PGCs). A flurry of recent studies have employed technical advances to generate global profiles of methylation and hydroxymethylation in these cells, unravelling the dynamics of methylation erasure at single locus resolution. Active demethylation in the zygote, involving extensive oxidation, is followed by passive loss over early cell divisions. Certain gamete-contributed methylation marks appear to have evolved non-canonical mechanisms for targeted maintenance of methylation in the face of these processes. These protected sequences include the imprinting control regions (ICRs) required for parental imprinting but also a surprising number of other regions. Such targeted maintenance mechanisms may also operate at certain sequences during early PGC migration when global passive demethylation occurs. In later gonadal PGCs, imprints must be reset and this may be achieved through the targeting of active mechanisms including oxidation. Thus, emerging evidence paints a complex picture whereby active and passive demethylation pathways operate synergistically and in parallel to ensure robust erasure in the early embryo and PGCs.
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