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Orjuela S, Machlab D, Menigatti M, Marra G, Robinson MD. DAMEfinder: a method to detect differential allele-specific methylation. Epigenetics Chromatin 2020; 13:25. [PMID: 32487212 PMCID: PMC7268773 DOI: 10.1186/s13072-020-00346-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation is a highly studied epigenetic signature that is associated with regulation of gene expression, whereby genes with high levels of promoter methylation are generally repressed. Genomic imprinting occurs when one of the parental alleles is methylated, i.e., when there is inherited allele-specific methylation (ASM). A special case of imprinting occurs during X chromosome inactivation in females, where one of the two X chromosomes is silenced, to achieve dosage compensation between the sexes. Another more widespread form of ASM is sequence dependent (SD-ASM), where ASM is linked to a nearby heterozygous single nucleotide polymorphism (SNP). Results We developed a method to screen for genomic regions that exhibit loss or gain of ASM in samples from two conditions (treatments, diseases, etc.). The method relies on the availability of bisulfite sequencing data from multiple samples of the two conditions. We leverage other established computational methods to screen for these regions within a new R package called DAMEfinder. It calculates an ASM score for all CpG sites or pairs in the genome of each sample, and then quantifies the change in ASM between conditions. It then clusters nearby CpG sites with consistent change into regions. In the absence of SNP information, our method relies only on reads to quantify ASM. This novel ASM score compares favorably to current methods that also screen for ASM. Not only does it easily discern between imprinted and non-imprinted regions, but also females from males based on X chromosome inactivation. We also applied DAMEfinder to a colorectal cancer dataset and observed that colorectal cancer subtypes are distinguishable according to their ASM signature. We also re-discover known cases of loss of imprinting. Conclusion We have designed DAMEfinder to detect regions of differential ASM (DAMEs), which is a more refined definition of differential methylation, and can therefore help in breaking down the complexity of DNA methylation and its influence in development and disease.
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Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Dania Machlab
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Dumont ELP, Tycko B, Do C. CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation. Bioinformatics 2020; 36:3558-3560. [PMID: 32119067 PMCID: PMC7267820 DOI: 10.1093/bioinformatics/btaa149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/28/2020] [Accepted: 02/25/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Methods for quantifying the imbalance in CpG methylation between alleles genome-wide have been described but their algorithmic time complexity is quadratic and their practical use requires painstaking attention to infrastructure choice, implementation and execution. To solve this problem, we developed CloudASM, a scalable, ultra-efficient, turn-key, portable pipeline on Google Cloud Platform (GCP) that uses a novel pipeline manager and GCP's serverless enterprise data warehouse. AVAILABILITY AND IMPLEMENTATION CloudASM is freely available in the GitHub repository https://github.com/TyckoLab/CloudASM and a sample dataset and its results are also freely available at https://console.cloud.google.com/storage/browser/cloudasm. CONTACT emmanuel.dumont@hmh-cdi.org.
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Affiliation(s)
- Emmanuel L P Dumont
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
- Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ 07110, USA
- Lombardi Comprehensive Cancer, Center Georgetown University, Washington, DC 20007, USA
| | - Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
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53
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Wu Y, Qi T, Wang H, Zhang F, Zheng Z, Phillips-Cremins JE, Deary IJ, McRae AF, Wray NR, Zeng J, Yang J. Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data. Nat Commun 2020; 11:2061. [PMID: 32345984 PMCID: PMC7188843 DOI: 10.1038/s41467-020-15587-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 03/12/2020] [Indexed: 01/15/2023] Open
Abstract
Promoter-anchored chromatin interactions (PAIs) play a pivotal role in transcriptional regulation. Current high-throughput technologies for detecting PAIs, such as promoter capture Hi-C, are not scalable to large cohorts. Here, we present an analytical approach that uses summary-level data from cohort-based DNA methylation (DNAm) quantitative trait locus (mQTL) studies to predict PAIs. Using mQTL data from human peripheral blood ([Formula: see text]), we predict 34,797 PAIs which show strong overlap with the chromatin contacts identified by previous experimental assays. The promoter-interacting DNAm sites are enriched in enhancers or near expression QTLs. Genes whose promoters are involved in PAIs are more actively expressed, and gene pairs with promoter-promoter interactions are enriched for co-expression. Integration of the predicted PAIs with GWAS data highlight interactions among 601 DNAm sites associated with 15 complex traits. This study demonstrates the use of mQTL data to predict PAIs and provides insights into the role of PAIs in complex trait variation.
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Affiliation(s)
- Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ting Qi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Huanwei Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhili Zheng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Institute for Advanced Research, Wenzhou Medical University, 325027, Wenzhou, Zhejiang, China
| | | | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Institute for Advanced Research, Wenzhou Medical University, 325027, Wenzhou, Zhejiang, China.
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54
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Freeman DM, Lou D, Li Y, Martos SN, Wang Z. The conserved DNMT1-dependent methylation regions in human cells are vulnerable to neurotoxicant rotenone exposure. Epigenetics Chromatin 2020; 13:17. [PMID: 32178731 PMCID: PMC7076959 DOI: 10.1186/s13072-020-00338-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Allele-specific DNA methylation (ASM) describes genomic loci that maintain CpG methylation at only one inherited allele rather than having coordinated methylation across both alleles. The most prominent of these regions are germline ASMs (gASMs) that control the expression of imprinted genes in a parent of origin-dependent manner and are associated with disease. However, our recent report reveals numerous ASMs at non-imprinted genes. These non-germline ASMs are dependent on DNA methyltransferase 1 (DNMT1) and strikingly show the feature of random, switchable monoallelic methylation patterns in the mouse genome. The significance of these ASMs to human health has not been explored. Due to their shared allelicity with gASMs, herein, we propose that non-traditional ASMs are sensitive to exposures in association with human disease. RESULTS We first explore their conservancy in the human genome. Our data show that our putative non-germline ASMs were in conserved regions of the human genome and located adjacent to genes vital for neuronal development and maturation. We next tested the hypothesized vulnerability of these regions by exposing human embryonic kidney cell HEK293 with the neurotoxicant rotenone for 24 h. Indeed,14 genes adjacent to our identified regions were differentially expressed from RNA-sequencing. We analyzed the base-resolution methylation patterns of the predicted non-germline ASMs at two neurological genes, HCN2 and NEFM, with potential to increase the risk of neurodegeneration. Both regions were significantly hypomethylated in response to rotenone. CONCLUSIONS Our data indicate that non-germline ASMs seem conserved between mouse and human genomes, overlap important regulatory factor binding motifs, and regulate the expression of genes vital to neuronal function. These results support the notion that ASMs are sensitive to environmental factors such as rotenone and may alter the risk of neurological disease later in life by disrupting neuronal development.
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Affiliation(s)
- Dana M Freeman
- Laboratory of Environmental Epigenomes, Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Dan Lou
- Laboratory of Environmental Epigenomes, Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Yanqiang Li
- Laboratory of Environmental Epigenomes, Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Suzanne N Martos
- Laboratory of Environmental Epigenomes, Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Zhibin Wang
- Laboratory of Environmental Epigenomes, Department of Environmental Health & Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
- The State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, Hubei, China.
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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55
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Kubo S, Murata C, Okamura H, Sakasegawa T, Sakurai C, Hatsuzawa K, Hori N. Oct motif variants in Beckwith–Wiedemann syndrome patients disrupt maintenance of the hypomethylated state of the
H19/IGF2
imprinting control region. FEBS Lett 2020; 594:1517-1531. [DOI: 10.1002/1873-3468.13750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/27/2019] [Accepted: 01/20/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Shuichi Kubo
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
| | - Chihiro Murata
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
| | - Hanayo Okamura
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
| | - Taku Sakasegawa
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
| | - Chiye Sakurai
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
| | - Kiyotaka Hatsuzawa
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
| | - Naohiro Hori
- Division of Molecular Biology Faculty of Medicine School of Life Sciences Tottori University Yonago Japan
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56
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Beiter T, Nieß AM, Moser D. Transcriptional memory in skeletal muscle. Don't forget (to) exercise. J Cell Physiol 2020; 235:5476-5489. [PMID: 31967338 DOI: 10.1002/jcp.29535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
Transcriptional memory describes an ancient and highly conserved form of cellular learning that enables cells to benefit from recent experience by retaining a mitotically inheritable but reversible memory of the initial transcriptional response when encountering an environmental or physiological stimulus. Herein, we will review recent progress made in the understanding of how cells can make use of diverse constituents of the epigenetic toolbox to retain a transcriptional memory of past states and perturbations. Specifically, we will outline how these mechanisms will help to improve our understanding of skeletal muscle plasticity in health and disease. We describe the epigenetic road map that allows skeletal muscle fibers to navigate through training-induced adaptation processes, and how epigenetic memory marks can preserve an autobiographical history of lifestyle behavior changes, pathological challenges, and aging. We will further consider some key findings in the field of exercise epigenomics to emphasize major challenges when interpreting dynamic changes in the chromatin landscape in response to acute exercise and training.
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Affiliation(s)
- Thomas Beiter
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Andreas M Nieß
- Department of Sports Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
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57
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Bertozzi TM, Ferguson-Smith AC. Metastable epialleles and their contribution to epigenetic inheritance in mammals. Semin Cell Dev Biol 2020; 97:93-105. [PMID: 31551132 DOI: 10.1016/j.semcdb.2019.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023]
Abstract
Many epigenetic differences between individuals are driven by genetic variation. Mammalian metastable epialleles are unusual in that they show variable DNA methylation states between genetically identical individuals. The occurrence of such states across generations has resulted in their consideration by many as strong evidence for epigenetic inheritance in mammals, with the classic Avy and AxinFu mouse models - each products of repeat element insertions - being the most widely accepted examples. Equally, there has been interest in exploring their use as epigenetic biosensors given their susceptibility to environmental compromise. Here we review the classic murine metastable epialleles as well as more recently identified candidates, with the aim of providing a more holistic understanding of their biology. We consider the extent to which epigenetic inheritance occurs at metastable epialleles and explore the limited mechanistic insights into the establishment of their variable epigenetic states. We discuss their environmental modulation and their potential relevance in genome regulation. In light of recent whole-genome screens for novel metastable epialleles, we point out the need to reassess their biological relevance in multi-generational studies and we highlight their value as a model to study repeat element silencing as well as the mechanisms and consequences of mammalian epigenetic stochasticity.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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58
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Abstract
The prevalence of autism spectrum disorder (ASD) has been increasing steadily over the last 20 years; however, the molecular basis for the majority of ASD cases remains unknown. Recent advances in next-generation sequencing and detection of DNA modifications have made methylation-dependent regulation of transcription an attractive hypothesis for being a causative factor in ASD etiology. Evidence for abnormal DNA methylation in ASD can be seen on multiple levels, from genetic mutations in epigenetic machinery to loci-specific and genome-wide changes in DNA methylation. Epimutations in DNA methylation can be acquired throughout life, as global DNA methylation reprogramming is dynamic during embryonic development and the early postnatal period that corresponds to the peak time of synaptogenesis. However, technical advances and causative evidence still need to be established before abnormal DNA methylation and ASD can be confidently associated.
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Affiliation(s)
- Martine W Tremblay
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA
| | - Yong-Hui Jiang
- Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA.,Departments of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
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59
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Kravitz SN, Gregg C. New subtypes of allele-specific epigenetic effects: implications for brain development, function and disease. Curr Opin Neurobiol 2019; 59:69-78. [PMID: 31153086 PMCID: PMC7476552 DOI: 10.1016/j.conb.2019.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/24/2019] [Indexed: 01/15/2023]
Abstract
Typically, it is assumed that the maternal and paternal alleles for most genes are equally expressed. Known exceptions include canonical imprinted genes, random X-chromosome inactivation, olfactory receptors and clustered protocadherins. Here, we highlight recent studies showing that allele-specific expression is frequent in the genome and involves subtypes of epigenetic allelic effects that differ in terms of heritability, clonality and stability over time. Different forms of epigenetic allele regulation could have different roles in brain development, function, and disease. An emerging area involves understanding allelic effects in a cell-type and developmental stage-specific manner and determining how these effects influence the impact of genetic variants and mutations on the brain. A deeper understanding of epigenetics at the allele and cellular level in the brain could help clarify the mechanisms underlying phenotypic variance.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA
| | - Christopher Gregg
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, UT 84132-3401, USA; Department of Human Genetics, University of Utah, Salt Lake City, UT 84132-3401, USA.
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Ben Maamar M, King SE, Nilsson E, Beck D, Skinner MK. Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations. Dev Biol 2019; 458:106-119. [PMID: 31682807 PMCID: PMC6987017 DOI: 10.1016/j.ydbio.2019.10.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Epigenetic transgenerational inheritance potentially impacts disease etiology, phenotypic variation, and evolution. An increasing number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease. Previous observations have demonstrated that the agricultural fungicide vinclozolin and pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation, ncRNA, and histone modifications or retention. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in the MOC F4 generation male prostate, kidney, obesity, and multiple diseases through a maternal allelic transmission. The POC F4 generation female offspring had increased pathology incidence for kidney, obesity and multiple types of diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner. The parent-of-origin allelic transmission observed appears similar to the process involved with imprinted-like genes.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Stephanie E King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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61
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Yamada Y, Sasaki S. A method for identifying allele-specific hydroxymethylation. Epigenetics 2019; 15:231-250. [PMID: 31533538 DOI: 10.1080/15592294.2019.1664228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We previously identified sequence-dependent allele-specific methylation (sd-ASM) in adult human peripheral blood leukocytes, in which ASM occurs in cis depending on adjacent polymorphic sequences. A number of groups have identified sd-ASM sites in the human and mouse genomes, illustrating the prevalence of sd-ASM in mammalian genomes. In addition, sd-ASM can lead to sequence-dependent allele-specific expression of neighbouring genes. Imprinted genes also often exhibit parent-of-origin-dependent allele-specific methylation (pd-ASM), which causes parent-of-origin-dependent allele-specific expression. However, whether most of the already known sd-ASM and pd-ASM sites are methylated or hydroxymethylated remains unclear due to technical restrictions. Accordingly, a novel method that enables examination of allelic methylation and hydroxymethylation status and also overcomes the drawbacks of conventional methods is needed. Such a method could also be used to elucidate the mechanisms underlying polymorphism-associated inter-individual differences in disease susceptibility and the mechanism of genomic imprinting. Here, we developed a simple method to determine allelic hydroxymethylation status and identified novel sequence- and parent-of-origin-dependent allele-specific hydroxymethylation sites. Correlation analyses of TF binding sequences and methylation or hydroxymethylation between three mouse strains revealed the involvement of Pax5 in strain-specific methylation and hydroxymethylation in exon 7 of Pdgfrb.
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Affiliation(s)
- Yoichi Yamada
- Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Sho Sasaki
- Division of Electrical and Computer Engineering, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
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Yang J, Adli M. Mapping and Making Sense of Noncoding Mutations in the Genome. Cancer Res 2019; 79:4309-4314. [PMID: 31387922 DOI: 10.1158/0008-5472.can-19-0905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022]
Abstract
Whole-genome sequencing efforts of tumors and normal tissues have identified numerous genetic mutations, both somatic and germline, that do not overlap with coding genomic sequences. Attributing a functional role to these noncoding mutations and characterizing them using experimental methods has been more challenging compared with coding mutations. In this review, we provide a brief introduction to the world of noncoding mutations. We discuss recent progress in identifying noncoding mutations and the analytic and experimental approaches utilized to interpret their functional roles. We also highlight the potential mechanisms by which a noncoding mutation may exert its effect and discuss future challenges and opportunities.
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Affiliation(s)
- Jiekun Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Mazhar Adli
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.
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63
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Genomic imprinting disorders: lessons on how genome, epigenome and environment interact. Nat Rev Genet 2019; 20:235-248. [PMID: 30647469 DOI: 10.1038/s41576-018-0092-0] [Citation(s) in RCA: 249] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genomic imprinting, the monoallelic and parent-of-origin-dependent expression of a subset of genes, is required for normal development, and its disruption leads to human disease. Imprinting defects can involve isolated or multilocus epigenetic changes that may have no evident genetic cause, or imprinting disruption can be traced back to alterations of cis-acting elements or trans-acting factors that control the establishment, maintenance and erasure of germline epigenetic imprints. Recent insights into the dynamics of the epigenome, including the effect of environmental factors, suggest that the developmental outcomes and heritability of imprinting disorders are influenced by interactions between the genome, the epigenome and the environment in germ cells and early embryos.
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64
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Pilvar D, Reiman M, Pilvar A, Laan M. Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy. Clin Epigenetics 2019; 11:94. [PMID: 31242935 PMCID: PMC6595585 DOI: 10.1186/s13148-019-0692-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background Genomic imprinting, mediated by parent-of-origin-specific epigenetic silencing, adjusts the gene expression dosage in mammals. We aimed to clarify parental allelic expression in the human placenta for 396 claimed candidate imprinted genes and to assess the evidence for the proposed enrichment of imprinted expression in the placenta. The study utilized RNA-Seq-based transcriptome and genotyping data from 54 parental-placental samples representing the three trimesters of gestation, and term cases of preeclampsia, gestational diabetes, and fetal growth disturbances. Results Almost half of the targeted genes (n = 179; 45%) were either not transcribed or showed limited expression in the human placenta. After filtering for the presence of common exonic SNPs, adequacy of sequencing reads and informative families, 91 genes were retained (43 loci form Geneimprint database; 48 recently proposed genes). Only 11/91 genes (12.1%) showed confident signals of imprinting (binomial test, Bonferroni corrected P < 0.05; > 90% transcripts originating from one parental allele). The confirmed imprinted genes exhibit enriched placental expression (PHLDA2, H19, IGF2, MEST, ZFAT, PLAGL1, AIM1) or are transcribed additionally only in the adrenal gland (MEG3, RTL1, PEG10, DLK1). Parental monoallelic expression showed extreme stability across gestation and in term pregnancy complications. A distinct group of additional 14 genes exhibited a statistically significant bias in parental allelic proportions defined as having 65–90% of reads from one parental allele (e.g., KLHDC10, NLRP2, RHOBTB3, DNMT1). Molecular mechanisms behind biased parental expression are still to be clarified. However, 66 of 91 (72.5%) analyzed candidate imprinted genes showed no signals of deviation from biallelic expression. Conclusions As placental tissue is not included in The Genotype-Tissue Expression (GTEx) project, the study contributed to fill the gap in the knowledge concerning parental allelic expression. A catalog of parental allelic proportions and gene expression of analyzed loci across human gestation and in term pregnancy complications is provided as additional files. The study outcome suggested that true imprinting in the human placenta is restricted to well-characterized loci. High expression of imprinted genes during mid-pregnancy supports their critical role in developmental programming. Consistent with the data on other GTEx tissues, the number of human imprinted genes appears to be overestimated. Electronic supplementary material The online version of this article (10.1186/s13148-019-0692-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana Pilvar
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Str, 19 50411, Tartu, Estonia
| | - Mario Reiman
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Str, 19 50411, Tartu, Estonia
| | - Arno Pilvar
- Veeuss OÜ, Jaama tn 185-49, 50705, Tartu, Tartu, Estonia
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila Str, 19 50411, Tartu, Estonia.
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Identification of Disease Risk DNA Variations is Shaping the Future of Precision Health. Genes (Basel) 2019; 10:genes10060450. [PMID: 31200548 PMCID: PMC6627794 DOI: 10.3390/genes10060450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 11/17/2022] Open
Abstract
In recent years, the knowledge generated by decoding the human genome has allowed groundbreaking genetic research to better understand genomic architecture and heritability in healthy and disease states. The vast amount of data generated over time and yet to be generated provides the basis for translational research towards the development of preventive and therapeutic strategies for many conditions. In this special issue, we highlight the discoveries of disease-associated and protective DNA variations in common human diseases and developmental disorders.
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66
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Lesch BJ, Tothova Z, Morgan EA, Liao Z, Bronson RT, Ebert BL, Page DC. Intergenerational epigenetic inheritance of cancer susceptibility in mammals. eLife 2019; 8:e39380. [PMID: 30963999 PMCID: PMC6456297 DOI: 10.7554/elife.39380] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Susceptibility to cancer is heritable, but much of this heritability remains unexplained. Some 'missing' heritability may be mediated by epigenetic changes in the parental germ line that do not involve transmission of genetic variants from parent to offspring. We report that deletion of the chromatin regulator Kdm6a (Utx) in the paternal germ line results in elevated tumor incidence in genetically wild type mice. This effect increases following passage through two successive generations of Kdm6a male germline deletion, but is lost following passage through a wild type germ line. The H3K27me3 mark is redistributed in sperm of Kdm6a mutants, and we define approximately 200 H3K27me3-marked regions that exhibit increased DNA methylation, both in sperm of Kdm6a mutants and in somatic tissue of progeny. Hypermethylated regions in enhancers may alter regulation of genes involved in cancer initiation or progression. Epigenetic changes in male gametes may therefore impact cancer susceptibility in adult offspring.
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Affiliation(s)
| | - Zuzana Tothova
- Department of Medicine, Division of HematologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Elizabeth A Morgan
- Department of PathologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Zhicong Liao
- Department of GeneticsYale School of MedicineNew HavenUnited States
- Yale Cancer CenterYale School of MedicineNew HavenUnited States
| | - Roderick T Bronson
- Department of PathologyTufts University School of Medicine and Veterinary MedicineNorth GraftonUnited States
| | - Benjamin L Ebert
- Department of Medicine, Division of HematologyBrigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - David C Page
- Whitehead InstituteCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Whitehead InstituteCambridgeUnited States
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Schulz H, Ruppert AK, Zara F, Madia F, Iacomino M, S Vari M, Balagura G, Minetti C, Striano P, Bianchi A, Marini C, Guerrini R, Weber YG, Becker F, Lerche H, Kapser C, Schankin CJ, Kunz WS, Møller RS, Oliver KL, Bellows ST, Mullen SA, Berkovic SF, Scheffer IE, Caglayan H, Ozbek U, Hoffmann P, Schramm S, Tsortouktzidis D, Becker AJ, Sander T. No evidence for a BRD2 promoter hypermethylation in blood leukocytes of Europeans with juvenile myoclonic epilepsy. Epilepsia 2019; 60:e31-e36. [PMID: 30719712 DOI: 10.1111/epi.14657] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/31/2023]
Abstract
Juvenile myoclonic epilepsy (JME) is a common syndrome of genetic generalized epilepsies (GGEs). Linkage and association studies suggest that the gene encoding the bromodomain-containing protein 2 (BRD2) may increase risk of JME. The present methylation and association study followed up a recent report highlighting that the BRD2 promoter CpG island (CpG76) is differentially hypermethylated in lymphoblastoid cells from Caucasian patients with JME compared to patients with other GGE subtypes and unaffected relatives. In contrast, we found a uniform low average percentage of methylation (<4.5%) for 13 CpG76-CpGs in whole blood cells from 782 unrelated European Caucasians, including 116 JME patients, 196 patients with genetic absence epilepsies, and 470 control subjects. We also failed to confirm an allelic association of the BRD2 promoter single nucleotide polymorphism (SNP) rs3918149 with JME (Armitage trend test, P = 0.98), and we did not detect a substantial impact of SNP rs3918149 on CpG76 methylation in either 116 JME patients (methylation quantitative trait loci [meQTL], P = 0.29) or 470 German control subjects (meQTL, P = 0.55). Our results do not support the previous observation that a high DNA methylation level of the BRD2 promoter CpG76 island is a prevalent epigenetic motif associated with JME in Caucasians.
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Affiliation(s)
- Herbert Schulz
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, G. Gaslini Institute, Genoa, Italy
| | - Francesca Madia
- Laboratory of Neurogenetics and Neuroscience, G. Gaslini Institute, Genoa, Italy
| | - Michele Iacomino
- Laboratory of Neurogenetics and Neuroscience, G. Gaslini Institute, Genoa, Italy
| | - Maria S Vari
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Ganna Balagura
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Carlo Minetti
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa, G. Gaslini Institute, Genoa, Italy
| | - Amedeo Bianchi
- Division of Neurology, Hospital San Donato Arezzo, Arezzo, Italy
| | - Carla Marini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Felicitas Becker
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany.,Department of Neurology, University of Ulm, Ulm, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- Department of Neurology, Großhadern Hospital, University of Munich, Munich, Germany
| | - Christoph J Schankin
- Department of Neurology, Großhadern Hospital, University of Munich, Munich, Germany.,Department of Neurology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Wolfram S Kunz
- Department of Epileptology, Institute of Experimental Epileptology and Cognition Research, University of Bonn Medical Center, Bonn, Germany
| | - Rikke S Møller
- Danish Epilepsy Center, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Karen L Oliver
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Susannah T Bellows
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Saul A Mullen
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria, Australia
| | - Hande Caglayan
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey.,Izmir Biomedicine and Genome Center, Izmir, Turkey
| | - Ugur Ozbek
- Department of Medical Genetics, Faculty of Medicine, Acibadem University, Istanbul, Turkey
| | - Per Hoffmann
- Department of Genomics, Life and Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital of Basel, Basel, Switzerland
| | - Sara Schramm
- Institute of Medical Informatics, Biometry, and Epidemiology, University of Duisburg-Essen, Essen, Germany
| | - Despina Tsortouktzidis
- Translational Epilepsy Research, Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Albert J Becker
- Translational Epilepsy Research, Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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