1
|
Raitoharju E, Rajić S, Marttila S. Non-coding 886 ( nc886/ vtRNA2-1), the epigenetic odd duck - implications for future studies. Epigenetics 2024; 19:2332819. [PMID: 38525792 DOI: 10.1080/15592294.2024.2332819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
Collapse
Affiliation(s)
- Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
| |
Collapse
|
2
|
Vidal AC, Sosnowski DW, Marchesoni J, Grenier C, Thorp J, Murphy SK, Johnson SB, Schlief W, Hoyo C. Maternal adverse childhood experiences (ACEs) and offspring imprinted gene DMR methylation at birth. Epigenetics 2024; 19:2293412. [PMID: 38100614 PMCID: PMC10730185 DOI: 10.1080/15592294.2023.2293412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Adverse childhood experiences (ACEs) contribute to numerous negative health outcomes across the life course and across generations. Here, we extend prior work by examining the association of maternal ACEs, and their interaction with financial stress and discrimination, with methylation status within eight differentially methylated regions (DMRs) in imprinted domains in newborns. ACEs, financial stress during pregnancy, and experience of discrimination were self-reported among 232 pregnant women. DNA methylation was assessed at PEG10/SGCE, NNAT, IGF2, H19, PLAGL1, PEG3, MEG3-IG, and DLK1/MEG3 regulatory sequences using pyrosequencing. Using multivariable linear regression models, we found evidence to suggest that financial stress was associated with hypermethylation of MEG3-IG in non-Hispanic White newborns; discrimination was associated with hypermethylation of IGF2 and NNAT in Hispanic newborns, and with hypomethylation of PEG3 in non-Hispanic Black newborns. We also found evidence that maternal ACEs interacted with discrimination to predict offspring PLAGL1 altered DMR methylation, in addition to interactions between maternal ACEs score and discrimination predicting H19 and SGCE/PEG10 altered methylation in non-Hispanic White newborns. However, these interactions were not statistically significant after multiple testing corrections. Findings from this study suggest that maternal ACEs, discrimination, and financial stress are associated with newborn aberrant methylation in imprinted gene regions.
Collapse
Affiliation(s)
- Adriana C. Vidal
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - David W. Sosnowski
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joddy Marchesoni
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - John Thorp
- Department of Obstetrics and Gynecology, Maternal and Child Health, UNC Gillings School of Public Health, UNC, Chapel Hill, NC, USA
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Sara B. Johnson
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Population, Family & Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William Schlief
- Johns Hopkins All Children’s Pediatric Biorepository, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| |
Collapse
|
3
|
da Fonseca LLCG, Rocha DN, Cintra HA, de Araújo LL, dos Santos GLM, de Faria LL, Salú MDS, Leite SHDS, Rocha AD, Lopes MDCB, Ferreira IR, Gomes LHF, Guida LC. Establishing a Standardized DNA Extraction Method Using NaCl from Oral Mucosa Cells for Its Application in Imprinting Diseases Such as Prader-Willi and Angelman Syndromes: A Preliminary Investigation. Genes (Basel) 2024; 15:641. [PMID: 38790270 PMCID: PMC11120874 DOI: 10.3390/genes15050641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/11/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Diagnosing imprinting defects in neonates and young children presents challenges, often necessitating molecular analysis for a conclusive diagnosis. The isolation of genetic material from oral swabs becomes crucial, especially in settings where blood sample collection is impractical or for vulnerable populations like newborns, who possess limited blood volumes and are often too fragile for invasive procedures. Oral swab samples emerge as an excellent source of DNA, effectively overcoming obstacles associated with rare diseases. METHODS In our study, we specifically addressed the determination of the quality and quantity of DNA extracted from oral swab samples using NaCl procedures. RESULTS We compared these results with extractions performed using a commercial kit. Subsequently, the obtained material underwent MS-HRM analysis for loci associated with imprinting diseases such as Prader-Willi and Angelman syndromes. CONCLUSIONS Our study emphasizes the significance of oral swab samples as a reliable source for obtaining DNA for MS-HRM analysis. NaCl extraction stands out as a practical and cost-effective method for genetic studies, contributing to a molecular diagnosis that proves particularly beneficial for patients facing delays in characterization, ultimately influencing their treatment.
Collapse
Affiliation(s)
- Letícia Lopes Cabral Guimarães da Fonseca
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Danielle Nascimento Rocha
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Hiago Azevedo Cintra
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Luiza Loureiro de Araújo
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Gabrielle Leal Monteiro dos Santos
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Leonardo Lima de Faria
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Margarida dos Santos Salú
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Silvia Helena dos Santos Leite
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Adriana Duarte Rocha
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Maria da Conceição Borges Lopes
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Igor Ribeiro Ferreira
- Rural and Remote Support Services, Department of Health, Integrated Cardiovascular Clinical Network SA, Adelaide 5042, Australia
| | - Leonardo Henrique Ferreira Gomes
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| | - Letícia Cunha Guida
- Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira–Fundação Oswaldo Cruz, Rio de Janeiro 22250-020, Brazil (H.A.C.); (L.L.d.A.); (L.L.d.F.)
| |
Collapse
|
4
|
Verruma CG, Santos RS, Marchesi JAP, Sales SLA, Vila RA, Rios ÁFL, Furtado CLM, Ramos ES. Dynamic methylation pattern of H19DMR and KvDMR1 in bovine oocytes and preimplantation embryos. J Assist Reprod Genet 2024; 41:333-345. [PMID: 38231285 PMCID: PMC10894807 DOI: 10.1007/s10815-023-03011-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
PURPOSE This study aimed to evaluate the epigenetic reprogramming of ICR1 (KvDMR1) and ICR2 (H19DMR) and expression of genes controlled by them as well as those involved in methylation, demethylation, and pluripotency. METHODS We collected germinal vesicle (GV) and metaphase II (MII) oocytes, and preimplantation embryos at five stages [zygote, 4-8 cells, 8-16 cells, morula, and expanded blastocysts (ExB)]. DNA methylation was assessed by BiSeq, and the gene expression was evaluated using qPCR. RESULTS H19DMR showed an increased DNA methylation from GV to MII oocytes (68.04% and 98.05%, respectively), decreasing in zygotes (85.83%) until morula (61.65%), and ExB (63.63%). H19 and IGF2 showed increased expression in zygotes, which decreased in further stages. KvDMR1 was hypermethylated in both GV (71.82%) and MII (69.43%) and in zygotes (73.70%) up to morula (77.84%), with a loss of methylation at the ExB (36.64%). The zygote had higher expression of most genes, except for CDKN1C and PHLDA2, which were highly expressed in MII and GV oocytes, respectively. DNMTs showed increased expression in oocytes, followed by a reduction in the earliest stages of embryo development. TET1 was downregulated until 4-8-cell and upregulated in 8-16-cell embryos. TET2 and TET3 showed higher expression in oocytes, and a downregulation in MII oocytes and 4-8-cell embryo. CONCLUSION We highlighted the heterogeneity in the DNA methylation of H19DMR and KvDMR1 and a dynamic expression pattern of genes controlled by them. The expression of DNMTs and TETs genes was also dynamic owing to epigenetic reprogramming.
Collapse
Affiliation(s)
- Carolina G Verruma
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Renan S Santos
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Jorge A P Marchesi
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Sarah L A Sales
- Postgraduate Program in Physiology and Pharmacology, Drug Research and Development Center (NPDM), Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Reginaldo A Vila
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Álvaro F L Rios
- Biotechnology Laboratory, Center of Bioscience and Biotechnology, State University of North Fluminense Darcy Ribeiro, Goitacazes Campus, Rio de Janeiro, Brazil
| | - Cristiana L M Furtado
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza - UNIFOR, Fortaleza, CE, 60811-905, Brazil
- Drug Research and Development Center (NPDM), Postgraduate Program in Translational Medicine, Federal University of Ceara (UFC), Fortaleza, CE, 60430-275, Brazil
| | - Ester S Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
| |
Collapse
|
5
|
Villicaña S, Castillo-Fernandez J, Hannon E, Christiansen C, Tsai PC, Maddock J, Kuh D, Suderman M, Power C, Relton C, Ploubidis G, Wong A, Hardy R, Goodman A, Ong KK, Bell JT. Genetic impacts on DNA methylation help elucidate regulatory genomic processes. Genome Biol 2023; 24:176. [PMID: 37525248 PMCID: PMC10391992 DOI: 10.1186/s13059-023-03011-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Pinpointing genetic impacts on DNA methylation can improve our understanding of pathways that underlie gene regulation and disease risk. RESULTS We report heritability and methylation quantitative trait locus (meQTL) analysis at 724,499 CpGs profiled with the Illumina Infinium MethylationEPIC array in 2358 blood samples from three UK cohorts. Methylation levels at 34.2% of CpGs are affected by SNPs, and 98% of effects are cis-acting or within 1 Mbp of the tested CpG. Our results are consistent with meQTL analyses based on the former Illumina Infinium HumanMethylation450 array. Both SNPs and CpGs with meQTLs are overrepresented in enhancers, which have improved coverage on this platform compared to previous approaches. Co-localisation analyses across genetic effects on DNA methylation and 56 human traits identify 1520 co-localisations across 1325 unique CpGs and 34 phenotypes, including in disease-relevant genes, such as USP1 and DOCK7 (total cholesterol levels), and ICOSLG (inflammatory bowel disease). Enrichment analysis of meQTLs and integration with expression QTLs give insights into mechanisms underlying cis-meQTLs (e.g. through disruption of transcription factor binding sites for CTCF and SMC3) and trans-meQTLs (e.g. through regulating the expression of ACD and SENP7 which can modulate DNA methylation at distal sites). CONCLUSIONS Our findings improve the characterisation of the mechanisms underlying DNA methylation variability and are informative for prioritisation of GWAS variants for functional follow-ups. The MeQTL EPIC Database and viewer are available online at https://epicmeqtl.kcl.ac.uk .
Collapse
Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | | | | | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Pei-Chien Tsai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jane Maddock
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Christine Power
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - George Ploubidis
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing, Institute of Cardiovascular Science, University College London, London, UK
| | - Rebecca Hardy
- School of Sport, Exercise & Health Sciences, Loughborough University, Loughborough, UK
- UCL Social Research Institute, University College London, London, UK
| | - Alissa Goodman
- Centre for Longitudinal Studies, Institute of Education, University College London, London, UK
| | - Ken K Ong
- MRC Epidemiology Unit and Department of Paediatrics, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| |
Collapse
|
6
|
CRISPR/dCas9-Dnmt3a-mediated targeted DNA methylation of APP rescues brain pathology in a mouse model of Alzheimer’s disease. Transl Neurodegener 2022; 11:41. [PMID: 36109806 PMCID: PMC9476342 DOI: 10.1186/s40035-022-00314-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/19/2022] [Indexed: 01/05/2023] Open
Abstract
Background Aberrant DNA methylation patterns have been observed in neurodegenerative diseases, including Alzheimer's disease (AD), and dynamic changes in DNA methylation are closely associated with the onset and progression of these diseases. Particularly, hypomethylation of the amyloid precursor protein gene (APP) has been reported in patients with AD. Methods In this study, we used catalytically inactivated Cas9 (dCas9) fused with Dnmt3a for targeted DNA methylation of APP, and showed that the CRISPR/dCas9-Dnmt3a-mediated DNA methylation system could efficiently induce targeted DNA methylation of APP both in vivo and in vitro. Results We hypothesized that the targeted methylation of the APP promoter might rescue AD-related neuronal cell death by reducing APP mRNA expression. The cultured APP-KI mouse primary neurons exhibited an altered DNA-methylation pattern on the APP promoter after dCas9-Dnmt3a treatment. Likewise, the APP mRNA level was significantly reduced in the dCas9-Dnmt3a-treated wild-type and APP-KI mouse primary neurons. We also observed decreased amyloid-beta (Aβ) peptide level and Aβ42/40 ratio in the dCas9-Dnmt3a-treated APP-KI mouse neurons compared to the control APP-KI mouse neurons. In addition, neuronal cell death was significantly decreased in the dCas9-Dnmt3a-treated APP-KI mouse neurons. Furthermore, the in vivo methylation of APP in the brain via dCas9-Dnmt3a treatment altered Aβ plaques and attenuated cognitive and behavioral impairments in the APP-KI mouse model. Conclusions These results suggest that the targeted methylation of APP via dCas9-Dnmt3a treatment can be a potential therapeutic strategy for AD. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-022-00314-0.
Collapse
|
7
|
Zheng Y, Joyce B, Hwang SJ, Ma J, Liu L, Allen N, Krefman A, Wang J, Gao T, Nannini D, Zhang H, Jacobs DR, Gross M, Fornage M, Lewis CE, Schreiner PJ, Sidney S, Chen D, Greenland P, Levy D, Hou L, Lloyd-Jones D. Association of Cardiovascular Health Through Young Adulthood With Genome-Wide DNA Methylation Patterns in Midlife: The CARDIA Study. Circulation 2022; 146:94-109. [PMID: 35652342 PMCID: PMC9348746 DOI: 10.1161/circulationaha.121.055484] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cardiovascular health (CVH) from young adulthood is strongly associated with an individual's future risk of cardiovascular disease (CVD) and total mortality. Defining epigenomic biomarkers of lifelong CVH exposure and understanding their roles in CVD development may help develop preventive and therapeutic strategies for CVD. METHODS In 1085 CARDIA study (Coronary Artery Risk Development in Young Adults) participants, we defined a clinical cumulative CVH score that combines body mass index, blood pressure, total cholesterol, and fasting glucose measured longitudinally from young adulthood through middle age over 20 years (mean age, 25-45). Blood DNA methylation at >840 000 methylation markers was measured twice over 5 years (mean age, 40 and 45). Epigenome-wide association analyses on the cumulative CVH score were performed in CARDIA and compared in the FHS (Framingham Heart Study). We used penalized regression to build a methylation-based risk score to evaluate the risk of incident coronary artery calcification and clinical CVD events. RESULTS We identified 45 methylation markers associated with cumulative CVH at false discovery rate <0.01 (P=4.7E-7-5.8E-17) in CARDIA and replicated in FHS. These associations were more pronounced with methylation measured at an older age. CPT1A, ABCG1, and SREBF1 appeared as the most prominent genes. The 45 methylation markers were mostly located in transcriptionally active chromatin and involved lipid metabolism, insulin secretion, and cytokine production pathways. Three methylation markers located in genes SARS1, SOCS3, and LINC-PINT statistically mediated 20.4% of the total effect between CVH and risk of incident coronary artery calcification. The methylation risk score added information and significantly (P=0.004) improved the discrimination capacity of coronary artery calcification status versus CVH score alone and showed association with risk of incident coronary artery calcification 5 to 10 years later independent of cumulative CVH score (odds ratio, 1.87; P=9.66E-09). The methylation risk score was also associated with incident clinical CVD in FHS (hazard ratio, 1.28; P=1.22E-05). CONCLUSIONS Cumulative CVH from young adulthood contributes to midlife epigenetic programming over time. Our findings demonstrate the role of epigenetic markers in response to CVH changes and highlight the potential of epigenomic markers for precision CVD prevention, and earlier detection of subclinical CVD, as well.
Collapse
Affiliation(s)
- Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Brian Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiantao Ma
- Tufts University Friedman School of Nutrition Science and Policy, Boston, Massachusetts, USA
| | - Lei Liu
- Division of Biostatistics, Washington University, St. Louis, Missouri, USA
| | - Norrina Allen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amy Krefman
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jun Wang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Drew Nannini
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, China
| | - David R. Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Cora E. Lewis
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephen Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Dongquan Chen
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Donald Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| |
Collapse
|
8
|
OUP accepted manuscript. Hum Reprod Update 2022; 28:629-655. [DOI: 10.1093/humupd/dmac010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Indexed: 11/13/2022] Open
|
9
|
Ducreux B, Frappier J, Bruno C, Doukani A, Guilleman M, Simon E, Martinaud A, Bourc’his D, Barberet J, Fauque P. Genome-Wide Analysis of DNA Methylation in Buccal Cells of Children Conceived through IVF and ICSI. Genes (Basel) 2021; 12:1912. [PMID: 34946866 PMCID: PMC8701402 DOI: 10.3390/genes12121912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/25/2022] Open
Abstract
Early life periconceptional exposures during assisted reproductive technology (ART) procedures could alter the DNA methylation profiles of ART children, notably in imprinted genes and repetitive elements. At the genome scale, DNA methylation differences have been reported in ART conceptions at birth, but it is still unclear if those differences remain at childhood. Here, we performed an epigenome-wide DNA methylation association study using Illumina InfiniumEPIC BeadChip to assess the effects of the mode of conception on the methylome of buccal cells from 7- to 8-year-old children (48 children conceived after ART or naturally (control, CTL)) and according to the embryo culture medium in which they were conceived. We identified 127 differentially methylated positions (DMPs) and 16 differentially methylated regions (DMRs) (FDR < 0.05) with low delta beta differences between the two groups (ART vs. CTL). DMPs were preferentially located inside promoter proximal regions and CpG islands and were mostly hypermethylated with ART. We highlighted that the use of distinct embryo culture medium was not associated with DNA methylation differences in childhood. Overall, we bring additional evidence that children conceived via ART display limited genome-wide DNA methylation variation compared with those conceived naturally.
Collapse
Affiliation(s)
- Bastien Ducreux
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
| | - Jean Frappier
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Céline Bruno
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Abiba Doukani
- Faculté de Médecine, Sorbonne Université, UMS 37 PASS Plateforme P3S, 91, Bd de l’hôpital, F-75634 Paris, France;
| | - Magali Guilleman
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Emmanuel Simon
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Service de Gynécologie-Obstétrique, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Aurélie Martinaud
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Déborah Bourc’his
- Institut Curie, PSL University, CNRS, INSERM, 26 Rue d’Ulm, F-75248 Paris, France;
| | - Julie Barberet
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Patricia Fauque
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| |
Collapse
|
10
|
Villicaña S, Bell JT. Genetic impacts on DNA methylation: research findings and future perspectives. Genome Biol 2021; 22:127. [PMID: 33931130 PMCID: PMC8086086 DOI: 10.1186/s13059-021-02347-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple recent studies highlight that genetic variants can have strong impacts on a significant proportion of the human DNA methylome. Methylation quantitative trait loci, or meQTLs, allow for the exploration of biological mechanisms that underlie complex human phenotypes, with potential insights for human disease onset and progression. In this review, we summarize recent milestones in characterizing the human genetic basis of DNA methylation variation over the last decade, including heritability findings and genome-wide identification of meQTLs. We also discuss challenges in this field and future areas of research geared to generate insights into molecular processes underlying human complex traits.
Collapse
Affiliation(s)
- Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, St. Thomas’ Hospital, King’s College London, 3rd Floor, South Wing, Block D, London, SE1 7EH UK
| |
Collapse
|
11
|
Akbari V, Garant JM, O'Neill K, Pandoh P, Moore R, Marra MA, Hirst M, Jones SJM. Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase. Genome Biol 2021; 22:68. [PMID: 33618748 PMCID: PMC7898412 DOI: 10.1186/s13059-021-02283-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/29/2021] [Indexed: 02/08/2023] Open
Abstract
The ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no complete software for detecting SNPs, phasing haplotypes, and mapping methylation to these from nanopore sequence data. Here, we present NanoMethPhase, a software tool to phase 5-methylcytosine from nanopore sequencing. We also present SNVoter, which can post-process nanopore SNV calls to improve accuracy in low coverage regions. Together, these tools can accurately detect allele-specific methylation genome-wide using nanopore sequence data with low coverage of about ten-fold redundancy.
Collapse
Affiliation(s)
- Vahid Akbari
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Kieran O'Neill
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin Hirst
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.,Department of Microbiology and Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
12
|
Lorgen-Ritchie M, Murray AD, Staff R, Ferguson-Smith AC, Richards M, Horgan GW, Phillips LH, Hoad G, McNeil C, Ribeiro A, Haggarty P. Imprinting methylation predicts hippocampal volumes and hyperintensities and the change with age in later life. Sci Rep 2021; 11:943. [PMID: 33441584 PMCID: PMC7806645 DOI: 10.1038/s41598-020-78062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/16/2020] [Indexed: 12/29/2022] Open
Abstract
Epigenetic imprinting is important for neurogenesis and brain function. Hippocampal volumes and brain hyperintensities in late life have been associated with early life circumstances. Epigenetic imprinting may underpin these associations. Methylation was measured at 982 sites in 13 imprinted locations in blood samples from a longitudinal cohort by bisulphite amplicon sequencing. Hippocampal volumes and hyperintensities were determined at age 64y and 72y using MRI. Hyperintensities were determined in white matter, grey matter and infratentorial regions. Permutation methods were used to adjust for multiple testing. At 64y, H19/IGF2 and NESPAS methylation predicted hippocampal volumes. PEG3 predicted hyperintensities in hippocampal grey matter, and white matter. GNASXL predicted grey matter hyperintensities. Changes with age were predicted for hippocampal volume (MEST1, KvDMR, L3MBTL, GNASXL), white matter (MEST1, PEG3) and hippocampal grey matter hyperintensities (MCTS2, GNASXL, NESPAS, L3MBTL, MCTS2, SNRPN, MEST1). Including childhood cognitive ability, years in education, or socioeconomic status as additional explanatory variables in regression analyses did not change the overall findings. Imprinting methylation in multiple genes predicts brain structures, and their change over time. These findings are potentially relevant to the development of novel tests of brain structure and function across the life-course, strategies to improve cognitive outcomes, and our understanding of early influences on brain development and function.
Collapse
Affiliation(s)
- Marlene Lorgen-Ritchie
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | | | | | - Marcus Richards
- MRC Unit for Lifelong Health and Ageing at UCL, University College London, London, UK
| | - Graham W Horgan
- Biomathematics and Statistics Scotland, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Louise H Phillips
- School of Psychology, University of Aberdeen, Aberdeen, AB24 3FX, UK
| | - Gwen Hoad
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Chris McNeil
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Antonio Ribeiro
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Paul Haggarty
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
| |
Collapse
|
13
|
Rousseaux S, Seyve E, Chuffart F, Bourova-Flin E, Benmerad M, Charles MA, Forhan A, Heude B, Siroux V, Slama R, Tost J, Vaiman D, Khochbin S, Lepeule J. Immediate and durable effects of maternal tobacco consumption alter placental DNA methylation in enhancer and imprinted gene-containing regions. BMC Med 2020; 18:306. [PMID: 33023569 PMCID: PMC7542140 DOI: 10.1186/s12916-020-01736-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although exposure to cigarette smoking during pregnancy has been associated with alterations of DNA methylation in the cord blood or placental cells, whether such exposure before pregnancy could induce epigenetic alterations in the placenta of former smokers has never been investigated. METHODS Our approach combined the analysis of placenta epigenomic (ENCODE) data with newly generated DNA methylation data obtained from 568 pregnant women, the largest cohort to date, either actively smoking during their pregnancy or formerly exposed to tobacco smoking. RESULTS This strategy resulted in several major findings. First, among the 203 differentially methylated regions (DMRs) identified by the epigenome-wide association study, 152 showed "reversible" alterations of DNA methylation, only present in the placenta of current smokers, whereas 26 were also found altered in former smokers, whose placenta had not been exposed directly to cigarette smoking. Although the absolute methylation changes were smaller than those observed in other contexts, such as in some congenital diseases, the observed alterations were consistent within each DMR. This observation was further supported by a demethylation of LINE-1 sequences in the placentas of both current (beta-coefficient (β) (95% confidence interval (CI)), - 0.004 (- 0.008; 0.001)) and former smokers (β (95% CI), - 0.006 (- 0.011; - 0.001)) compared to nonsmokers. Second, the 203 DMRs were enriched in epigenetic marks corresponding to enhancer regions, including monomethylation of lysine 4 and acetylation of lysine 27 of histone H3 (respectively H3K4me1 and H3K27ac). Third, smoking-associated DMRs were also found near and/or overlapping 10 imprinted genes containing regions (corresponding to 16 genes), notably including the NNAT, SGCE/PEG10, and H19/MIR675 loci. CONCLUSIONS Our results pointing towards genomic regions containing the imprinted genes as well as enhancers as preferential targets suggest mechanisms by which tobacco could directly impact the fetus and future child. The persistence of significant DNA methylation changes in the placenta of former smokers supports the hypothesis of an "epigenetic memory" of exposure to cigarette smoking before pregnancy. This observation not only is conceptually revolutionary, but these results also bring crucial information in terms of public health concerning potential long-term detrimental effects of smoking in women.
Collapse
Affiliation(s)
- Sophie Rousseaux
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Emie Seyve
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Florent Chuffart
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | | | - Meriem Benmerad
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Marie-Aline Charles
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, Paris, France
| | - Valérie Siroux
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Remy Slama
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Evry, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Saadi Khochbin
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France
| | - Johanna Lepeule
- Université Grenoble Alpes, Inserm, CNRS, IAB, 38000, Grenoble, France.
| | | |
Collapse
|
14
|
Orjuela S, Machlab D, Menigatti M, Marra G, Robinson MD. DAMEfinder: a method to detect differential allele-specific methylation. Epigenetics Chromatin 2020; 13:25. [PMID: 32487212 PMCID: PMC7268773 DOI: 10.1186/s13072-020-00346-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/21/2020] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation is a highly studied epigenetic signature that is associated with regulation of gene expression, whereby genes with high levels of promoter methylation are generally repressed. Genomic imprinting occurs when one of the parental alleles is methylated, i.e., when there is inherited allele-specific methylation (ASM). A special case of imprinting occurs during X chromosome inactivation in females, where one of the two X chromosomes is silenced, to achieve dosage compensation between the sexes. Another more widespread form of ASM is sequence dependent (SD-ASM), where ASM is linked to a nearby heterozygous single nucleotide polymorphism (SNP). Results We developed a method to screen for genomic regions that exhibit loss or gain of ASM in samples from two conditions (treatments, diseases, etc.). The method relies on the availability of bisulfite sequencing data from multiple samples of the two conditions. We leverage other established computational methods to screen for these regions within a new R package called DAMEfinder. It calculates an ASM score for all CpG sites or pairs in the genome of each sample, and then quantifies the change in ASM between conditions. It then clusters nearby CpG sites with consistent change into regions. In the absence of SNP information, our method relies only on reads to quantify ASM. This novel ASM score compares favorably to current methods that also screen for ASM. Not only does it easily discern between imprinted and non-imprinted regions, but also females from males based on X chromosome inactivation. We also applied DAMEfinder to a colorectal cancer dataset and observed that colorectal cancer subtypes are distinguishable according to their ASM signature. We also re-discover known cases of loss of imprinting. Conclusion We have designed DAMEfinder to detect regions of differential ASM (DAMEs), which is a more refined definition of differential methylation, and can therefore help in breaking down the complexity of DNA methylation and its influence in development and disease.
Collapse
Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Dania Machlab
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| |
Collapse
|
15
|
Granot-Hershkovitz E, Wu P, Karasik D, Peter I, Peloso GM, Levy D, Vasan RS, Adrienne Cupples L, Liu CT, Meigs JB, Siscovick DS, Dupuis J, Friedlander Y, Hochner H. Searching for parent-of-origin effects on cardiometabolic traits in imprinted genomic regions. Eur J Hum Genet 2020; 28:646-655. [PMID: 31896779 PMCID: PMC7170899 DOI: 10.1038/s41431-019-0568-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/08/2022] Open
Abstract
Cardiometabolic traits pose a major global public health burden. Large-scale genome-wide association studies (GWAS) have identified multiple loci accounting for up to 30% of the genetic variance in complex traits such as cardiometabolic traits. However, the contribution of parent-of-origin effects (POEs) to complex traits has been largely ignored in GWAS. Family-based studies enable the assessment of POEs in genetic association analyses. We investigated POEs on a range of complex traits in 3 family-based studies. The discovery phase was carried out in large pedigrees from the Kibbutzim Family Study (n = 901 individuals) and in 872 parent-offspring trios from the Jerusalem Perinatal Study. Focusing on imprinted genomic regions, we examined parent-specific associations with 12 complex traits (i.e., body-size, blood pressure, lipids), mostly cardiometabolic risk traits. Forty five of the 11,967 SNPs initially found to have POE were evaluated for replication (p value < 1 × 10-4) in Framingham Heart Study families (max n = 8000 individuals). Three common variants yielded evidence of POE in the meta-analysis. Two variants, located on chr6 in the HLA region, showed a paternal effect on height (rs1042136: βpaternal = -0.023, p value = 1.5 × 10-8 and rs1431403: βpaternal = -0.011, p value = 5.4 × 10-6). The corresponding maternally-derived effects were statistically nonsignificant. The variant rs9332053, located on chr13 in RCBTB2 gene, demonstrated a maternal effect on hip circumference (βmaternal = -4.24, p value = 9.6 × 10-6; βpaternal = 1.29, p value = 0.23). These findings provide evidence for the utility of incorporating POEs into association studies of cardiometabolic traits, especially anthropometric traits. The study highlights the benefits of using family-based data for deciphering the genetic architecture of complex traits.
Collapse
Affiliation(s)
| | - Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Daniel Levy
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Ramachandran S Vasan
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Sections of Preventive medicine and Epidemiology, and cardiovascular medicine, Departments of Medicine and Epidemiology, Boston University Schools of Medicine and Public health, Boston, MA, 02118, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - James B Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David S Siscovick
- Institute for Urban Health, New York Academy of Medicine, New York, NY, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Yechiel Friedlander
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel
| | - Hagit Hochner
- Braun School of Public Health, The Hebrew University of Jerusalem, 99112102, Jerusalem, Israel.
| |
Collapse
|
16
|
Busto-Moner L, Morival J, Ren H, Fahim A, Reitz Z, Downing TL, Read EL. Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation. PLoS Comput Biol 2020; 16:e1007195. [PMID: 32275652 PMCID: PMC7176288 DOI: 10.1371/journal.pcbi.1007195] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 04/22/2020] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
DNA methylation is a heritable epigenetic modification that plays an essential role in mammalian development. Genomic methylation patterns are dynamically maintained, with DNA methyltransferases mediating inheritance of methyl marks onto nascent DNA over cycles of replication. A recently developed experimental technique employing immunoprecipitation of bromodeoxyuridine labeled nascent DNA followed by bisulfite sequencing (Repli-BS) measures post-replication temporal evolution of cytosine methylation, thus enabling genome-wide monitoring of methylation maintenance. In this work, we combine statistical analysis and stochastic mathematical modeling to analyze Repli-BS data from human embryonic stem cells. We estimate site-specific kinetic rate constants for the restoration of methyl marks on >10 million uniquely mapped cytosines within the CpG (cytosine-phosphate-guanine) dinucleotide context across the genome using Maximum Likelihood Estimation. We find that post-replication remethylation rate constants span approximately two orders of magnitude, with half-lives of per-site recovery of steady-state methylation levels ranging from shorter than ten minutes to five hours and longer. Furthermore, we find that kinetic constants of maintenance methylation are correlated among neighboring CpG sites. Stochastic mathematical modeling provides insight to the biological mechanisms underlying the inference results, suggesting that enzyme processivity and/or collaboration can produce the observed kinetic correlations. Our combined statistical/mathematical modeling approach expands the utility of genomic datasets and disentangles heterogeneity in methylation patterns arising from replication-associated temporal dynamics versus stable cell-to-cell differences.
Collapse
Affiliation(s)
- Luis Busto-Moner
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
- Dept. of Chemical & Biomolecular Engineering, University of California, Irvine, California, United States of America
| | - Julien Morival
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Honglei Ren
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, United States of America
| | - Arjang Fahim
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Zachary Reitz
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
| | - Timothy L. Downing
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California, United States of America
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| | - Elizabeth L. Read
- Dept. of Chemical & Biomolecular Engineering, University of California, Irvine, California, United States of America
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, Irvine, California, United States of America
| |
Collapse
|
17
|
Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC. Methylome Dynamics of Bovine Gametes and in vivo Early Embryos. Front Genet 2019; 10:512. [PMID: 31191619 PMCID: PMC6546829 DOI: 10.3389/fgene.2019.00512] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/10/2019] [Indexed: 01/12/2023] Open
Abstract
DNA methylation undergoes drastic fluctuation during early mammalian embryogenesis. The dynamics of global DNA methylation in bovine embryos, however, have mostly been studied by immunostaining. We adopted the whole genome bisulfite sequencing (WGBS) method to characterize stage-specific genome-wide DNA methylation in bovine sperm, immature oocytes, oocytes matured in vivo and in vitro, as well as in vivo developed single embryos at the 2-, 4-, 8-, and 16-cell stages. We found that the major wave of genome-wide DNA demethylation was complete by the 8-cell stage when de novo methylation became prominent. Sperm and oocytes were differentially methylated in numerous regions (DMRs), which were primarily intergenic, suggesting that these non-coding regions may play important roles in gamete specification. DMRs were also identified between in vivo and in vitro matured oocytes, suggesting environmental effects on epigenetic modifications. In addition, virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, by using RNA-seq data generated from embryos at the same developmental stages, we revealed a weak inverse correlation between gene expression and promoter methylation. This comprehensive analysis provides insight into the critical features of the bovine embryo methylome, and serves as an important reference for embryos produced in vitro, such as by in vitro fertilization and cloning. Lastly, these data can also provide a model for the epigenetic dynamics in human early embryos.
Collapse
Affiliation(s)
- Jingyue Ellie Duan
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Zongliang Carl Jiang
- School of Animal Science, AgCenter, Louisiana State University, Baton Rouge, LA, United States
| | - Fahad Alqahtani
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, United States
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xiuchun Cindy Tian
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| |
Collapse
|
18
|
Zeng Y, Amador C, Xia C, Marioni R, Sproul D, Walker RM, Morris SW, Bretherick A, Canela-Xandri O, Boutin TS, Clark DW, Campbell A, Rawlik K, Hayward C, Nagy R, Tenesa A, Porteous DJ, Wilson JF, Deary IJ, Evans KL, McIntosh AM, Navarro P, Haley CS. Parent of origin genetic effects on methylation in humans are common and influence complex trait variation. Nat Commun 2019; 10:1383. [PMID: 30918249 PMCID: PMC6437195 DOI: 10.1038/s41467-019-09301-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 02/28/2019] [Indexed: 01/11/2023] Open
Abstract
Parent-of-origin effects (POE) exist when there is differential expression of alleles inherited from the two parents. A genome-wide scan for POE on DNA methylation at 639,238 CpGs in 5,101 individuals identifies 733 independent methylation CpGs potentially influenced by POE at a false discovery rate ≤ 0.05 of which 331 had not previously been identified. Cis and trans methylation quantitative trait loci (mQTL) regulate methylation variation through POE at 54% (399/733) of the identified POE-influenced CpGs. The combined results provide strong evidence for previously unidentified POE-influenced CpGs at 171 independent loci. Methylation variation at 14 of the POE-influenced CpGs is associated with multiple metabolic traits. A phenome-wide association analysis using the POE mQTL SNPs identifies a previously unidentified imprinted locus associated with waist circumference. These results provide a high resolution population-level map for POE on DNA methylation sites, their local and distant regulators and potential consequences for complex traits.
Collapse
Affiliation(s)
- Yanni Zeng
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carmen Amador
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Charley Xia
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Riccardo Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Rosie M Walker
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew Bretherick
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Oriol Canela-Xandri
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Thibaud S Boutin
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Konrad Rawlik
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Caroline Hayward
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Reka Nagy
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Albert Tenesa
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - James F Wilson
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathryn L Evans
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Division of Psychiatry, University of Edinburgh, Edinburgh, EH10 5HF, UK
| | - Pau Navarro
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Chris S Haley
- MRC Human Genetic Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, Edinburgh, EH25 9RG, UK.
| |
Collapse
|
19
|
Miranda Furtado CL, Salomão KB, Verruma CG, Paulino Leite SB, Lopes Rios ÁF, Bialecka M, Moustakas I, Mei H, de Paz CCP, Duarte G, Chuva de Sousa Lopes SM, Ramos ES. Variation in DNA methylation in the KvDMR1 (ICR2) region in first-trimester human pregnancies. Fertil Steril 2019; 111:1186-1193. [PMID: 30922639 DOI: 10.1016/j.fertnstert.2019.01.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To investigate the levels of DNA methylation in the KvDMR1 (KvLQT1 differentially methylated region 1) in embryonic and extra-embryonic tissues. DESIGN Cross-sectional study. SETTING University medical center and clinical hospital. PATIENT(S) Embryonic and/or extraembryonic tissues (umbilical cord, chorionic villus, chorion, decidua, and/or amnion) collected from 27 first-trimester pregnancies (up to 12 weeks of gestation, single embryos) from elective abortions, extravillous trophoblasts (EVTs) from the top of individual chorionic villi, and chorionic villi from 10 normal full-term placentas collected after birth. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) DNA methylation of the KvDMR1 region evaluated using quantitative analysis of DNA methylation followed by real-time polymerase chain reaction (qAMP) and bisulfite sequencing (bis-seq) analysis. RESULT(S) The results showed variability in KvDMR1 DNA methylation in different tissues from the same pregnancy. The average of DNA methylation was not different between the embryo, umbilical cord, amnion, and chorionic villi, despite the relatively low level of methylation observed in the amnion (33.50% ± 14.48%). Chorionic villi from term placentas showed a normal methylation pattern at KvDMR1 (42.60% ± 6.08%). The normal methylation pattern at KvDMR1 in chorionic villi (as well as in EVTs) from first-trimester placentas was confirmed by bis-seq. CONCLUSION(S) Our results highlight an existing heterogeneity in DNA methylation of the KvDMR1 region during first trimester and a consistent hypomethylation in the amnion in this period of gestation.
Collapse
Affiliation(s)
- Cristiana Libardi Miranda Furtado
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil; Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | - Karina Bezerra Salomão
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Carolina Gennari Verruma
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Álvaro Fabrício Lopes Rios
- Biotechnology Laboratory, Center of Bioscience and Biotechnology, State University of North Fluminense Darcy Ribeiro, Campos dos Goitacazes, Rio de Janeiro, Brazil
| | - Monika Bialecka
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ioannis Moustakas
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Claudia Cristina Paro de Paz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil; Instituto de Zootecnia, Centro APTA de Bovinos de Corte, São Paulo, Brazil
| | - Geraldo Duarte
- Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
20
|
O'Doherty AM, Rue-Albrecht KC, Magee DA, Ahting S, Irwin RE, Hall TJ, Browne JA, Nalpas NC, Walsh CP, Gordon SV, Wojewodzic MW, MacHugh DE. The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. Sci Rep 2019; 9:1510. [PMID: 30728374 PMCID: PMC6365515 DOI: 10.1038/s41598-018-37618-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is pivotal in orchestrating gene expression patterns in various mammalian biological processes. Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. The methylomes of bAM infected with M. bovis were compared to those of non-infected bAM 24 hours post-infection (hpi). No differences in DNA methylation (CpG or non-CpG) were observed. Analysis of DNA methylation at proximal promoter regions uncovered >250 genes harbouring intermediately methylated (IM) promoters (average methylation of 33–66%). Gene ontology analysis, focusing on genes with low, intermediate or highly methylated promoters, revealed that genes with IM promoters were enriched for immune-related GO categories; this enrichment was not observed for genes in the high or low methylation groups. Targeted analysis of genes in the IM category confirmed the WGBS observation. This study is the first in cattle examining genome-wide DNA methylation at single nucleotide resolution in an important bovine cellular host-pathogen interaction model, providing evidence for IM promoter methylation in bAM.
Collapse
Affiliation(s)
- Alan Mark O'Doherty
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.
| | - Kevin Christophe Rue-Albrecht
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, Oxford, OX3 7FY, UK
| | - David Andrew Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Simone Ahting
- Institute of Molecular Medicine, Trinity College Dublin, Dublin, D08 W9RT, Ireland
| | - Rachelle Elizabeth Irwin
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA, UK
| | - Thomas Jonathan Hall
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - John Arthur Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Nicolas Claude Nalpas
- Quantitative Proteomics and Proteome Centre Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Colum Patrick Walsh
- Genomic Medicine Research Group, Biomedical Sciences Research Institute, Centre for Molecular Biosciences, University of Ulster, Coleraine, BT52 1SA, UK
| | - Stephen Vincent Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | | | - David Evan MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| |
Collapse
|
21
|
Cowley M, Skaar DA, Jima DD, Maguire RL, Hudson KM, Park SS, Sorrow P, Hoyo C. Effects of Cadmium Exposure on DNA Methylation at Imprinting Control Regions and Genome-Wide in Mothers and Newborn Children. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:037003. [PMID: 29529597 PMCID: PMC6071808 DOI: 10.1289/ehp2085] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Imprinted genes are defined by their preferential expression from one of the two parental alleles. This unique mode of gene expression is dependent on allele-specific DNA methylation profiles established at regulatory sequences called imprinting control regions (ICRs). These loci have been used as biosensors to study how environmental exposures affect methylation and transcription. However, a critical unanswered question is whether they are more, less, or equally sensitive to environmental stressors as the rest of the genome. OBJECTIVES Using cadmium exposure in humans as a model, we aimed to determine the relative sensitivity of ICRs to perturbation of methylation compared to similar, nonimprinted loci in the genome. METHODS We assayed DNA methylation genome-wide using bisulfite sequencing of 19 newborn cord blood and 20 maternal blood samples selected on the basis of maternal blood cadmium levels. Differentially methylated regions (DMRs) associated with cadmium exposure were identified. RESULTS In newborn cord blood and maternal blood, 641 and 1,945 cadmium-associated DMRs were identified, respectively. DMRs were more common at the 15 maternally methylated ICRs than at similar nonimprinted loci in newborn cord blood (p=5.64×10-8) and maternal blood (p=6.22×10-14), suggesting a higher sensitivity for ICRs to cadmium. Genome-wide, Enrichr analysis indicated that the top three functional categories for genes that overlapped DMRs in maternal blood were body mass index (BMI) (p=2.0×10-5), blood pressure (p=3.8×10-5), and body weight (p=0.0014). In newborn cord blood, the top three functional categories were BMI, atrial fibrillation, and hypertension, although associations were not significant after correction for multiple testing (p=0.098). These findings suggest that epigenetic changes may contribute to the etiology of cadmium-associated diseases. CONCLUSIONS We analyzed cord blood and maternal blood DNA methylation profiles genome-wide at nucleotide resolution in individuals selected for high and low blood cadmium levels in the first trimester. Our findings suggest that ICRs may be hot spots for perturbation by cadmium, motivating further study of these loci to investigate potential mechanisms of cadmium action. https://doi.org/10.1289/EHP2085.
Collapse
Affiliation(s)
- Michael Cowley
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- W.M. Keck Center for Behavioral Biology , North Carolina State University , Raleigh, North Carolina, USA
| | - David A Skaar
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Dereje D Jima
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University , Raleigh, North Carolina, USA
| | - Rachel L Maguire
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Kathleen M Hudson
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Sarah S Park
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Patricia Sorrow
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment and Department of Biological Sciences, North Carolina State University , Raleigh, North Carolina, USA
| |
Collapse
|
22
|
Stranger BE, Brigham LE, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber WF, Lonsdale JT, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas JA, Walters G, Washington M, Wheeler J, Bridge J, Foster BA, Gillard BM, Karasik E, Kumar R, Miklos M, Moser MT, Jewell SD, Montroy RG, Rohrer DC, Valley D, Davis DA, Mash DC, Gould SE, Guan P, Koester S, Little AR, Martin C, Moore HM, Rao A, Struewing JP, Volpi S, Hansen KD, Hickey PF, Rizzardi LF, Hou L, Liu Y, Molinie B, Park Y, Rinaldi N, Wang LB, Van Wittenberghe N, Claussnitzer M, Gelfand ET, Li Q, Linder S, Smith KS, Tsang EK, Demanelis K, Doherty JA, Jasmine F, Kibriya MG, Jiang L, Lin S, Wang M, Jian R, Li X, Chan J, Bates D, Diegel M, Halow J, Haugen E, Johnson A, Kaul R, Lee K, Maurano MT, Nelson J, Neri FJ, Sandstrom R, Fernando MS, Linke C, Oliva M, Skol A, Wu F, Akey JM, Feinberg AP, Li JB, Pierce BL, Stamatoyannopoulos JA, Tang H, Ardlie KG, Kellis M, Snyder MP, Montgomery SB. Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. Nat Genet 2017; 49:1664-1670. [PMID: 29019975 PMCID: PMC6636856 DOI: 10.1038/ng.3969] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic variants have been associated with myriad molecular phenotypes that provide new insight into the range of mechanisms underlying genetic traits and diseases. Identifying any particular genetic variant's cascade of effects, from molecule to individual, requires assaying multiple layers of molecular complexity. We introduce the Enhancing GTEx (eGTEx) project that extends the GTEx project to combine gene expression with additional intermediate molecular measurements on the same tissues to provide a resource for studying how genetic differences cascade through molecular phenotypes to impact human health.
Collapse
Affiliation(s)
- Barbara E. Stranger
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
- Center for Data Intensive Science, The University of Chicago, Chicago, IL 60637, USA
| | - Lori E. Brigham
- Washington Regional Transplant Community, Annandale, VA 22003, USA
| | - Richard Hasz
- Gift of Life Donor Program, Philadelphia, PA 19103, USA
| | | | | | | | - Gene Kopen
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | | | - John T. Lonsdale
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | - Alisa McDonald
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | | | | | | | | | - Saboor Shad
- National Disease Research Interchange, Philadelphia, PA 19103, USA
| | | | | | | | - Joseph Wheeler
- Center for Organ Recovery and Education, Pittsburgh, PA 15238, USA
| | | | - Barbara A. Foster
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Bryan M. Gillard
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Ellen Karasik
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Rachna Kumar
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Mark Miklos
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Michael T. Moser
- Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | | | | | | | - Dana Valley
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David A. Davis
- Brain Endowment Bank, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Deborah C. Mash
- Brain Endowment Bank, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Sarah E. Gould
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Ping Guan
- Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Susan Koester
- Division of Neuroscience and Basic Behavioral Science, National Institute of Mental Health, NIH, Bethesda, MD 20892, USA
| | - A. Roger Little
- National Institute on Drug Abuse, NIH, Bethesda, MD 20892, USA
| | - Casey Martin
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Helen M. Moore
- Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Abhi Rao
- Biorepositories and Biospecimen Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jeffery P. Struewing
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Simona Volpi
- Division of Genomic Medicine, National Human Genome Research Institute, Rockville, MD 20852, USA
| | - Kasper D. Hansen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Peter F. Hickey
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lindsay F. Rizzardi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lei Hou
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Yaping Liu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Benoit Molinie
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Yongjin Park
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Nicola Rinaldi
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Li B. Wang
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Nicholas Van Wittenberghe
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Melina Claussnitzer
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Technical University Munich, 8350 Freising, Germany
| | - Ellen T. Gelfand
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Linder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kevin S. Smith
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Emily K. Tsang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305, USA
| | - Kathryn Demanelis
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Jennifer A. Doherty
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Shin Lin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Meng Wang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Xiao Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joanne Chan
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Bates
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Morgan Diegel
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Jessica Halow
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Audra Johnson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Rajinder Kaul
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Kristen Lee
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Matthew T. Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jemma Nelson
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Fidencio J. Neri
- Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | | | - Marian S. Fernando
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Caroline Linke
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Meritxell Oliva
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Andrew Skol
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
- Center for Data Intensive Science, The University of Chicago, Chicago, IL 60637, USA
| | - Fan Wu
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Brandon L. Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | | | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kristin G. Ardlie
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|