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Hofmeister RJ, Rubinacci S, Ribeiro DM, Buil A, Kutalik Z, Delaneau O. Parent-of-Origin inference for biobanks. Nat Commun 2022; 13:6668. [PMID: 36335127 PMCID: PMC9637181 DOI: 10.1038/s41467-022-34383-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Identical genetic variations can have different phenotypic effects depending on their parent of origin. Yet, studies focusing on parent-of-origin effects have been limited in terms of sample size due to the lack of parental genomes or known genealogies. We propose a probabilistic approach to infer the parent-of-origin of individual alleles that does not require parental genomes nor prior knowledge of genealogy. Our model uses Identity-By-Descent sharing with second- and third-degree relatives to assign alleles to parental groups and leverages chromosome X data in males to distinguish maternal from paternal groups. We combine this with robust haplotype inference and haploid imputation to infer the parent-of-origin for 26,393 UK Biobank individuals. We screen 99 phenotypes for parent-of-origin effects and replicate the discoveries of 6 GWAS studies, confirming signals on body mass index, type 2 diabetes, standing height and multiple blood biomarkers, including the known maternal effect at the MEG3/DLK1 locus on platelet phenotypes. We also report a novel maternal effect at the TERT gene on telomere length, thereby providing new insights on the heritability of this phenotype. All our summary statistics are publicly available to help the community to better characterize the molecular mechanisms leading to parent-of-origin effects and their implications for human health.
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Affiliation(s)
- Robin J Hofmeister
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Simone Rubinacci
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Diogo M Ribeiro
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark.,Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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2
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Webb T, Craigon C, Ciulli A. Targeting epigenetic modulators using PROTAC degraders: Current status and future perspective. Bioorg Med Chem Lett 2022; 63:128653. [PMID: 35257896 DOI: 10.1016/j.bmcl.2022.128653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023]
Abstract
Epigenetic modulators perform critical functions in gene expression for rapid adaption to external stimuli and are prevalent in all higher-order organisms. The establishment of a link between dysregulation of epigenetic processes and disease pathogenesis, particularly in cancer, has led to much interest in identifying drug targets. This prompted the development of small molecule inhibitors, primarily in haematological malignancies. While there have been epigenetic-targeting drugs to receive FDA approval for the treatment of cancers, many suffer from limited applicability, toxicity and the onset of drug resistance, as our understanding of the biology remains incomplete. The recent advent of genome-wide RNAi and CRISPR screens has shed new light on loss of specific proteins causing vulnerabilities of specific cancer types, highlighting the potential for exploiting synthetic lethality as a therapeutic approach. However, small molecule inhibitors have largely been unable to recapitulate phenotypic effects observed using genome-wide knockdown approaches. This mechanistic disconnect and gap are set to be addressed by targeted protein degradation. Degraders such as PROTACs targeting epigenetic proteins recapitulate CRISPR mediated genetic knockdown at the post-translational level and therefore can better exploit target druggability. Here, we review the current landscape of epigenetic drug discovery, the rationale behind and progress made in the development of PROTAC degraders, and look at future perspectives for the field.
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Affiliation(s)
- Thomas Webb
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Conner Craigon
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom.
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3
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Zeng Y, Amador C, Gao C, Walker RM, Morris SW, Campbell A, Frkatović A, Madden RA, Adams MJ, He S, Bretherick AD, Hayward C, Porteous DJ, Wilson JF, Evans KL, McIntosh AM, Navarro P, Haley CS. Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome. EBioMedicine 2021; 74:103730. [PMID: 34883445 PMCID: PMC8654798 DOI: 10.1016/j.ebiom.2021.103730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/19/2021] [Accepted: 11/19/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND parent-of-origin effects (POE) play important roles in complex disease and thus understanding their regulation and associated molecular and phenotypic variation are warranted. Previous studies mainly focused on the detection of genomic regions or phenotypes regulated by POE. Understanding whether POE may be modified by environmental or genetic exposures is important for understanding of the source of POE-associated variation, but only a few case studies addressing modifiable POE exist. METHODS in order to understand this high order of POE regulation, we screened 101 genetic and environmental factors such as 'predicted mRNA expression levels' of DNA methylation/imprinting machinery genes and environmental exposures. POE-mQTL-modifier interaction models were proposed to test the potential of these factors to modify POE at DNA methylation using data from Generation Scotland: The Scottish Family Health Study(N=2315). FINDINGS a set of vulnerable/modifiable POE-CpGs were identified (modifiable-POE-regulated CpGs, N=3). Four factors, 'lifetime smoking status' and 'predicted mRNA expression levels' of TET2, SIRT1 and KDM1A, were found to significantly modify the POE on the three CpGs in both discovery and replication datasets. We further identified plasma protein and health-related phenotypes associated with the methylation level of one of the identified CpGs. INTERPRETATION the modifiable POE identified here revealed an important yet indirect path through which genetic background and environmental exposures introduce their effect on DNA methylation, motivating future comprehensive evaluation of the role of these modifiers in complex diseases. FUNDING NSFC (81971270),H2020-MSCA-ITN(721815), Wellcome (204979/Z/16/Z,104036/Z/14/Z), MRC (MC_UU_00007/10, MC_PC_U127592696), CSO (CZD/16/6,CZB/4/276, CZB/4/710), SFC (HR03006), EUROSPAN (LSHG-CT-2006-018947), BBSRC (BBS/E/D/30002276), SYSU, Arthritis Research UK, NHLBI, NIH.
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Affiliation(s)
- Yanni Zeng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China.
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Chenhao Gao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, Chancellor's Building, The University of Edinburgh, Edinburgh, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Azra Frkatović
- Genos Glycoscience Research Laboratory, Borongajska cesta 83h, 10000 Zagreb, Croatia
| | - Rebecca A Madden
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Mark J Adams
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Shuai He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Chris S Haley
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
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Qazi S, Raza K. In silico approach to understand epigenetics of POTEE in ovarian cancer. J Integr Bioinform 2021; 18:jib-2021-0028. [PMID: 34788504 PMCID: PMC8709732 DOI: 10.1515/jib-2021-0028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
Ovarian cancer is the third leading cause of cancer-related deaths in India. Epigenetics mechanisms seemingly plays an important role in ovarian cancer. This paper highlights the crucial epigenetic changes that occur in POTEE that get hypomethylated in ovarian cancer. We utilized the POTEE paralog mRNA sequence to identify major motifs and also performed its enrichment analysis. We identified 6 motifs of varying lengths, out of which only three motifs, including CTTCCAGCAGATGTGGATCA, GGAACTGCC, and CGCCACATGCAGGC were most likely to be present in the nucleotide sequence of POTEE. By enrichment and occurrences identification analyses, we rectified the best match motif as CTTCCAGCAGATGT. Since there is no experimentally verified structure of POTEE paralog, thus, we predicted the POTEE structure using an automated workflow for template-based modeling using the power of a deep neural network. Additionally, to validate our predicted model we used AlphaFold predicted POTEE structure and observed that the residual stretch starting from 237-958 had a very high confidence per residue. Furthermore, POTEE predicted model stability was evaluated using replica exchange molecular dynamic simulation for 50 ns. Our network-based epigenetic analysis discerns only 10 highly significant, direct, and physical associators of POTEE. Our finding aims to provide new insights about the POTEE paralog.
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Affiliation(s)
- Sahar Qazi
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
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Borba LA, Broseghini LDR, Manosso LM, de Moura AB, Botelho MEM, Arent CO, Behenck JP, Hilsendeger A, Kammer LH, Valvassori SS, Quevedo J, Réus GZ. Environmental enrichment improves lifelong persistent behavioral and epigenetic changes induced by early-life stress. J Psychiatr Res 2021; 138:107-116. [PMID: 33848966 PMCID: PMC10494235 DOI: 10.1016/j.jpsychires.2021.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 02/08/2023]
Abstract
This study aimed to evaluate the effects of environmental enrichment (EE) in Wistar rats subjected to maternal deprivation (MD). MD was performed in the first post-natal days (PND) ten for 3 h/day. The groups were: control; deprived without EE; and deprived with EE. The EE was applied for 3 h/day. Forced swimming test (FST) and open field test were performed, and histone deacetylase (HDAC) and DNA methyltransferase (DNMT) activities in the prefrontal cortex (PFC) and hippocampus were evaluated on 31, 41, and 61 PND. MD altered spontaneous locomotor activity and immobility time in FST, but the effects were sex- and developmental period dependent. In deprived females at PND 31, 41, and 61, HDAC and DNMT increased in the PFC and hippocampus. In females exposed to EE for 20 days, there was a decrease of HDAC in the hippocampus and DNMT in the PFC and hippocampus. Exposure of females to EE for 40 days can reverse HDAC and DNMT increase in all brain areas. In deprived males at PND 31, 41, and 61, HDAC and DNMT increased in the hippocampus, and in the group exposed to EE for 40 days, there was a decrease in hippocampal activity. In PFC of male deprived rats at PND 61 and EE for 40 days, there was a reduction of HDAC and DNMT. MD induced lifelong persistent behavioral and epigenetic changes, and such effects were more evident in female than male rats. EE can be considered an essential non-pharmacological strategy to treat long-term trauma-induced early life changes.
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Affiliation(s)
- Laura A Borba
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Lia D R Broseghini
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Luana M Manosso
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Airam B de Moura
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Maria Eduarda M Botelho
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Camila O Arent
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - João Paulo Behenck
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Amanda Hilsendeger
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Letícia H Kammer
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - Samira S Valvassori
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil
| | - João Quevedo
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil; Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Center of Excellence on Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA; Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Gislaine Z Réus
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciuma, SC, Brazil.
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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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8
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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: 1.0] [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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9
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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Ponsuksili S, Trakooljul N, Basavaraj S, Hadlich F, Murani E, Wimmers K. Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs. BMC Genomics 2019; 20:492. [PMID: 31195974 PMCID: PMC6567458 DOI: 10.1186/s12864-019-5880-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/04/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in particular the DNA methylation state, of specific loci are driven by genetic variation. In this sense, polymorphism with major gene effects on metabolic and cell signaling processes, like the variation of the ryanodine receptors in skeletal muscle, may affect DNA methylation. METHODS DNA-Methylation profiles were generated applying Reduced Representation Bisulfite Sequencing (RRBS) on 17 Musculus longissimus dorsi samples. We examined DNA methylation in skeletal muscle of pig breeds differing in metabolic type, Duroc and Pietrain. We also included F2 crosses of these breeds to get a first clue to DNA methylation sites that may contribute to breed differences. Moreover, we compared DNA methylation in muscle tissue of Pietrain pigs differing in genotypes at the gene encoding the Ca2+ release channel (RYR1) that largely affects muscle physiology. RESULTS More than 2000 differently methylated sites were found between breeds including changes in methylation profiles of METRNL, IDH3B, COMMD6, and SLC22A18, genes involved in lipid metabolism. Depending on RYR1 genotype there were 1060 differently methylated sites including some functionally related genes, such as CABP2 and EHD, which play a role in buffering free cytosolic Ca2+ or interact with the Na+/Ca2+ exchanger. CONCLUSIONS The change in the level of methylation between the breeds is probably the result of the long-term selection process for quantitative traits involving an infinite number of genes, or it may be the result of a major gene mutation that plays an important role in muscle metabolism and triggers extensive compensatory processes.
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Affiliation(s)
- Siriluck Ponsuksili
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Rostock, Germany
| | - Nares Trakooljul
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Rostock, Germany
| | - Sajjanar Basavaraj
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Rostock, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Rostock, Germany
| | - Eduard Murani
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Rostock, Germany
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), Institute for Genome Biology, Functional Genome Analysis Research Unit, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Rostock, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
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Liu Y, Xu C, Tang X, Pei S, Jin D, Guo M, Yang M, Zhang Y. Genomic methylation and transcriptomic profiling provides insights into heading depression in inbred Brassica rapa L. ssp. pekinensis. Gene 2018; 665:119-126. [PMID: 29705127 DOI: 10.1016/j.gene.2018.04.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape. Transcriptome analysis by RNA-Seq revealed that genes in auxin-response and synthesis pathways were differentially expressed in the inbreeding depression lines. Interestingly, methylation levels of some of those genes were also changed. Furthermore, endogenous IAA content was decreased in inbred plants, in agreement with expression and methylation data. Chemical inhibition of auxin also replicated the degenerated phenotype in normal plants, while exogenous IAA application had no effect in inbred depression plants, suggesting a more complex mechanism. These data indicate DNA methylation-regulated auxin pathways play a role in establishing inbred depression phenotypes in plants. Our findings reveal new insights into inbreeding depression and leafy head development in Chinese cabbage.
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Affiliation(s)
- Yan Liu
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Cui Xu
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Xuebing Tang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, PR China
| | - Di Jin
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Minghao Guo
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Meng Yang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China
| | - Yaowei Zhang
- College of Horticulture, Northeast Agricultural University, Harbin 150030, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin 150030, PR China.
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12
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Coluccio A, Ecco G, Duc J, Offner S, Turelli P, Trono D. Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells. Epigenetics Chromatin 2018; 11:7. [PMID: 29482634 PMCID: PMC6389204 DOI: 10.1186/s13072-018-0177-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/16/2018] [Indexed: 01/18/2023] Open
Abstract
Background The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in repressing transposable elements (TEs) and maintaining parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of genome-wide reprogramming that precedes implantation. In naïve murine embryonic stem cells (mESCs), the genome is maintained highly hypomethylated by a combination of TET-mediated active demethylation and lack of de novo methylation, yet KAP1 is tethered by sequence-specific KZFPs to ICRs and TEs where it recruits histone and DNA methyltransferases to impose heterochromatin formation and DNA methylation. Results Here, upon removing either KAP1 or the cognate KZFP, we observed rapid TET2-dependent accumulation of 5hmC at both ICRs and TEs. In the absence of the KZFP/KAP1 complex, ICRs lost heterochromatic histone marks and underwent both active and passive DNA demethylation. For KAP1-bound TEs, 5mC hydroxylation correlated with transcriptional reactivation. Using RNA-seq, we further compared the expression profiles of TEs upon Kap1 removal in wild-type, Dnmt and Tet triple knockout mESCs. While we found that KAP1 represents the main effector of TEs repression in all three settings, we could additionally identify specific groups of TEs further controlled by DNA methylation. Furthermore, we observed that in the absence of TET proteins, activation upon Kap1 depletion was blunted for some TE integrants and increased for others. Conclusions Our results indicate that the KZFP/KAP1 complex maintains heterochromatin and DNA methylation at ICRs and TEs in naïve embryonic stem cells partly by protecting these loci from TET-mediated demethylation. Our study further unveils an unsuspected level of complexity in the transcriptional control of the endovirome by demonstrating often integrant-specific differential influences of histone-based heterochromatin modifications, DNA methylation and 5mC oxidation in regulating TEs expression. Electronic supplementary material The online version of this article (10.1186/s13072-018-0177-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Coluccio
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Gabriela Ecco
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Station 19, 1015, Lausanne, Switzerland.
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13
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Jasiulionis MG. Abnormal Epigenetic Regulation of Immune System during Aging. Front Immunol 2018; 9:197. [PMID: 29483913 PMCID: PMC5816044 DOI: 10.3389/fimmu.2018.00197] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to the study of mechanisms controlling the chromatin structure, which has fundamental role in the regulation of gene expression and genome stability. Epigenetic marks, such as DNA methylation and histone modifications, are established during embryonic development and epigenetic profiles are stably inherited during mitosis, ensuring cell differentiation and fate. Under the effect of intrinsic and extrinsic factors, such as metabolic profile, hormones, nutrition, drugs, smoke, and stress, epigenetic marks are actively modulated. In this sense, the lifestyle may affect significantly the epigenome, and as a result, the gene expression profile and cell function. Epigenetic alterations are a hallmark of aging and diseases, such as cancer. Among biological systems compromised with aging is the decline of immune response. Different regulators of immune response have their promoters and enhancers susceptible to the modulation by epigenetic marks, which is fundamental to the differentiation and function of immune cells. Consistent evidence has showed the regulation of innate immune cells, and T and B lymphocytes by epigenetic mechanisms. Therefore, age-dependent alterations in epigenetic marks may result in the decline of immune function and this might contribute to the increased incidence of diseases in old people. In order to maintain health, we need to better understand how to avoid epigenetic alterations related to immune aging. In this review, the contribution of epigenetic mechanisms to the loss of immune function during aging will be discussed, and the promise of new means of disease prevention and management will be pointed.
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Affiliation(s)
- Miriam G Jasiulionis
- Laboratory of Ontogeny and Epigenetics, Pharmacology Department, Universidade Federal de São Paulo, São Paulo, Brazil
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14
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Abstract
DNA methylation is a dynamic epigenetic mark that characterizes different cellular developmental stages, including tissue-specific profiles. This CpG dinucleotide modification cooperates in the regulation of the output of the cellular genetic content, in both healthy and pathological conditions. According to endogenous and exogenous stimuli, DNA methylation is involved in gene transcription, alternative splicing, imprinting, X-chromosome inactivation, and control of transposable elements. When these dinucleotides are organized in dense regions are called CpG islands (CGIs), being commonly known as transcriptional regulatory regions frequently associated with the promoter region of several genes. In cancer, promoter DNA hypermethylation events sustained the mechanistic hypothesis of epigenetic transcriptional silencing of an increasing number of tumor suppressor genes. CGI hypomethylation-mediated reactivation of oncogenes was also documented in several cancer types. In this chapter, we aim to summarize the functional consequences of the differential DNA methylation at CpG dinucleotides in cancer, focused in CGIs. Interestingly, cancer methylome is being recently explored, looking for biomarkers for diagnosis, prognosis, and predictors of drug response.
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Affiliation(s)
- Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.
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15
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Durzynska J, Lesniewicz K, Poreba E. Human papillomaviruses in epigenetic regulations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 772:36-50. [PMID: 28528689 DOI: 10.1016/j.mrrev.2016.09.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/01/2016] [Accepted: 09/17/2016] [Indexed: 12/12/2022]
Abstract
Human Papillomaviruses (HPVs) are double-stranded DNA viruses, that infect epithelial cells and are etiologically involved in the development of human cancer. Today, over 200 types of human papillomaviruses are known. They are divided into low-risk and high-risk HPVs depending on their potential to induce carcinogenesis, driven by two major viral oncoproteins, E6 and E7. By interacting with cellular partners, these proteins are involved in interdependent viral and cell cycles in stratified differentiating epithelium, and concomitantly induce epigenetic changes in infected cells and those undergoing malignant transformation. E6 and E7 oncoproteins interact with and/or modulate expression of many proteins involved in epigenetic regulation, including DNA methyltransferases, histone-modifying enzymes and subunits of chromatin remodeling complexes, thereby influencing host cell transcription program. Furthermore, HPV oncoproteins modulate expression of cellular micro RNAs. Most of these epigenetic actions in a complex dynamic interplay participate in the maintenance of persistent infection, cell transformation, and development of invasive cancer by a considerable deregulation of tumor suppressor and oncogenes. In this study, we have undertaken to discuss a number of studies concerning epigenetic regulations in HPV-dependent cells and to focus on those that have biological relevance to cancer progression.
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Affiliation(s)
- Julia Durzynska
- Department of Molecular Virology, Institute of Experimental Biology, A. Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Elzbieta Poreba
- Department of Molecular Virology, Institute of Experimental Biology, A. Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.
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16
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Abstract
With the impressive advancement in high-throughput 'omics' technologies over the past two decades, epigenetic mechanisms have emerged as the regulatory interface between the genome and environmental factors. These mechanisms include DNA methylation, histone modifications, ATP-dependent chromatin remodeling and RNA-based mechanisms. Their highly interdependent and coordinated action modulates the chromatin structure controlling access of the transcription machinery and thereby regulating expression of target genes. Given the rather limited proliferative capability of human cardiomyocytes, epigenetic regulation appears to play a particularly important role in the myocardium. The highly dynamic nature of the epigenome allows the heart to adapt to environmental challenges and to respond quickly and properly to cardiac stress. It is now becoming evident that histone-modifying and chromatin-remodeling enzymes as well as numerous non-coding RNAs play critical roles in cardiac development and function, while their dysregulation contributes to the onset and development of pathological cardiac remodeling culminating in HF. This review focuses on up-to-date knowledge about the epigenetic mechanisms and highlights their emerging role in the healthy and failing heart. Uncovering the determinants of epigenetic regulation holds great promise to accelerate the development of successful new diagnostic and therapeutic strategies in human cardiac disease.
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Affiliation(s)
- José Marín-García
- The Molecular Cardiology and Neuromuscular Institute, 75 Raritan Ave., Highland Park, NJ, 08904, USA,
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17
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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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18
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Abstract
Genomic imprinting refers to the epigenetic mechanism that results in the mono-allelic expression of a subset of genes in a parent-of-origin manner. These haploid genes are highly active in the placenta and are functionally implicated in the appropriate development of the fetus. Furthermore, the epigenetic marks regulating imprinted expression patterns are established early in development. These characteristics make genomic imprinting a potentially useful biomarker for environmental insults, especially during the in utero or early development stages, and for health outcomes later in life. Herein, we critically review the current literature regarding environmental influences on imprinted genes and summarize findings that suggest that imprinted loci are sensitive to known teratogenic agents, such as alcohol and tobacco, as well as less established factors with the potential to manipulate the in utero environment, including assisted reproductive technology. Finally, we discuss the potential of genomic imprinting to serve as an environmental sensor during early development.
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19
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Anvar Z, Cammisa M, Riso V, Baglivo I, Kukreja H, Sparago A, Girardot M, Lad S, De Feis I, Cerrato F, Angelini C, Feil R, Pedone PV, Grimaldi G, Riccio A. ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells. Nucleic Acids Res 2015; 44:1118-32. [PMID: 26481358 PMCID: PMC4756812 DOI: 10.1093/nar/gkv1059] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/01/2015] [Indexed: 12/15/2022] Open
Abstract
Imprinting Control Regions (ICRs) need to maintain their parental allele-specific DNA methylation during early embryogenesis despite genome-wide demethylation and subsequent de novo methylation. ZFP57 and KAP1 are both required for maintaining the repressive DNA methylation and H3-lysine-9-trimethylation (H3K9me3) at ICRs. In vitro, ZFP57 binds a specific hexanucleotide motif that is enriched at its genomic binding sites. We now demonstrate in mouse embryonic stem cells (ESCs) that SNPs disrupting closely-spaced hexanucleotide motifs are associated with lack of ZFP57 binding and H3K9me3 enrichment. Through a transgenic approach in mouse ESCs, we further demonstrate that an ICR fragment containing three ZFP57 motif sequences recapitulates the original methylated or unmethylated status when integrated into the genome at an ectopic position. Mutation of Zfp57 or the hexanucleotide motifs led to loss of ZFP57 binding and DNA methylation of the transgene. Finally, we identified a sequence variant of the hexanucleotide motif that interacts with ZFP57 both in vivo and in vitro. The presence of multiple and closely located copies of ZFP57 motif variants emerges as a distinct characteristic that is required for the faithful maintenance of repressive epigenetic marks at ICRs and other ZFP57 binding sites.
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Affiliation(s)
- Zahra Anvar
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Marco Cammisa
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Vincenzo Riso
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Harpreet Kukreja
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Angela Sparago
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Shraddha Lad
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | - Italia De Feis
- Istituto per le Applicazioni del Calcolo 'Mauro Picone' (IAC), CNR, 80131 Naples, Italy
| | - Flavia Cerrato
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo 'Mauro Picone' (IAC), CNR, 80131 Naples, Italy
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR5535 and University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Paolo V Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Giovanna Grimaldi
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Ceinge Biotecnologie Avanzate s.c.a.r.l., 80145 Naples, Italy
| | - Andrea Riccio
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
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20
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Soellner L, Monk D, Rezwan FI, Begemann M, Mackay D, Eggermann T. Congenital imprinting disorders: Application of multilocus and high throughput methods to decipher new pathomechanisms and improve their management. Mol Cell Probes 2015; 29:282-90. [DOI: 10.1016/j.mcp.2015.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022]
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21
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Hoffmann A, Daniel G, Schmidt-Edelkraut U, Spengler D. Roles of imprinted genes in neural stem cells. Epigenomics 2015; 6:515-32. [PMID: 25431944 DOI: 10.2217/epi.14.42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Imprinted genes and neural stem cells (NSC) play an important role in the developing and mature brain. A central theme of imprinted gene function in NSCs is cell survival and G1 arrest to control cell division, cell-cycle exit, migration and differentiation. Moreover, genomic imprinting can be epigenetically switched off at some genes to ensure stem cell quiescence and differentiation. At the genome scale, imprinted genes are organized in dynamic networks formed by interchromosomal interactions and transcriptional coregulation of imprinted and nonimprinted genes. Such multilayered networks may synchronize NSC activity with the demand from the niche resembling their roles in adjusting fetal size.
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Affiliation(s)
- Anke Hoffmann
- Max Planck Institute of Psychiatry, Translational Research, Kraepelinstrasse 2-10, 80804 Munich, Germany
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22
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Kiguchi N, Saika F, Kobayashi Y, Kishioka S. Epigenetic regulation of CC-chemokine ligand 2 in nonresolving inflammation. Biomol Concepts 2015; 5:265-73. [PMID: 25372758 DOI: 10.1515/bmc-2014-0022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/06/2014] [Indexed: 12/31/2022] Open
Abstract
Inflammation mediated by the crosstalk between leukocytes and resident tissue cells is crucial for the maintenance of homeostasis. Because chemokine ligands and receptors, which recruit a variety of leukocytes, are widely distributed among tissues, it is important to understand the mechanisms regulating inflammatory disease. Chemokines such as CC-chemokine ligand 2 (CCL2) amplify and maintain inflammation through chemokine-cytokine networks after the recruitment of circulating leukocytes. Chemokine-dependent nonresolving inflammation occurs in the peripheral and central nervous systems, and underlies several intractable diseases, including cancer and neuropathic pain. The chronic upregulation of chemokines is often mediated by epigenetic mechanisms consisting of DNA methylation, histone modification, and nucleosome positioning. In particular, histone acetylation and methylation have been shown to play important roles in the upregulation of chemokine expression. In addition to CCL2, several other chemokines strongly contribute to neuropathic pain through epigenetic induction. Consequently, targeting epigenetic changes may have therapeutic potential for nonresolving inflammatory diseases such as neuropathic pain. Further research into the epigenetics of inflammatory diseases should promote the development of novel and effective treatment strategies for intractable inflammatory diseases.
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Sanli I, Feil R. Chromatin mechanisms in the developmental control of imprinted gene expression. Int J Biochem Cell Biol 2015; 67:139-47. [PMID: 25908531 DOI: 10.1016/j.biocel.2015.04.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
Hundreds of protein-coding genes and regulatory non-coding RNAs (ncRNAs) are subject to genomic imprinting. The mono-allelic DNA methylation marks that control imprinted gene expression are somatically maintained throughout development, and this process is linked to specific chromatin features. Yet, at many imprinted genes, the mono-allelic expression is lineage or tissue-specific. Recent studies provide mechanistic insights into the developmentally-restricted action of the 'imprinting control regions' (ICRs). At several imprinted domains, the ICR expresses a long ncRNA that mediates chromatin repression in cis (and probably in trans as well). ICRs at other imprinted domains mediate higher-order chromatin structuration that enhances, or prevents, transcription of close-by genes. Here, we present how chromatin and ncRNAs contribute to developmental control of imprinted gene expression and discuss implications for disease. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
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Affiliation(s)
- Ildem Sanli
- Institute of Molecular Genetics (IGMM), UMR-5535, CNRS, University of Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), UMR-5535, CNRS, University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
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24
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Eggermann T, Netchine I, Temple IK, Tümer Z, Monk D, Mackay D, Grønskov K, Riccio A, Linglart A, Maher ER. Congenital imprinting disorders: EUCID.net - a network to decipher their aetiology and to improve the diagnostic and clinical care. Clin Epigenetics 2015; 7:23. [PMID: 25784961 PMCID: PMC4362648 DOI: 10.1186/s13148-015-0050-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
Imprinting disorders (IDs) are a group of eight rare but probably underdiagnosed congenital diseases affecting growth, development and metabolism. They are caused by similar molecular changes affecting regulation, dosage or the genomic sequence of imprinted genes. Each ID is characterised by specific clinical features, and, as each appeared to be associated with specific imprinting defects, they have been widely regarded as separate entities. However, they share clinical characteristics and can show overlapping molecular alterations. Nevertheless, IDs are usually studied separately despite their common underlying (epi)genetic aetiologies, and their basic pathogenesis and long-term clinical consequences remain largely unknown. Efforts to elucidate the aetiology of IDs are currently fragmented across Europe, and standardisation of diagnostic and clinical management is lacking. The new consortium EUCID.net (European network of congenital imprinting disorders) now aims to promote better clinical care and scientific investigation of imprinting disorders by establishing a concerted multidisciplinary alliance of clinicians, researchers, patients and families. By encompassing all IDs and establishing a wide ranging and collaborative network, EUCID.net brings together a wide variety of expertise and interests to engender new collaborations and initiatives.
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Affiliation(s)
- Thomas Eggermann
- Department of Human Genetics, RWTH Aachen, Aachen, 52074 Germany ; Department of Human Genetics, University Hospital, RWTH Aachen, Pauwelsstr. 30, 52074 Aachen, Germany
| | - Irène Netchine
- INSERM, UMR_S 938, CDR Saint-Antoine, Paris, F-75012 France ; UMR_S 938, CDR Saint-Antoine, UPMC Univ Paris 06, Sorbonne Universites, Paris, F-75012 France ; Pediatric Endocrinology, 3APHP, Armand Trousseau Hospital, Paris, 75012 France
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA UK
| | - Zeynep Tümer
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, 2600 Denmark
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Hospital Duran i Reynals, 08907 Barcelona, Spain
| | - Deborah Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine University of Southampton, Wessex Clinical Genetics Service, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA UK
| | - Karin Grønskov
- Clinical Genetic Clinic, Kennedy Center, Rigshospitalet, Copenhagen University Hospital, Glostrup, 2600 Denmark
| | - Andrea Riccio
- DiSTABiF, Seconda Università degli Studi di Napoli, 81100 Caserta, Italy ; Institute of Genetics and Biophysics-ABT, CNR, Napoli, Italy
| | - Agnès Linglart
- Endocrinology and Diabetology for Children and Reference Center for Rare Disorders of Calcium and Phosphorus Metabolism, Bicêtre Paris Sud, APHP, Le Kremlin-Bicêtre, 94276 Paris France ; INSERM U986, INSERM, Le Kremlin-Bicêtre, 94276 Paris, France
| | - Eamonn R Maher
- Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, CB2 OXY UK
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Bruno C, Carmignac V, Netchine I, Choux C, Duffourd Y, Faivre L, Thauvin-Robinet C, Le Bouc Y, Sagot P, Bourc'his D, Fauque P. Germline correction of an epimutation related to Silver-Russell syndrome. Hum Mol Genet 2015; 24:3314-21. [DOI: 10.1093/hmg/ddv079] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/26/2015] [Indexed: 12/23/2022] Open
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Eggermann T, Soellner L, Buiting K, Kotzot D. Mosaicism and uniparental disomy in prenatal diagnosis. Trends Mol Med 2015; 21:77-87. [DOI: 10.1016/j.molmed.2014.11.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/18/2014] [Accepted: 11/26/2014] [Indexed: 01/21/2023]
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DNA methylation: the pivotal interaction between early-life nutrition and glucose metabolism in later life. Br J Nutr 2014; 112:1850-7. [PMID: 25327140 DOI: 10.1017/s0007114514002827] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Traditionally, it has been widely acknowledged that genes together with adult lifestyle factors determine the risk of developing some metabolic diseases such as insulin resistance, obesity and diabetes mellitus in later life. However, there is now substantial evidence that prenatal and early-postnatal nutrition play a critical role in determining susceptibility to these diseases in later life. Maternal nutrition has historically been a key determinant for offspring health, and gestation is the critical time window that can affect the growth and development of offspring. The Developmental Origins of Health and Disease (DOHaD) hypothesis proposes that exposures during early life play a critical role in determining the risk of developing metabolic diseases in adulthood. Currently, there are substantial epidemiological studies and experimental animal models that have demonstrated that nutritional disturbances during the critical periods of early-life development can significantly have an impact on the predisposition to developing some metabolic diseases in later life. The hypothesis that epigenetic mechanisms may link imbalanced early-life nutrition with altered disease risk has been widely accepted in recent years. Epigenetics can be defined as the study of heritable changes in gene expression that do not involve alterations in the DNA sequence. Epigenetic processes play a significant role in regulating tissue-specific gene expression, and hence alterations in these processes may induce long-term changes in gene function and metabolism that persist throughout the life course. The present review focuses on how nutrition in early life can alter the epigenome, produce different phenotypes and alter disease susceptibilities, especially for impaired glucose metabolism.
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Steyaert S, Van Criekinge W, De Paepe A, Denil S, Mensaert K, Vandepitte K, Vanden Berghe W, Trooskens G, De Meyer T. SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data. Nucleic Acids Res 2014; 42:e157. [PMID: 25237057 PMCID: PMC4227762 DOI: 10.1093/nar/gku847] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but only few examples are known. One important reason is that current, cost-affordable truly genome-wide methods to assess DNA-methylation are based on sequencing post-enrichment. Here, we present a new methodology based on classical population genetic theory, i.e. the Hardy–Weinberg theorem, that combines methylomic data from MethylCap-seq with associated SNP profiles to identify monoallelically methylated loci. Applied on 334 MethylCap-seq samples of very diverse origin, this resulted in the identification of 80 genomic regions featured by monoallelic DNA-methylation. Of these 80 loci, 49 are located in genic regions of which 25 have already been linked to imprinting. Further analysis revealed statistically significant enrichment of these loci in promoter regions, further establishing the relevance and usefulness of the method. Additional validation was done using both 14 whole-genome bisulfite sequencing data sets and 16 mRNA-seq data sets. Importantly, the developed approach can be easily applied to other enrichment-based sequencing technologies, like the ChIP-seq-based identification of monoallelic histone modifications.
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Affiliation(s)
- Sandra Steyaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Ayla De Paepe
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Klaas Mensaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | | | - Wim Vanden Berghe
- PPES, Department of Biomedical Sciences, University of Antwerp, Wilrijk 2610, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent 9000, Belgium
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Cheng CT, Kuo CY, Ann DK. KAPtain in charge of multiple missions: Emerging roles of KAP1. World J Biol Chem 2014; 5:308-320. [PMID: 25225599 PMCID: PMC4160525 DOI: 10.4331/wjbc.v5.i3.308] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/21/2014] [Accepted: 06/20/2014] [Indexed: 02/05/2023] Open
Abstract
KAP1/TRIM28/TIF1β was identified nearly twenty years ago as a universal transcriptional co-repressor because it interacts with a large KRAB-containing zinc finger protein (KRAB-ZFP) transcription factor family. Many studies demonstrate that KAP1 affects gene expression by regulating the transcription of KRAB-ZFP-specific loci, trans-repressing as a transcriptional co-repressor or epigenetically modulating chromatin structure. Emerging evidence suggests that KAP1 also functions independent of gene regulation by serving as a SUMO/ubiquitin E3 ligase or signaling scaffold protein to mediate signal transduction. KAP1 is subjected to multiple post-translational modifications (PTMs), including serine/tyrosine phosphorylation, SUMOylation, and acetylation, which coordinately regulate KAP1 function and its protein abundance. KAP1 is involved in multiple aspects of cellular activities, including DNA damage response, virus replication, cytokine production and stem cell pluripotency. Moreover, knockout of KAP1 results in embryonic lethality, indicating that KAP1 is crucial for embryonic development and possibly impacts a wide-range of (patho)physiological manifestations. Indeed, studies from conditional knockout mouse models reveal that KAP1-deficiency significantly impairs vital physiological processes, such as immune maturation, stress vulnerability, hepatic metabolism, gamete development and erythropoiesis. In this review, we summarize and evaluate current literatures involving the biochemical and physiological functions of KAP1. In addition, increasing studies on the clinical relevance of KAP1 in cancer will also be discussed.
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Iglesias-Platas I, Martin-Trujillo A, Petazzi P, Guillaumet-Adkins A, Esteller M, Monk D. Altered expression of the imprinted transcription factor PLAGL1 deregulates a network of genes in the human IUGR placenta. Hum Mol Genet 2014; 23:6275-85. [PMID: 24993786 DOI: 10.1093/hmg/ddu347] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomic imprinting is the epigenetic process that results in monoallelic expression of genes depending on parental origin. These genes are known to be critical for placental development and fetal growth in mammals. Aberrant epigenetic profiles at imprinted loci, such as DNA methylation defects, are surprisingly rare in pregnancies with compromised fetal growth, while variations in transcriptional output from the expressed alleles of imprinted genes are more commonly reported in pregnancies complicated with intrauterine growth restriction (IUGR). To determine if PLAGL1 and HYMAI, two imprinted transcripts deregulated in Transient Neonatal Diabetes Mellitus, are involved in non-syndromic IUGR we compared the expression and DNA methylation levels in a large cohort of placental biopsies from IUGR and uneventful pregnancies. This revealed that despite appropriate maternal methylation at the shared PLAGL1/HYMAI promoter, there was a loss of correlation between PLAGL1 and HYMAI expression in IUGR. This incongruity was due to higher HYMAI expression in IUGR gestations, coupled with PLAGL1 down-regulation in placentas from IUGR girls, but not boys. The PLAGL1 protein is a zinc-finger transcription factor that has been shown to be a master coordinator of a genetic growth network in mice. We observe PLAGL1 binding to the H19/IGF2 shared enhancers in placentae, with significant correlations between PLAGL1 levels with H19 and IGF2 expression levels. In addition, PLAGL1 binding and expression also correlate with expression levels of metabolic regulator genes SLC2A4, TCF4 and PPARγ1. Our results strongly suggest that fetal growth can be influenced by altered expression of the PLAGL1 gene network in human placenta.
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Affiliation(s)
- Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona 08950, Spain,
| | | | - Paolo Petazzi
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut D'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08907, Spain
| | - Amy Guillaumet-Adkins
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona 08950, Spain, Imprinting and Cancer Group
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut D'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08907, Spain, Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona 08097, Spain and Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain
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Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE. Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits. Anim Genet 2014; 45 Suppl 1:25-39. [PMID: 24990393 DOI: 10.1111/age.12168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/30/2022]
Abstract
The phenomenon of genomic imprinting, whereby a subset of mammalian genes display parent-of-origin-specific monoallelic expression, is one of the most active areas of epigenetics research. Over the past two decades, more than 100 imprinted mammalian genes have been identified, while considerable advances have been made in elucidating the molecular mechanisms governing imprinting. These studies have helped to unravel the epigenome--a separate layer of regulatory information contained in eukaryotic chromosomes that influences gene expression and phenotypes without involving changes to the underlying DNA sequence. Although most studies of genomic imprinting in mammals have focussed on mouse models or human biomedical disorders, there is burgeoning interest in the phenotypic effects of imprinted genes in domestic livestock species. In particular, research has focused on imprinted genes influencing foetal growth and development, which are associated with economically important production traits in cattle, sheep and pigs. These findings, when coupled with the data emerging from the various different livestock genome projects, have major implications for the future of animal breeding, health and management. Here, we review current scientific knowledge regarding genomic imprinting in livestock species and evaluate how this information can be used in modern livestock improvement programmes.
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Affiliation(s)
- D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
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Abstract
PURPOSE OF REVIEW Genomic imprinting is an epigenetically-driven phenomenon that responds to environmental stimuli to determine the fetal growth trajectory. This review aims at describing the transgenerational meaning of genomic imprinting while supporting the study of genomic imprinting in placenta for the determination of an important biomarker of chronic and developmental disorders in children as driven by the environment. RECENT FINDINGS Recent work has shown that genomic imprinting reaches beyond the basic significance of an epigenetic mark regulating gene expression. Genomic imprinting has been theorized as the main determinant of epigenetic inheritance. Concomitantly, new studies in the field of molecular epidemiology became available that tie the fetal growth trajectory to genomic imprinting in response to environmental stimuli, making of genomic imprinting the driving force of the fetal growth. When carried out in placenta, the effector of the intrauterine environment as conveyed by the maternal exposure to the general life environment, the study of genomic imprinting may reveal critical information on alterations of the fetal growth trajectory. SUMMARY The study of genomic imprinting profiles in placentas from birth cohorts of individuals exposed to different environmental stimuli can provide a new, much needed, tool for the elaboration of effective public health intervention plans for child health.
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Wolf JB, Oakey RJ, Feil R. Imprinted gene expression in hybrids: perturbed mechanisms and evolutionary implications. Heredity (Edinb) 2014; 113:167-75. [PMID: 24619185 DOI: 10.1038/hdy.2014.11] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 01/24/2014] [Accepted: 01/28/2014] [Indexed: 01/21/2023] Open
Abstract
Diverse mechanisms contribute to the evolution of reproductive barriers, a process that is critical in speciation. Amongst these are alterations in gene products and in gene dosage that affect development and reproductive success in hybrid offspring. Because of its strict parent-of-origin dependence, genomic imprinting is thought to contribute to the aberrant phenotypes observed in interspecies hybrids in mammals and flowering plants, when the abnormalities depend on the directionality of the cross. In different groups of mammals, hybrid incompatibility has indeed been linked to loss of imprinting. Aberrant expression levels have been reported as well, including imprinted genes involved in development and growth. Recent studies in humans emphasize that genetic diversity within a species can readily perturb imprinted gene expression and phenotype as well. Despite novel insights into the underlying mechanisms, the full extent of imprinted gene perturbation still remains to be determined in the different hybrid systems. Here we review imprinted gene expression in intra- and interspecies hybrids and examine the evolutionary scenarios under which imprinting could contribute to hybrid incompatibilities. We discuss effects on development and reproduction and possible evolutionary implications.
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Affiliation(s)
- J B Wolf
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK
| | - R J Oakey
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - R Feil
- Institute of Molecular Genetics (IGMM), CNRS, UMR-5535 and University of Montpellier, Montpellier, France
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Miller JL, Grant PA. The role of DNA methylation and histone modifications in transcriptional regulation in humans. Subcell Biochem 2014; 61:289-317. [PMID: 23150256 DOI: 10.1007/978-94-007-4525-4_13] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although the field of genetics has grown by leaps and bounds within the last decade due to the completion and availability of the human genome sequence, transcriptional regulation still cannot be explained solely by an individual's DNA sequence. Complex coordination and communication between a plethora of well-conserved chromatin modifying factors are essential for all organisms. Regulation of gene expression depends on histone post translational modifications (HPTMs), DNA methylation, histone variants, remodeling enzymes, and effector proteins that influence the structure and function of chromatin, which affects a broad spectrum of cellular processes such as DNA repair, DNA replication, growth, and proliferation. If mutated or deleted, many of these factors can result in human disease at the level of transcriptional regulation. The common goal of recent studies is to understand disease states at the stage of altered gene expression. Utilizing information gained from new high-throughput techniques and analyses will aid biomedical research in the development of treatments that work at one of the most basic levels of gene expression, chromatin. This chapter will discuss the effects of and mechanism by which histone modifications and DNA methylation affect transcriptional regulation.
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Affiliation(s)
- Jaime L Miller
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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35
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Skaar DA, Li Y, Bernal AJ, Hoyo C, Murphy SK, Jirtle RL. The human imprintome: regulatory mechanisms, methods of ascertainment, and roles in disease susceptibility. ILAR J 2014; 53:341-58. [PMID: 23744971 DOI: 10.1093/ilar.53.3-4.341] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Imprinted genes form a special subset of the genome, exhibiting monoallelic expression in a parent-of-origin-dependent fashion. This monoallelic expression is controlled by parental-specific epigenetic marks, which are established in gametogenesis and early embryonic development and are persistent in all somatic cells throughout life. We define this specific set of cis-acting epigenetic regulatory elements as the imprintome, a distinct and specially tasked subset of the epigenome. Imprintome elements contain DNA methylation and histone modifications that regulate monoallelic expression by affecting promoter accessibility, chromatin structure, and chromatin configuration. Understanding their regulation is critical because a significant proportion of human imprinted genes are implicated in complex diseases. Significant species variation in the repertoire of imprinted genes and their epigenetic regulation, however, will not allow model organisms solely to be used for this crucial purpose. Ultimately, only the human will suffice to accurately define the human imprintome.
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Affiliation(s)
- David A Skaar
- Department of Oncology, Duke University Medical Center, Durham, North Carolina, USA
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Girardot M, Feil R, Llères D. Epigenetic deregulation of genomic imprinting in humans: causal mechanisms and clinical implications. Epigenomics 2013; 5:715-28. [DOI: 10.2217/epi.13.66] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mammalian genes controlled by genomic imprinting play important roles in development and diverse postnatal processes. A growing number of congenital disorders have been linked to genomic imprinting. Each of these is caused by perturbed gene expression at one principal imprinted domain. Some imprinting disorders, including the Prader–Willi and Angelman syndromes, are caused almost exclusively by genetic mutations. In several others, including the Beckwith–Wiedemann and Silver–Russell growth syndromes, and transient neonatal diabetes mellitus, imprinted expression is perturbed mostly by epigenetic alterations at ‘imprinting control regions’ and at other specific regulatory sequences. In a minority of these patients, DNA methylation is altered at multiple imprinted loci, suggesting that common trans-acting factors are affected. Here, we review the epimutations involved in congenital imprinting disorders and the associated clinical features. Trans-acting factors known to be causally involved are discussed and other trans-acting factors that are potentially implicated are also presented.
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Affiliation(s)
- Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
| | - David Llères
- Institute of Molecular Genetics (IGMM), CNRS UMR-5535, 1919 Route de Mende, 34293 Montpellier, France
- Universities of Montpellier I & II, Montpellier, France
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Biémont C, Vieira C. Could interallelic interactions be a key to the epigenetic aspects of fitness-trait inbreeding depression? Heredity (Edinb) 2013; 112:219-20. [PMID: 24105439 DOI: 10.1038/hdy.2013.80] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- C Biémont
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - C Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
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Buckberry S, Bianco-Miotto T, Roberts CT. Imprinted and X-linked non-coding RNAs as potential regulators of human placental function. Epigenetics 2013; 9:81-9. [PMID: 24081302 DOI: 10.4161/epi.26197] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pregnancy outcome is inextricably linked to placental development, which is strictly controlled temporally and spatially through mechanisms that are only partially understood. However, increasing evidence suggests non-coding RNAs (ncRNAs) direct and regulate a considerable number of biological processes and therefore may constitute a previously hidden layer of regulatory information in the placenta. Many ncRNAs, including both microRNAs and long non-coding transcripts, show almost exclusive or predominant expression in the placenta compared with other somatic tissues and display altered expression patterns in placentas from complicated pregnancies. In this review, we explore the results of recent genome-scale and single gene expression studies using human placental tissue, but include studies in the mouse where human data are lacking. Our review focuses on the ncRNAs epigenetically regulated through genomic imprinting or X-chromosome inactivation and includes recent evidence surrounding the H19 lincRNA, the imprinted C19MC cluster microRNAs, and X-linked miRNAs associated with pregnancy complications.
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Affiliation(s)
- Sam Buckberry
- The Robinson Institute; Research Centre for Reproductive Health; School of Paediatrics and Reproductive Health; The University of Adelaide; Adelaide, SA Australia
| | - Tina Bianco-Miotto
- The Robinson Institute; Research Centre for Reproductive Health; School of Paediatrics and Reproductive Health; The University of Adelaide; Adelaide, SA Australia; School of Agriculture Food & Wine; The University of Adelaide; Adelaide, SA Australia
| | - Claire T Roberts
- The Robinson Institute; Research Centre for Reproductive Health; School of Paediatrics and Reproductive Health; The University of Adelaide; Adelaide, SA Australia
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Jacobs DI, Mao Y, Fu A, Kelly WK, Zhu Y. Dysregulated methylation at imprinted genes in prostate tumor tissue detected by methylation microarray. BMC Urol 2013; 13:37. [PMID: 23890537 PMCID: PMC3751920 DOI: 10.1186/1471-2490-13-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/15/2013] [Indexed: 11/18/2022] Open
Abstract
Background Imprinting is an important epigenetic regulator of gene expression that is often disrupted in cancer. While loss of imprinting (LOI) has been reported for two genes in prostate cancer (IGF2 and TFPI2), disease-related changes in methylation across all imprinted gene regions has not been investigated. Methods Using an Illumina Infinium Methylation Assay, we analyzed methylation of 396 CpG sites in the promoter regions of 56 genes in a pooled sample of 12 pairs of prostate tumor and adjacent normal tissue. Selected LOI identified from the array was validated using the Sequenom EpiTYPER assay for individual samples and further confirmed by expression data from publicly available datasets. Results Methylation significantly increased in 52 sites and significantly decreased in 17 sites across 28 unique genes (P < 0.05), and the strongest evidence for loss of imprinting was demonstrated in tumor suppressor genes DLK1, PLAGL1, SLC22A18, TP73, and WT1. Differential expression of these five genes in prostate tumor versus normal tissue using array data from a publicly available database were consistent with the observed LOI patterns, and WT1 hypermethylation was confirmed using quantitative DNA methylation analysis. Conclusions Together, these findings suggest a more widespread dysregulation of genetic imprinting in prostate cancer than previously reported and warrant further investigation.
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Affiliation(s)
- Daniel I Jacobs
- Yale School of Public Health, Yale University School of Medicine, New Haven, CT, USA
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Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations. Proc Natl Acad Sci U S A 2013; 110:11946-51. [PMID: 23818637 DOI: 10.1073/pnas.1310704110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
When positioned into the integrin α-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.
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Erkek S, Hisano M, Liang CY, Gill M, Murr R, Dieker J, Schübeler D, van der Vlag J, Stadler MB, Peters AHFM. Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. Nat Struct Mol Biol 2013; 20:868-75. [PMID: 23770822 DOI: 10.1038/nsmb.2599] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/29/2013] [Indexed: 12/21/2022]
Abstract
In mammalian spermatozoa, most but not all of the genome is densely packaged by protamines. Here we reveal the molecular logic underlying the retention of nucleosomes in mouse spermatozoa, which contain only 1% residual histones. We observe high enrichment throughout the genome of nucleosomes at CpG-rich sequences that lack DNA methylation. Residual nucleosomes are largely composed of the histone H3.3 variant and are trimethylated at Lys4 of histone H3 (H3K4me3). Canonical H3.1 and H3.2 histones are also enriched at CpG-rich promoters marked by Polycomb-mediated H3K27me3, a modification predictive of gene repression in preimplantation embryos. Histone variant-specific nucleosome retention in sperm is strongly associated with nucleosome turnover in round spermatids. Our data show evolutionary conservation of the basic principles of nucleosome retention in mouse and human sperm, supporting a model of epigenetic inheritance by nucleosomes between generations.
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Affiliation(s)
- Serap Erkek
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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van Heesbeen HJ, Mesman S, Veenvliet JV, Smidt MP. Epigenetic mechanisms in the development and maintenance of dopaminergic neurons. Development 2013; 140:1159-69. [PMID: 23444349 DOI: 10.1242/dev.089359] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Mesodiencephalic dopaminergic (mdDA) neurons are located in the ventral mesodiencephalon and are involved in psychiatric disorders and severely affected in neurodegenerative diseases such as Parkinson's disease. mdDA neuronal development has received much attention in the last 15 years and many transcription factors involved in mdDA specification have been discovered. More recently however, the impact of epigenetic regulation has come into focus, and it's emerging that the processes of histone modification and DNA methylation form the basis of genetic switches that operate during mdDA development. Here, we review the epigenetic control of mdDA development, maturation and maintenance. As we highlight, epigenetic mechanisms play a pivotal role in all of these processes and the knowledge gathered from studying epigenetics in these contexts may aid our understanding of mdDA-related pathologies.
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Affiliation(s)
- Hendrikus J van Heesbeen
- Swammerdam Institute for Life Sciences, Science Park, University of Amsterdam, Amsterdam, The Netherlands
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43
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Ashbrook DG, Hager R. Empirical testing of hypotheses about the evolution of genomic imprinting in mammals. Front Neuroanat 2013; 7:6. [PMID: 23641202 PMCID: PMC3639422 DOI: 10.3389/fnana.2013.00006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/10/2013] [Indexed: 01/01/2023] Open
Abstract
The close interaction between mother and offspring in mammals is thought to contribute to the evolution of genomic imprinting or parent-of-origin dependent gene expression. Empirical tests of theories about the evolution of imprinting have been scant for several reasons. Models make different assumptions about the traits affected by imprinted genes and the scenarios in which imprinting is predicted to have been selected for. Thus, competing hypotheses cannot readily be tested against each other. Further, it is far from clear how predictions about expression patterns of genes with specific phenotypic effects can be tested given current methodology of assaying gene expression levels, be it in the brain or in other tissues. We first set out a scenario for testing competing hypotheses and delineate the different assumptions and predictions of models. We then outline how predictions may be tested using mouse models such as intercrosses or recombinant inbred (RI) systems that can be phenotyped for traits relevant to imprinting theories. Further, we briefly discuss different molecular approaches that may be used in conjunction with experiments to ascertain expression patterns of imprinted genes and thus the testing of predictions.
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Affiliation(s)
- David G Ashbrook
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester Manchester, UK
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Jacobs DI, Hansen J, Fu A, Stevens RG, Tjonneland A, Vogel UB, Zheng T, Zhu Y. Methylation alterations at imprinted genes detected among long-term shiftworkers. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:141-146. [PMID: 23193016 PMCID: PMC4993623 DOI: 10.1002/em.21752] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/19/2012] [Indexed: 06/02/2023]
Abstract
Exposure to light at night through shiftwork has been linked to alterations in DNA methylation and increased risk of cancer development. Using an Illumina Infinium Methylation Assay, we analyzed methylation levels of 397 CpG sites in the promoter regions of 56 normally imprinted genes to investigate whether shiftwork is associated with alteration of methylation patterns. Methylation was significantly higher at 20 CpG sites and significantly lower at 30 CpG sites (P < 0.05) in 10 female long-term shiftworkers as compared to 10 female age- and folate intake-matched day workers. The strongest evidence for altered methylation patterns in shiftworkers was observed for DLX5, IGF2AS, and TP73 based on the magnitude of methylation change and consistency in the direction of change across multiple CpG sites, and consistent results were observed using quantitative DNA methylation analysis. We conclude that long-term shiftwork may alter methylation patterns at imprinted genes, which may be an important mechanism by which shiftwork has carcinogenic potential and warrants further investigation.
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Affiliation(s)
- Daniel I. Jacobs
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Johnni Hansen
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Alan Fu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Anne Tjonneland
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Ulla B. Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Tongzhang Zheng
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yong Zhu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
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Epigenetics: How Genes and Environment Interact. ENVIRONMENTAL EPIGENOMICS IN HEALTH AND DISEASE 2013. [DOI: 10.1007/978-3-642-23380-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Eggermann T, Spengler S, Gogiel M, Begemann M, Elbracht M. Epigenetic and genetic diagnosis of Silver-Russell syndrome. Expert Rev Mol Diagn 2012; 12:459-71. [PMID: 22702363 DOI: 10.1586/erm.12.43] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Silver-Russell syndrome (SRS) is a congenital imprinting disorder characterized by intrauterine and postnatal growth restriction and further characteristic features. SRS is genetically heterogenous: 7-10% of patients carry a maternal uniparental disomy of chromosome 7; >38% show a hypomethylation in imprinting control region 1 in 11p15; and a further class of mutations are copy number variations affecting different chromosomes, but mainly 11p15 and 7. The diagnostic work-up should thus aim to detect these three molecular subtypes. Numerous techniques are currently applied in genetic SRS testing, but none of them covers all known (epi)mutations, and they should therefore be used synergistically. However, future next-generation sequencing approaches will allow a comprehensive analysis of all types of alterations in SRS.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, University Hospital Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany.
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Schagdarsurengin U, Paradowska A, Steger K. Analysing the sperm epigenome: roles in early embryogenesis and assisted reproduction. Nat Rev Urol 2012; 9:609-19. [PMID: 23045264 DOI: 10.1038/nrurol.2012.183] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An understanding of the epigenetic mechanisms involved in sperm production and their impact on the differentiating embryo is essential if we are to optimize fertilization and assisted reproduction techniques in the future. Male germ cells are unique in terms of size, robustness, and chromatin structure, which is highly condensed owing to the replacement of most histones by protamines. Analysis of sperm epigenetics requires specific techniques that enable the isolation of high quality chromatin and associated nucleic acids. Histone modification, DNA methylation and noncoding RNAs have important, but so far underestimated, roles in the production of fertile sperm. Aberrations in these epigenetic processes have detrimental consequences for both early embryo development and assisted reproductive technology. Emerging computational techniques are likely to improve our understanding of chromatin dynamics in the future.
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Affiliation(s)
- Undraga Schagdarsurengin
- Justus Liebig University, Department of Urology, Pediatric Urology and Andrology, Section Molecular Andrology, Giessen, Germany
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48
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Quantitative, high-resolution CpG methylation assays on the pyrosequencingplatform. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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49
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Eggermann T, Leisten I, Binder G, Begemann M, Spengler S. Disturbed methylation at multiple imprinted loci: an increasing observation in imprinting disorders. Epigenomics 2012; 3:625-37. [PMID: 22126250 DOI: 10.2217/epi.11.84] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The widely accepted association between aberrant methylation at specific imprinted loci and distinct imprinting disorders has recently been brought into question by the identification of methylation defects at multiple loci (multilocus methylation defect [MLMD]). Strikingly, in different imprinting disorders, the same MLMD patterns can be observed. The cause for this ambiguous epigenotype-phenotype correlation is currently unknown. Future strategies to solve this enigma have to include all levels of imprinting regulation, ranging from DNA methylation to chromatin organization, as any disturbance of the balanced interaction between the different players in imprinting regulation might cause disturbed expression of imprinted factors. The molecular analysis of MLMD will help in discovering these interactions and contribute to the understanding of genomic imprinting and its disturbances.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany.
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Abstract
Strong evidence suggests a potential link among epigenetics, microRNAs (miRNAs), and pregnancy complications. Much research still needs to be carried out to determine whether epigenetic factors are predictive in the pathogenesis of preeclampsia (PE), a life-threatening disease during pregnancy. Recently, the importance of maternal epigenetic features, including DNA methylation, histone modifications, epigenetically regulated miRNA, and the effect of imprinted or non-imprinted genes on trophoblast growth, invasion, as well as fetal development and hypertension in pregnancy, has been demonstrated in a series of articles. This article discusses the current evidence of this complicated network of miRNA and epigenetic factors as potential mechanisms that may underlie the theories of disease for PE. Translating these basic epigenetic findings to clinical practice could potentially serve as prognostic biomarkers for diagnosis in its early stages and could help in the development of prophylactic strategies.
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Affiliation(s)
- Mahua Choudhury
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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