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Liao Z, Zhang J, Sun S, Li Y, Xu Y, Li C, Cao J, Nie Y, Niu Z, Liu J, Lu F, Liu Z, Sun Q. Reprogramming mechanism dissection and trophoblast replacement application in monkey somatic cell nuclear transfer. Nat Commun 2024; 15:5. [PMID: 38228612 PMCID: PMC10791636 DOI: 10.1038/s41467-023-43985-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024] Open
Abstract
Somatic cell nuclear transfer (SCNT) successfully clones cynomolgus monkeys, but the efficiency remains low due to a limited understanding of the reprogramming mechanism. Notably, no rhesus monkey has been cloned through SCNT so far. Our study conducts a comparative analysis of multi-omics datasets, comparing embryos resulting from intracytoplasmic sperm injection (ICSI) with those from SCNT. Our findings reveal a widespread decrease in DNA methylation and the loss of imprinting in maternally imprinted genes within SCNT monkey blastocysts. This loss of imprinting persists in SCNT embryos cultured in-vitro until E17 and in full-term SCNT placentas. Additionally, histological examination of SCNT placentas shows noticeable hyperplasia and calcification. To address these defects, we develop a trophoblast replacement method, ultimately leading to the successful cloning of a healthy male rhesus monkey. These discoveries provide valuable insights into the reprogramming mechanism of monkey SCNT and introduce a promising strategy for primate cloning.
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Affiliation(s)
- Zhaodi Liao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jixiang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shiyu Sun
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuzhuo Li
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Yuting Xu
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Chunyang Li
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Jing Cao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Yanhong Nie
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Zhuoyue Niu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingwen Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Falong Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Liu
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China.
| | - Qiang Sun
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China.
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Sciorio R, Campos G, Tramontano L, Bulletti FM, Baldini GM, Vinciguerra M. Exploring the effect of cryopreservation in assisted reproductive technology and potential epigenetic risk. ZYGOTE 2023; 31:420-432. [PMID: 37409505 DOI: 10.1017/s0967199423000345] [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] [Indexed: 07/07/2023]
Abstract
Since the birth of the first baby by in vitro fertilization in 1978, more than 9 million children have been born worldwide using medically assisted reproductive treatments. Fertilization naturally takes place in the maternal oviduct where unique physiological conditions enable the early healthy development of the embryo. During this dynamic period of early development major waves of epigenetic reprogramming, crucial for the normal fate of the embryo, take place. Increasingly, over the past 20 years concerns relating to the increased incidence of epigenetic anomalies in general, and genomic-imprinting disorders in particular, have been raised following assisted reproduction technology (ART) treatments. Epigenetic reprogramming is particularly susceptible to environmental conditions during the periconceptional period and non-physiological conditions such as ovarian stimulation, in vitro fertilization and embryo culture, as well as cryopreservation procedure, might have the potential to independently or collectively contribute to epigenetic dysregulation. Therefore, this narrative review offers a critical reappraisal of the evidence relating to the association between embryo cryopreservation and potential epigenetic regulation and the consequences on gene expression together with long-term consequences for offspring health and wellbeing. Current literature suggests that epigenetic and transcriptomic profiles are sensitive to the stress induced by vitrification, in terms of osmotic shock, temperature and pH changes, and toxicity of cryoprotectants, it is therefore, critical to have a more comprehensive understanding and recognition of potential unanticipated iatrogenic-induced perturbations of epigenetic modifications that may or may not be a consequence of vitrification.
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Affiliation(s)
- Romualdo Sciorio
- Edinburgh Assisted Conception Programme, EFREC, Royal Infirmary of Edinburgh, UK
| | | | - Luca Tramontano
- Department of Women, Infants and Adolescents, Division of Obstetrics, Geneve University Hospitals, Boulevard de la Cluse 30, Geneve 14, Switzerland
| | - Francesco M Bulletti
- Department Obstetrics and Gynecology, University Hospital of Vaud, Lausanne, Switzerland
| | | | - Marina Vinciguerra
- Department of Biomedical Sciences and Human Oncology, Obstetrics and Gynaecology Section, University of Bari, Italy
- Clinic of Obstetrics and Gynecology 'Santa Caterina Novella', Galatina Hospital, Italy
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Sciorio R, Manna C, Fauque P, Rinaudo P. Can Cryopreservation in Assisted Reproductive Technology (ART) Induce Epigenetic Changes to Gametes and Embryos? J Clin Med 2023; 12:4444. [PMID: 37445479 DOI: 10.3390/jcm12134444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Since the birth of Louise Brown in 1978, more than nine million children have been conceived using assisted reproductive technologies (ARTs). While the great majority of children are healthy, there are concerns about the potential epigenetic consequences of gametes and embryo manipulation. In fact, during the preimplantation period, major waves of epigenetic reprogramming occur. Epigenetic reprogramming is susceptible to environmental changes induced by ovarian stimulation, in-vitro fertilization, and embryo culture, as well as cryopreservation procedures. This review summarizes the evidence relating to oocytes and embryo cryopreservation and potential epigenetic regulation. Overall, it appears that the stress induced by vitrification, including osmotic shock, temperature and pH changes, and toxicity of cryoprotectants, might induce epigenetic and transcriptomic changes in oocytes and embryos. It is currently unclear if these changes will have potential consequences for the health of future offspring.
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Affiliation(s)
- Romualdo Sciorio
- Edinburgh Assisted Conception Programme, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Claudio Manna
- Biofertility IVF and Infertility Center, 00198 Rome, Italy
| | - Patricia Fauque
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Development (GAD) INSERM UMR1231, F-21000 Dijon, France
- CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, F-21000 Dijon, France
| | - Paolo Rinaudo
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA 92037, USA
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Basak S, Duttaroy AK. Maternal PUFAs, Placental Epigenetics, and Their Relevance to Fetal Growth and Brain Development. Reprod Sci 2023; 30:408-427. [PMID: 35676498 DOI: 10.1007/s43032-022-00989-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/24/2022] [Indexed: 12/17/2022]
Abstract
Dietary polyunsaturated fatty acids (PUFAs), especially omega-3 (n-3) and n-6 long-chain (LC) PUFAs, are indispensable for the fetus' brain supplied by the placenta. Despite being highly unsaturated, n-3 LCPUFA-docosahexaenoic acid (DHA) plays a protective role as an antioxidant in the brain. Deficiency of DHA during fetal development may cause irreversible damages in neurodevelopment programming. Dietary PUFAs can impact placental structure and functions by regulating early placentation processes, such as angiogenesis. They promote remodeling of uteroplacental architecture to facilitate increased blood flow and surface area for nutrient exchange. The placenta's fatty acid transfer depends on the uteroplacental vascular development, ensuring adequate maternal circulatory fatty acids transport to fulfill the fetus' rapid growth and development requirements. Maternal n-3 PUFA deficiency predominantly leads to placental epigenetic changes than other fetal developing organs. A global shift in DNA methylation possibly transmits epigenetic instability in developing fetuses due to n-3 PUFA deficiency. Thus, an optimal level of maternal omega-3 (n-3) PUFAs may protect the placenta's structural and functional integrity and allow fetal growth by controlling the aberrant placental epigenetic changes. This narrative review summarizes the recent advances and underpins the roles of maternal PUFAs on the structure and functions of the placenta and their relevance to fetal growth and brain development.
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Affiliation(s)
- Sanjay Basak
- Molecular Biology Division, ICMR-National Institute of Nutrition, Indian Council of Medical Research, Hyderabad, India.
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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Krushkal J, Vural S, Jensen TL, Wright G, Zhao Y. Increased copy number of imprinted genes in the chromosomal region 20q11-q13.32 is associated with resistance to antitumor agents in cancer cell lines. Clin Epigenetics 2022; 14:161. [PMID: 36461044 PMCID: PMC9716673 DOI: 10.1186/s13148-022-01368-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Parent of origin-specific allelic expression of imprinted genes is epigenetically controlled. In cancer, imprinted genes undergo both genomic and epigenomic alterations, including frequent copy number changes. We investigated whether copy number loss or gain of imprinted genes in cancer cell lines is associated with response to chemotherapy treatment. RESULTS We analyzed 198 human imprinted genes including protein-coding genes and noncoding RNA genes using data from tumor cell lines from the Cancer Cell Line Encyclopedia and Genomics of Drug Sensitivity in Cancer datasets. We examined whether copy number of the imprinted genes in 35 different genome locations was associated with response to cancer drug treatment. We also analyzed associations of pretreatment expression and DNA methylation of imprinted genes with drug response. Higher copy number of BLCAP, GNAS, NNAT, GNAS-AS1, HM13, MIR296, MIR298, and PSIMCT-1 in the chromosomal region 20q11-q13.32 was associated with resistance to multiple antitumor agents. Increased expression of BLCAP and HM13 was also associated with drug resistance, whereas higher methylation of gene regions of BLCAP, NNAT, SGK2, and GNAS was associated with drug sensitivity. While expression and methylation of imprinted genes in several other chromosomal regions was also associated with drug response and many imprinted genes in different chromosomal locations showed a considerable copy number variation, only imprinted genes at 20q11-q13.32 had a consistent association of their copy number with drug response. Copy number values among the imprinted genes in the 20q11-q13.32 region were strongly correlated. They were also correlated with the copy number of cancer-related non-imprinted genes MYBL2, AURKA, and ZNF217 in that chromosomal region. Expression of genes at 20q11-q13.32 was associated with ex vivo drug response in primary tumor samples from the Beat AML 1.0 acute myeloid leukemia patient cohort. Association of the increased copy number of the 20q11-q13.32 region with drug resistance may be complex and could involve multiple genes. CONCLUSIONS Copy number of imprinted and non-imprinted genes in the chromosomal region 20q11-q13.32 was associated with cancer drug resistance. The genes in this chromosomal region may have a modulating effect on tumor response to chemotherapy.
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Affiliation(s)
- Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA.
| | - Suleyman Vural
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA.,Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | | | - George Wright
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD, 20850, USA
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Stankevičius V, Gibas P, Masiulionytė B, Gasiulė L, Masevičius V, Klimašauskas S, Vilkaitis G. Selective chemical tracking of Dnmt1 catalytic activity in live cells. Mol Cell 2022; 82:1053-1065.e8. [PMID: 35245449 PMCID: PMC8901439 DOI: 10.1016/j.molcel.2022.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/04/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022]
Abstract
Enzymatic methylation of cytosine to 5-methylcytosine in DNA is a fundamental epigenetic mechanism involved in mammalian development and disease. DNA methylation is brought about by collective action of three AdoMet-dependent DNA methyltransferases, whose catalytic interactions and temporal interplay are poorly understood. We used structure-guided engineering of the Dnmt1 methyltransferase to enable catalytic transfer of azide tags onto DNA from a synthetic cofactor analog, Ado-6-azide, in vitro. We then CRISPR-edited the Dnmt1 locus in mouse embryonic stem cells to install the engineered codon, which, following pulse internalization of the Ado-6-azide cofactor by electroporation, permitted selective azide tagging of Dnmt1-specific genomic targets in cellulo. The deposited covalent tags were exploited as “click” handles for reading adjoining sequences and precise genomic mapping of the methylation sites. The proposed approach, Dnmt-TOP-seq, enables high-resolution temporal tracking of the Dnmt1 catalysis in mammalian cells, paving the way to selective studies of other methylation pathways in eukaryotic systems. A single alanine substitution in Dnmt1 confers catalytic transfer of extended groups Electroporation permits facile delivery of AdoMet analogs into live mammalian cells Engineered Dnmt1 adds trackable azide tags at its native target sites in cellulo Dnmt-TOP-seq enables genome-wide tracking of Dnmt1 activity in live mammalian cells
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Affiliation(s)
- Vaidotas Stankevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Povilas Gibas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Bernadeta Masiulionytė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Liepa Gasiulė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania; Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Vilnius 03225, Lithuania
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.
| | - Giedrius Vilkaitis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania.
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Baulina N, Kiselev I, Favorova O. Imprinted Genes and Multiple Sclerosis: What Do We Know? Int J Mol Sci 2021; 22:1346. [PMID: 33572862 PMCID: PMC7866243 DOI: 10.3390/ijms22031346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disease of the central nervous system that arises from interplay between non-genetic and genetic risk factors. The epigenetics functions as a link between these factors, affecting gene expression in response to external influence, and therefore should be extensively studied to improve the knowledge of MS molecular mechanisms. Among others, the epigenetic mechanisms underlie the establishment of parent-of-origin effects that appear as phenotypic differences depending on whether the allele was inherited from the mother or father. The most well described manifestation of parent-of-origin effects is genomic imprinting that causes monoallelic gene expression. It becomes more obvious that disturbances in imprinted genes at the least affecting their expression do occur in MS and may be involved in its pathogenesis. In this review we will focus on the potential role of imprinted genes in MS pathogenesis.
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Affiliation(s)
- Natalia Baulina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
| | - Olga Favorova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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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: 2] [Impact Index Per Article: 0.7] [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.
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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.
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Yuan V, Hui D, Yin Y, Peñaherrera MS, Beristain AG, Robinson WP. Cell-specific characterization of the placental methylome. BMC Genomics 2021; 22:6. [PMID: 33407091 PMCID: PMC7788826 DOI: 10.1186/s12864-020-07186-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs. RESULTS The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation. CONCLUSIONS Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser ( https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/ ), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data.
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Affiliation(s)
- Victor Yuan
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Desmond Hui
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Yifan Yin
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Maria S. Peñaherrera
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Alexander G. Beristain
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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Rhon-Calderon EA, Vrooman LA, Riesche L, Bartolomei MS. The effects of Assisted Reproductive Technologies on genomic imprinting in the placenta. Placenta 2019; 84:37-43. [PMID: 30871810 DOI: 10.1016/j.placenta.2019.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 12/29/2022]
Abstract
The placenta is a complex and poorly understood organ, which serves as the connection between the mother and the developing fetus. Genomic imprinting, defined as a regulatory process resulting in the expression of a gene in a parent-of-origin-specific manner, plays an important role in fetal development and placental function. Disturbances that occur during the establishment and maintenance of imprinting could compromise the placenta and fetus, and ultimately, offspring health. Assisted Reproductive Technologies (ART) have been widely used to overcome infertility, however experimental studies have shown that ART procedures affect placentation and the expression of imprinted genes. Here we briefly review the role of imprinted genes in placental development and the evidence from mouse and human studies suggesting ART disrupts imprinted gene regulation in the placenta.
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Affiliation(s)
- Eric A Rhon-Calderon
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA
| | - Lisa A Vrooman
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA
| | - Laren Riesche
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA; Department of Family and Community Health, Claire M. Fagin School of Nursing, University of Pennsylvania, Philadelphia, PA, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Smilow Center for Translational Research, 3400 Civic Center Blvd, Bldg 421, Philadelphia, PA, 19104-6058, USA.
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Human placental methylome in the interplay of adverse placental health, environmental exposure, and pregnancy outcome. PLoS Genet 2019; 15:e1008236. [PMID: 31369552 PMCID: PMC6675049 DOI: 10.1371/journal.pgen.1008236] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The placenta is the interface between maternal and fetal circulations, integrating maternal and fetal signals to selectively regulate nutrient, gas, and waste exchange, as well as secrete hormones. In turn, the placenta helps create the in utero environment and control fetal growth and development. The unique epigenetic profile of the human placenta likely reflects its early developmental separation from the fetus proper and its role in mediating maternal–fetal exchange that leaves it open to a range of exogenous exposures in the maternal circulation. In this review, we cover recent advances in DNA methylation in the context of placental function and development, as well as the interaction between the pregnancy and the environment.
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12
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Lorgen-Ritchie M, Murray AD, Ferguson-Smith AC, Richards M, Horgan GW, Phillips LH, Hoad G, Gall I, Harrison K, McNeill G, Ito M, Haggarty P. Imprinting methylation in SNRPN and MEST1 in adult blood predicts cognitive ability. PLoS One 2019; 14:e0211799. [PMID: 30707743 PMCID: PMC6358095 DOI: 10.1371/journal.pone.0211799] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/21/2019] [Indexed: 01/01/2023] Open
Abstract
Genomic imprinting is important for normal brain development and aberrant imprinting has been associated with impaired cognition. We studied the imprinting status in selected imprints (H19, IGF2, SNRPN, PEG3, MEST1, NESPAS, KvDMR, IG-DMR and ZAC1) by pyrosequencing in blood samples from longitudinal cohorts born in 1936 (n = 485) and 1921 (n = 223), and anterior hippocampus, posterior hippocampus, periventricular white matter, and thalamus from brains donated to the Aberdeen Brain Bank (n = 4). MEST1 imprint methylation was related to childhood cognitive ability score (-0.416 95% CI -0.792,-0.041; p = 0.030), with the strongest effect evident in males (-0.929 95% CI -1.531,-0.326; p = 0.003). SNRPN imprint methylation was also related to childhood cognitive ability (+0.335 95%CI 0.008,0.663; p = 0.045). A significant association was also observed for SNRPN methylation and adult crystallised cognitive ability (+0.262 95%CI 0.007,0.517; p = 0.044). Further testing of significant findings in a second cohort from the same region, but born in 1921, resulted in similar effect sizes and greater significance when the cohorts were combined (MEST1; -0.371 95% CI -0.677,-0.065; p = 0.017; SNRPN; +0.361 95% CI 0.079,0.643; p = 0.012). For SNRPN and MEST1 and four other imprints the methylation levels in blood and in the five brain regions were similar. Methylation of the paternally expressed, maternally methylated genes SNRPN and MEST1 in adult blood was associated with cognitive ability in childhood. This is consistent with the known importance of the SNRPN containing 15q11-q13 and the MEST1 containing 7q31-34 regions in cognitive function. These findings, and their sex specific nature in MEST1, point to new mechanisms through which complex phenotypes such as cognitive ability may be inherited. These mechanisms are potentially relevant to both the heritable and non-heritable components of cognitive ability. The process of epigenetic imprinting—within SNRPN and MEST1 in particular—and the factors that influence it, are worthy of further study in relation to the determinants of cognitive ability.
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Affiliation(s)
- Marlene Lorgen-Ritchie
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Marcus Richards
- MRC Unit for Lifelong Health and Ageing, University College London, London, United Kingdom
| | - Graham W. Horgan
- Biomathematics and Statistics Scotland, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Gwen Hoad
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Ishbel Gall
- Department of Pathology, N.H.S. Grampian, Aberdeen, United Kingdom
| | - Kristina Harrison
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Geraldine McNeill
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Mitsuteru Ito
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Paul Haggarty
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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13
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Lorgen-Ritchie M, Murray AD, Ferguson-Smith AC, Richards M, Horgan GW, Phillips LH, Hoad G, Gall I, Harrison K, McNeill G, Ito M, Haggarty P. Imprinting methylation in SNRPN and MEST1 in adult blood predicts cognitive ability. PLoS One 2019; 14:e0211799. [PMID: 30707743 PMCID: PMC6358095 DOI: 10.1371/journal.pone.0211799 10.1371/journal.pone.0215422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genomic imprinting is important for normal brain development and aberrant imprinting has been associated with impaired cognition. We studied the imprinting status in selected imprints (H19, IGF2, SNRPN, PEG3, MEST1, NESPAS, KvDMR, IG-DMR and ZAC1) by pyrosequencing in blood samples from longitudinal cohorts born in 1936 (n = 485) and 1921 (n = 223), and anterior hippocampus, posterior hippocampus, periventricular white matter, and thalamus from brains donated to the Aberdeen Brain Bank (n = 4). MEST1 imprint methylation was related to childhood cognitive ability score (-0.416 95% CI -0.792,-0.041; p = 0.030), with the strongest effect evident in males (-0.929 95% CI -1.531,-0.326; p = 0.003). SNRPN imprint methylation was also related to childhood cognitive ability (+0.335 95%CI 0.008,0.663; p = 0.045). A significant association was also observed for SNRPN methylation and adult crystallised cognitive ability (+0.262 95%CI 0.007,0.517; p = 0.044). Further testing of significant findings in a second cohort from the same region, but born in 1921, resulted in similar effect sizes and greater significance when the cohorts were combined (MEST1; -0.371 95% CI -0.677,-0.065; p = 0.017; SNRPN; +0.361 95% CI 0.079,0.643; p = 0.012). For SNRPN and MEST1 and four other imprints the methylation levels in blood and in the five brain regions were similar. Methylation of the paternally expressed, maternally methylated genes SNRPN and MEST1 in adult blood was associated with cognitive ability in childhood. This is consistent with the known importance of the SNRPN containing 15q11-q13 and the MEST1 containing 7q31-34 regions in cognitive function. These findings, and their sex specific nature in MEST1, point to new mechanisms through which complex phenotypes such as cognitive ability may be inherited. These mechanisms are potentially relevant to both the heritable and non-heritable components of cognitive ability. The process of epigenetic imprinting-within SNRPN and MEST1 in particular-and the factors that influence it, are worthy of further study in relation to the determinants of cognitive ability.
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Affiliation(s)
- Marlene Lorgen-Ritchie
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Marcus Richards
- MRC Unit for Lifelong Health and Ageing, University College London, London, United Kingdom
| | - Graham W. Horgan
- Biomathematics and Statistics Scotland, University of Aberdeen, Aberdeen, United Kingdom
| | | | - Gwen Hoad
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Ishbel Gall
- Department of Pathology, N.H.S. Grampian, Aberdeen, United Kingdom
| | - Kristina Harrison
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
| | - Geraldine McNeill
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Mitsuteru Ito
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Paul Haggarty
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, United Kingdom
- * E-mail:
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14
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Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. PLoS Genet 2018; 14:e1007872. [PMID: 30586358 PMCID: PMC6324821 DOI: 10.1371/journal.pgen.1007872] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/08/2019] [Accepted: 12/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.
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MESH Headings
- Cells, Cultured
- Chromosome Painting/methods
- Chromosome Structures/chemistry
- Chromosome Structures/genetics
- Chromosome Structures/ultrastructure
- Chromosome Walking/methods
- Chromosomes, Human, Pair 19/chemistry
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/ultrastructure
- Female
- Fluorescent Dyes
- Humans
- Imaging, Three-Dimensional
- In Situ Hybridization, Fluorescence/methods
- Male
- Models, Genetic
- Oligonucleotide Probes
- Pedigree
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Affiliation(s)
- Guy Nir
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Irene Farabella
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cynthia Pérez Estrada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Carl G. Ebeling
- Bruker Nano Inc., Salt Lake City, Utah, United States of America
| | - Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Hiroshi M. Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - S. Dean Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Son C. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shyamtanu Chattoraj
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jumana AlHaj Abed
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nuno M. C. Martins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huy Q. Nguyen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sheikh Russell
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Neva C. Durand
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
| | - Suhas S. P. Rao
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paula Soler-Vila
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | | | | | - Jeff A. Stuckey
- Bruker Nano Inc., Middleton, Wisconsin, United States of America
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, United States of America
- Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, Texas, United States of America
| | - Marc A. Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
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15
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A genome-wide search for new imprinted genes in the human placenta identifies DSCAM as the first imprinted gene on chromosome 21. Eur J Hum Genet 2018; 27:49-60. [PMID: 30206355 DOI: 10.1038/s41431-018-0267-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 11/08/2022] Open
Abstract
We identified, through a genome-wide search for new imprinted genes in the human placenta, DSCAM (Down Syndrome Cellular Adhesion Molecule) as a paternally expressed imprinted gene. Our work revealed the presence of a Differentially Methylated Region (DMR), located within intron 1 that might regulate the imprinting in the region. This DMR showed a maternal allele methylation, compatible with its paternal expression. We showed that DSCAM is present in endothelial cells and the syncytiotrophoblast layer of the human placenta. In mouse, Dscam expression is biallelic in foetal brain and placenta excluding any possible imprinting in these tissues. This gene encodes a cellular adhesion molecule mainly known for its role in neurone development but its function in the placenta remains unclear. We report here the first imprinted gene located on human chromosome 21 with potential clinical implications.
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16
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Haffner MC, Esopi DM, Chaux A, Gürel M, Ghosh S, Vaghasia AM, Tsai H, Kim K, Castagna N, Lam H, Hicks J, Wyhs N, Biswal Shinohara D, Hurley PJ, Simons BW, Schaeffer EM, Lotan TL, Isaacs WB, Netto GJ, De Marzo AM, Nelson WG, An SS, Yegnasubramanian S. AIM1 is an actin-binding protein that suppresses cell migration and micrometastatic dissemination. Nat Commun 2017; 8:142. [PMID: 28747635 PMCID: PMC5529512 DOI: 10.1038/s41467-017-00084-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/01/2017] [Indexed: 01/05/2023] Open
Abstract
A defining hallmark of primary and metastatic cancers is the migration and invasion of malignant cells. These invasive properties involve altered dynamics of the cytoskeleton and one of its major structural components β-actin. Here we identify AIM1 (absent in melanoma 1) as an actin-binding protein that suppresses pro-invasive properties in benign prostate epithelium. Depletion of AIM1 in prostate epithelial cells increases cytoskeletal remodeling, intracellular traction forces, cell migration and invasion, and anchorage-independent growth. In addition, decreased AIM1 expression results in increased metastatic dissemination in vivo. AIM1 strongly associates with the actin cytoskeleton in prostate epithelial cells in normal tissues, but not in prostate cancers. In addition to a mislocalization of AIM1 from the actin cytoskeleton in invasive cancers, advanced prostate cancers often harbor AIM1 deletion and reduced expression. These findings implicate AIM1 as a key suppressor of invasive phenotypes that becomes dysregulated in primary and metastatic prostate cancer. Invasion of malignant cells involves changes in cytoskeleton dynamics. Here the authors identify absent in melanoma 1 as an actin binding protein and show that it regulates cytoskeletal remodeling and cell migration in prostate epithelial cells, acting as a metastatic suppressor in cancer cells.
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Affiliation(s)
- Michael C Haffner
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - David M Esopi
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Alcides Chaux
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Office of Scientific Research, Norte University, Asunción,, Paraguay
| | - Meltem Gürel
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Susmita Ghosh
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Ajay M Vaghasia
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Harrison Tsai
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Kunhwa Kim
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Nicole Castagna
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hong Lam
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jessica Hicks
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicolas Wyhs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | | | - Paula J Hurley
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Brian W Simons
- Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Edward M Schaeffer
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - William B Isaacs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - George J Netto
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Angelo M De Marzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - William G Nelson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Steven S An
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.,Johns Hopkins Physical Sciences in Oncology Center, Johns Hopkins University, Baltimore, MD, USA
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA. .,Department of Pathology, Johns Hopkins University, Baltimore, MD, USA. .,Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA. .,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, USA. .,Johns Hopkins Physical Sciences in Oncology Center, Johns Hopkins University, Baltimore, MD, USA.
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17
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A complex association between DNA methylation and gene expression in human placenta at first and third trimesters. PLoS One 2017; 12:e0181155. [PMID: 28704530 PMCID: PMC5509291 DOI: 10.1371/journal.pone.0181155] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022] Open
Abstract
The human placenta is a maternal-fetal organ essential for normal fetal development and maternal health. During pregnancy, the placenta undergoes many structural and functional changes in response to fetal needs and environmental exposures. Previous studies have demonstrated widespread epigenetic and gene expression changes from early to late pregnancy. However, on the global level, how DNA methylation changes impact on gene expression in human placenta is not yet well understood. We performed DNA methylome analysis by reduced representation bisulfite sequencing (RRBS) and gene expression analysis by RNA-Seq for both first and third trimester human placenta tissues. From first to third trimester, 199 promoters (corresponding to 189 genes) and 2,297 gene bodies were differentially methylated, with a clear dominance of hypermethylation (96.8% and 93.0% for promoters and gene bodies, respectively). A total of 2,447 genes were differentially expressed, of which 77.2% were down-regulated. Gene ontology analysis using differentially expressed genes were enriched for cell cycle and immune response functions. The correlation between DNA methylation and gene expression was non-linear and complex, depending on the genomic context (promoter or gene body) and gene expression levels. A wide range of DNA methylation and gene expression changes were observed at different gestational ages. The non-linear association between DNA methylation and gene expression indicates that epigenetic regulation of placenta development is more complex than previously envisioned.
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18
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Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B. Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biol 2017. [PMID: 28629478 PMCID: PMC5477265 DOI: 10.1186/s13059-017-1250-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS). Sequence variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistically linked to mQTLs and hap-ASM. Identifying these sites can point to disease-associated transcriptional pathways, with implications for targeted treatment and prevention.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Alyssa Shearer
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neurobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Taub Institute for Research on Alzheimer's disease and the Aging Brain, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
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19
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Bar S, Schachter M, Eldar-Geva T, Benvenisty N. Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells. Cell Rep 2017; 19:957-968. [DOI: 10.1016/j.celrep.2017.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/01/2017] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
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20
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Placental expression of DNA methyltransferase 1 (DNMT1): Gender-specific relation with human placental growth. Placenta 2016; 48:119-125. [DOI: 10.1016/j.placenta.2016.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 01/31/2023]
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21
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Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T. Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. Am J Hum Genet 2016; 99:1045-1058. [PMID: 27843122 DOI: 10.1016/j.ajhg.2016.08.021] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022] Open
Abstract
DNA methylation is globally reprogrammed after fertilization, and as a result, the parental genomes have similar DNA-methylation profiles after implantation except at the germline differentially methylated regions (gDMRs). We and others have previously shown that human blastocysts might contain thousands of transient maternally methylated gDMRs (transient mDMRs), whose maternal methylation is lost in embryonic tissues after implantation. In this study, we performed genome-wide allelic DNA methylation analyses of purified trophoblast cells from human placentas and, surprisingly, found that more than one-quarter of the transient-in-embryo mDMRs maintained their maternally biased DNA methylation. RNA-sequencing-based allelic expression analyses revealed that some of the placenta-specific mDMRs were associated with expression of imprinted genes (e.g., TIGAR, SLC4A7, PROSER2-AS1, and KLHDC10), and three imprinted gene clusters were identified. This approach also identified some X-linked gDMRs. Comparisons of the data with those from other mammals revealed that genomic imprinting in the placenta is highly variable. These findings highlight the incomplete erasure of germline DNA methylation in the human placenta; understanding this erasure is important for understanding normal placental development and the pathogenesis of developmental disorders with imprinting effects.
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22
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Benetatos L, Vartholomatos G. On the potential role of DNMT1 in acute myeloid leukemia and myelodysplastic syndromes: not another mutated epigenetic driver. Ann Hematol 2016; 95:1571-82. [PMID: 26983918 DOI: 10.1007/s00277-016-2636-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
DNA methylation is the most common epigenetic modification in the mammalian genome. DNA methylation is governed by the DNA methyltransferases mainly DNMT1, DNMT3A, and DNMT3B. DNMT1 methylates hemimethylated DNA ensuring accurate DNA methylation maintenance. DNMT1 is involved in the proper differentiation of hematopoietic stem cells (HSCs) through the interaction with effector molecules. DNMT1 is deregulated in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) as early as the leukemic stem cell stage. Through the interaction with fundamental transcription factors, non-coding RNAs, fusion oncogenes and by modulating core members of signaling pathways, it can affect leukemic cells biology. DNMT1 action might be also catalytic-independent highlighting a methylation-independent mode of action. In this review, we have gathered some current facts of DNMT1 role in AML and MDS and we also propose some perspectives for future studies.
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Novakovic B, Napier CE, Vryer R, Dimitriadis E, Manuelpillai U, Sharkey A, Craig JM, Reddel RR, Saffery R. DNA methylation mediated up-regulation of TERRA non-coding RNA is coincident with elongated telomeres in the human placenta. Mol Hum Reprod 2016; 22:791-799. [PMID: 27604461 DOI: 10.1093/molehr/gaw053] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION What factors regulate elongated telomere length in the human placenta? SUMMARY ANSWER Hypomethylation of TERRA promoters in the human placenta is associated with high TERRA expression, however, no clear mechanistic link between these phenomena and elongated telomere length in the human placenta was found. WHAT IS KNOWN ALREADY Human placenta tissue and trophoblasts show longer telomere lengths compared to gestational age-matched somatic cells. However, telomerase (hTERT) expression and activity in the placenta is low, suggesting a role for an alternative lengthening of telomeres (ALT). While ALT is observed in 10-15% of human cancers and in some mouse stem cells, ALT has never been reported in non-cancerous human tissues. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Human term placental tissue and matched cord blood mononuclear cells (CBMCs) were collected as part of the Peri/Postnatal Epigenetic Twins study (PETS). In addition, first trimester placental villi, purified cytotrophoblasts, choriocarcinoma cell lines and a panel of ALT-positive cancer cell lines were tested. Telomere length was determined using the Terminal Restriction Fragment (TRF) assay and a relative quantitative PCR method. DNA methylation levels at several CpG rich subtelomeric TERRA promoters were determined using bisulfite conversion and the SEQUENOM EpiTYPER platform. Expression of TERRA and hTERT was determined using quantitative RT-PCR. ALT was assessed using the C-circle assay (CCA). MAIN RESULTS AND THE ROLE OF CHANCE The human placenta tissue and purified first trimester trophoblasts showed low subtelomeric (TERRA) DNA methylation compared to matched CBMCs and other somatic cells. Interestingly placental TERRA methylation was lower than ALT-cancer cell lines, previously reported to be hypomethylated at these loci. Low TERRA methylation was associated with higher expression of TERRA RNA in placenta compared to matched CBMCs. Detectable levels of C-circles were observed in first trimester placental villi, but not term placenta, suggesting that the ALT mechanism may be active in specific placental cells in early gestation. C-circle analysis of purified first trimester trophoblasts and ALT-associated PML bodies (APB) staining of first trimester villi cross-sections failed to identify this specific cell type population. LIMITATIONS, REASONS FOR CAUTION While first trimester villi showed detectable levels of C-circles, these levels were very low compared with those observed in ALT-positive tumours and cell lines. This is consistent with a small sub-population of ALT-positive cells but this requires further investigation. Finally, no mechanistic link was established between TERRA DNA methylation, the presence of C-circles and longer telomere length. WIDER IMPLICATIONS OF THE FINDINGS Given the previously described role of TERRA ncRNA as a negative regulator of telomerase, the finding of elevated TERRA and long telomeres is counterintutive. ALT as a mechanism for telomere length maintenance has only been reported in certain human cancers, and recently in mouse embryonic stem cells and embryos. As with many aspects of cancer, it appears that ALT activity in tumours may be the inappropriate activation of a pathway found in very specific cell types in human development. Our data are the first supportive evidence for ALT in a non-cancerous human tissue, a result that requires further investigation and replication. The level of TERRA methylation in the human placenta is significantly lower than found in ALT cancer cell lines and somatic cells, raising the possibility of a novel mechanism in maintaining low methylation at subtelomeric regions. LARGE SCALE DATA Not applicable. STUDY FUNDING AND COMPETING INTERESTS This study was supported by NHMRC early career fellowship (B.N.), NHMRC Senior Research Fellowship (R.S.) and the Victoria Government Infrastructure Grant. R.R. holds a patent for the C-circle assay. No other conflicts declared.
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Affiliation(s)
- Boris Novakovic
- Murdoch Childrens Research Institute-Cancer and Disease Epigenetics, Royal Children's Hospital Flemington Road, Parkville, Melbourne, Victoria 3052, Australia
| | - Christine E Napier
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Regan Vryer
- Murdoch Childrens Research Institute-Cancer and Disease Epigenetics, Royal Children's Hospital Flemington Road, Parkville, Melbourne, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Parkville VIC 305 2
| | - Eva Dimitriadis
- Embryo Implantation Laboratory, Hudson Institute for Medical Research, Monash University, Clayton VIC 3168, Australia
| | - Ursula Manuelpillai
- Pregnancy Research Centre, Department of Perinatal Medicine, Royal Women's Hospital , Parkville, Victoria 3052, Australia.,Centre for Genetic Diseases, Hudson Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
| | - Andrew Sharkey
- Department of Pathology and Centre for Trophoblast Research, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Jeffrey M Craig
- Department of Paediatrics, University of Melbourne, Parkville VIC 305 2.,Early Life Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital , Parkville VIC 3052, Australia
| | - Roger R Reddel
- Cancer Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute-Cancer and Disease Epigenetics, Royal Children's Hospital Flemington Road, Parkville, Melbourne, Victoria 3052, Australia .,Department of Paediatrics, University of Melbourne, Parkville VIC 305 2
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Lesch BJ, Silber SJ, McCarrey JR, Page DC. Parallel evolution of male germline epigenetic poising and somatic development in animals. Nat Genet 2016; 48:888-94. [PMID: 27294618 DOI: 10.1038/ng.3591] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
Changes in gene regulation frequently underlie changes in morphology during evolution, and differences in chromatin state have been linked with changes in anatomical structure and gene expression across evolutionary time. Here we assess the relationship between evolution of chromatin state in germ cells and evolution of gene regulatory programs governing somatic development. We examined the poised (H3K4me3/H3K27me3 bivalent) epigenetic state in male germ cells from five mammalian and one avian species. We find that core genes poised in germ cells from multiple amniote species are ancient regulators of morphogenesis that sit at the top of transcriptional hierarchies controlling somatic tissue development, whereas genes that gain poising in germ cells from individual species act downstream of core poised genes during development in a species-specific fashion. We propose that critical regulators of animal development gained an epigenetically privileged state in germ cells, manifested in amniotes by H3K4me3/H3K27me3 poising, early in metazoan evolution.
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Affiliation(s)
| | - Sherman J Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, Missouri, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, USA
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25
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Pervjakova N, Kasela S, Morris AP, Kals M, Metspalu A, Lindgren CM, Salumets A, Mägi R. Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues. Epigenomics 2016; 8:789-99. [PMID: 27004446 PMCID: PMC5066126 DOI: 10.2217/epi.16.8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 03/03/2016] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is an epigenetic feature characterized by parent-specific monoallelic gene expression. The aim of this study was to compare the DNA methylation status of imprinted genes and imprinting control regions (ICRs), harboring differentially methylated regions (DMRs) in a comprehensive panel of 18 somatic tissues. The germline DMRs analyzed were divided into ubiquitously imprinted and placenta-specific DMRs, which show identical and different methylation imprints in adult somatic and placental tissues, respectively. We showed that imprinted genes and ICR DMRs maintain methylation patterns characterized by intermediate methylation levels in somatic tissues, which are pronounced in a specific region of the promoter area, located 200-1500 bp from the transcription start site. This intermediate methylation is concordant with gene expression from a single unmethylated allele and silencing of a reciprocal parental allele through DNA methylation. The only exceptions were seen for ICR DMRs of placenta-specific imprinted genes, which showed low levels of methylation, suggesting that these genes escape parent-specific epigenetic regulation in somatic tissues.
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Affiliation(s)
- Natalia Pervjakova
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- National Institute for Health & Welfare, University of Helsinki, Helsinki FI-00271, Finland
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Silva Kasela
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GA, UK
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu 50409, Estonia
| | - Andres Metspalu
- Department of Biotechnology, Institute of Molecular & Cell Biology, University of Tartu, Tartu 51010, Estonia
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Big Data Institute, University of Oxford, Oxford, OX3 7BN, UK
- Broad Institute of the Massachusetts Institute of Technology & Harvard University, Cambridge, MA 02142, USA
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu 50410, Estonia
- Department of Obstetrics & Gynecology, University of Tartu, Tartu 51014, Estonia
- Institute of Bio- & Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
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26
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Bianco-Miotto T, Mayne BT, Buckberry S, Breen J, Rodriguez Lopez CM, Roberts CT. Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction 2016; 152:R23-30. [PMID: 27026712 PMCID: PMC5064761 DOI: 10.1530/rep-16-0014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/29/2016] [Indexed: 12/20/2022]
Abstract
Epigenetic modifications, and particularly DNA methylation, have been studied in many tissues, both healthy and diseased, and across numerous developmental stages. The placenta is the only organ that has a transient life of 9 months and undergoes rapid growth and dynamic structural and functional changes across gestation. Additionally, the placenta is unique because although developing within the mother, its genome is identical to that of the foetus. Given these distinctive characteristics, it is not surprising that the epigenetic landscape affecting placental gene expression may be different to that in other healthy tissues. However, the role of epigenetic modifications, and particularly DNA methylation, in placental development remains largely unknown. Of particular interest is the fact that the placenta is the most hypomethylated human tissue and is characterized by the presence of large partially methylated domains (PMDs) containing silenced genes. Moreover, how and why the placenta is hypomethylated and what role DNA methylation plays in regulating placental gene expression across gestation are poorly understood. We review genome-wide DNA methylation studies in the human placenta and highlight that the different cell types that make up the placenta have very different DNA methylation profiles. Summarizing studies on DNA methylation in the placenta and its relationship with pregnancy complications are difficult due to the limited number of studies available for comparison. To understand the key steps in placental development and hence what may be perturbed in pregnancy complications requires large-scale genome-wide DNA methylation studies coupled with transcriptome analyses.
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Affiliation(s)
- Tina Bianco-Miotto
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin T Mayne
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical ResearchThe University of Western Australia, Crawley, Western Australia, Australia Plant Energy BiologyARC Centre of Excellence, The University of Western Australia, Crawley, Western Australia, Australia
| | - James Breen
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia Bioinformatics HubUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Carlos M Rodriguez Lopez
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Claire T Roberts
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
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27
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Hanna CW, Peñaherrera MS, Saadeh H, Andrews S, McFadden DE, Kelsey G, Robinson WP. Pervasive polymorphic imprinted methylation in the human placenta. Genome Res 2016; 26:756-67. [PMID: 26769960 PMCID: PMC4889973 DOI: 10.1101/gr.196139.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 01/07/2016] [Indexed: 01/19/2023]
Abstract
The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are established in the germline and maintained after fertilization. There are a large number of germline DMRs that have not yet been associated with imprinting, and their function in development is unknown. In this study, we developed a genome-wide approach to identify novel imprinted DMRs in the human placenta and investigated the dynamics of these imprinted DMRs during development in somatic and extraembryonic tissues. DNA methylation was evaluated using the Illumina HumanMethylation450 array in 134 human tissue samples, publicly available reduced representation bisulfite sequencing in the human embryo and germ cells, and targeted bisulfite sequencing in term placentas. Forty-three known and 101 novel imprinted DMRs were identified in the human placenta by comparing methylation between diandric and digynic triploid conceptions in addition to female and male gametes. Seventy-two novel DMRs showed a pattern consistent with placental-specific imprinting, and this monoallelic methylation was entirely maternal in origin. Strikingly, these DMRs exhibited polymorphic imprinted methylation between placental samples. These data suggest that imprinting in human development is far more extensive and dynamic than previously reported and that the placenta preferentially maintains maternal germline-derived DNA methylation.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Maria S Peñaherrera
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Deborah E McFadden
- Department of Pathology, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada; Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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28
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Monk D. Genomic imprinting in the human placenta. Am J Obstet Gynecol 2015; 213:S152-62. [PMID: 26428495 DOI: 10.1016/j.ajog.2015.06.032] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 12/22/2022]
Abstract
With the launch of the National Institute of Child Health and Human Development/National Institutes of Health Human Placenta Project, the anticipation is that this often-overlooked organ will be the subject of much intense research. Compared with somatic tissues, the cells of the placenta have a unique epigenetic profile that dictates its transcription patterns, which when disturbed may be associated with adverse pregnancy outcomes. One major class of genes that is dependent on strict epigenetic regulation in the placenta is subject to genomic imprinting, the parent-of-origin-dependent monoallelic gene expression. This review discusses the differences in allelic expression and epigenetic profiles of imprinted genes that are identified between different species, which reflect the continuous evolutionary adaption of this form of epigenetic regulation. These observations divulge that placenta-specific imprinted gene that is reliant on repressive histone signatures in mice are unlikely to be imprinted in humans, whereas intense methylation profiling in humans has uncovered numerous maternally methylated regions that are restricted to the placenta that are not conserved in mice. Imprinting has been proposed to be a mechanism that regulates parental resource allocation and ultimately can influence fetal growth, with the placenta being the key in this process. Furthermore, I discuss the developmental dynamics of both classic and transient placenta-specific imprinting and examine the evidence for an involvement of these genes in intrauterine growth restriction and placenta-associated complications. Finally, I focus on examples of genes that are regulated aberrantly in complicated pregnancies, emphasizing their application as pregnancy-related disease biomarkers to aid the diagnosis of at-risk pregnancies early in gestation.
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Affiliation(s)
- David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain.
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29
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Januar V, Desoye G, Novakovic B, Cvitic S, Saffery R. Epigenetic regulation of human placental function and pregnancy outcome: considerations for causal inference. Am J Obstet Gynecol 2015; 213:S182-96. [PMID: 26428498 DOI: 10.1016/j.ajog.2015.07.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetic mechanisms, often defined as regulating gene activity independently of underlying DNA sequence, are crucial for healthy development. The sum total of epigenetic marks within a cell or tissue (the epigenome) is sensitive to environmental influence, and disruption of the epigenome in utero has been associated with adverse pregnancy outcomes. Not surprisingly, given its multifaceted functions and important role in regulating pregnancy outcome, the placenta shows unique epigenetic features. Interestingly however, many of these are only otherwise seen in human malignancy (the pseudomalignant placental epigenome). Epigenetic variation in the placenta is now emerging as a candidate mediator of environmental influence on placental functioning and a key regulator of pregnancy outcome. However, replication of findings is generally lacking, most likely due to small sample sizes and a lack of standardization of analytical approaches. Defining DNA methylation "signatures" in the placenta associated with maternal and fetal outcomes offers tremendous potential to improve pregnancy outcomes, but care must be taken in interpretation of findings. Future placental epigenetic research would do well to address the issues present in epigenetic epidemiology more generally, including careful consideration of sample size, potentially confounding factors, issues of tissue heterogeneity, reverse causation, and the role of genetics in modulating epigenetic profile. The importance of animal or in vitro models in establishing a functional role of epigenetic variation identified in human beings, which is key to establishing causation, should not be underestimated.
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Affiliation(s)
- Vania Januar
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Boris Novakovic
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Silvija Cvitic
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Pediatrics, University of Melbourne, Parkville, Australia.
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30
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Harrison K, Hoad G, Scott P, Simpson L, Horgan GW, Smyth E, Heys SD, Haggarty P. Breast cancer risk and imprinting methylation in blood. Clin Epigenetics 2015; 7:92. [PMID: 26347357 PMCID: PMC4560070 DOI: 10.1186/s13148-015-0125-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 08/17/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Altered DNA methylation of imprinted genes has been implicated in a range of cancers. Imprinting is established early in development, and some are maintained throughout the life course in multiple tissues, providing a plausible mechanism linking known early life factors to cancer risk. This study investigated methylation status of seven imprinted differentially methylated regions-PLAGL1/ZAC1, H19-ICR1, IGF2-DMR2, KvDMR-ICR2, RB1, SNRPN-DMR1 and PEG3-in blood samples from 189 women with the most common type of invasive breast cancer (invasive ductal carcinoma-IDC), 41 women with in situ breast cancer (ductal carcinoma in situ-DCIS) and 363 matched disease-free controls. RESULTS There was no evidence that imprinted gene methylation levels varied with age (between 25 and 87 years old), weight or height. Higher PEG3 methylation was associated with an elevated risk of IDC (odds ratio (OR) 1.065; 95 % confidence interval (CI) 1.002, 1.132; p = 0.042) and DCIS (OR 1.139; 95 % CI 1.027, 1.263; p = 0.013). The effect was stronger when in situ and invasive breast cancer were combined (OR 1.079; 95 % CI 1.020, 1.142; p = 0.008). DCIS breast cancer risk increased with higher KvDMR-ICR2 methylation (OR 1.395; 95 % CI 1.190, 1.635; p < 0.001) and lower PLAGL1/ZAC1 methylation (OR 0.905; 95 % CI 0.833, 0.982; p = 0.017). In a combined model, only KvDMR-ICR2 methylation remained significantly associated. CONCLUSIONS These findings may help to improve our understanding of the aetiology of breast cancer and the importance of early life factors in particular. Imprinting methylation status also has the potential to contribute to the development of improved screening and treatment strategies for women with, or at risk of, breast cancer.
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Affiliation(s)
- Kristina Harrison
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
| | - Gwen Hoad
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
| | - Paula Scott
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
| | - Louise Simpson
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, University Medical Buildings, Foresterhill, Aberdeen, UK
| | | | - Elizabeth Smyth
- Aberdeen Royal Infirmary, Ward 308, Foresterhill, Aberdeen, UK
| | - Steven D Heys
- Division of Applied Medicine, School of Medicine and Dentistry, University of Aberdeen, University Medical Buildings, Foresterhill, Aberdeen, UK
| | - Paul Haggarty
- Division of Lifelong Health, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen, UK
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Metsalu T, Viltrop T, Tiirats A, Rajashekar B, Reimann E, Kõks S, Rull K, Milani L, Acharya G, Basnet P, Vilo J, Mägi R, Metspalu A, Peters M, Haller-Kikkatalo K, Salumets A. Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta. Epigenetics 2015; 9:1397-409. [PMID: 25437054 DOI: 10.4161/15592294.2014.970052] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Given the possible critical importance of placental gene imprinting and random monoallelic expression on fetal and infant health, most of those genes must be identified, in order to understand the risks that the baby might meet during pregnancy and after birth. Therefore, the aim of the current study was to introduce a workflow and tools for analyzing imprinted and random monoallelic gene expression in human placenta, by applying whole-transcriptome (WT) RNA sequencing of placental tissue and genotyping of coding DNA variants in family trios. Ten family trios, each with a healthy spontaneous single-term pregnancy, were recruited. Total RNA was extracted for WT analysis, providing the full sequence information for the placental transcriptome. Parental and child blood DNA genotypes were analyzed by exome SNP genotyping microarrays, mapping the inheritance and estimating the abundance of parental expressed alleles. Imprinted genes showed consistent expression from either parental allele, as demonstrated by the SNP content of sequenced transcripts, while monoallelically expressed genes had random activity of parental alleles. We revealed 4 novel possible imprinted genes (LGALS8, LGALS14, PAPPA2 and SPTLC3) and confirmed the imprinting of 4 genes (AIM1, PEG10, RHOBTB3 and ZFAT-AS1) in human placenta. The major finding was the identification of 4 genes (ABP1, BCLAF1, IFI30 and ZFAT) with random allelic bias, expressing one of the parental alleles preferentially. The main functions of the imprinted and monoallelically expressed genes included: i) mediating cellular apoptosis and tissue development; ii) regulating inflammation and immune system; iii) facilitating metabolic processes; and iv) regulating cell cycle.
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Key Words
- ASE, allele-specific expression
- FDR, false discovery rate
- GEO, Gene Expression Omnibus
- IUGR, intrauterine growth restriction
- MAF, minor allele frequency
- MHC, major histocompatibility complex
- NK cells, natural killer cells
- RNA sequencing
- RNA-Seq, RNA-sequencing
- RPKM, reads per kilobase per million
- UCSC, University of California Santa Cruz
- WT, whole-transcriptome
- allele-specific expression
- imprinting
- placenta
- random monoallelic expression
- short read mapping
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Affiliation(s)
- Tauno Metsalu
- a Institute of Computer Science ; University of Tartu ; Tartu , Estonia
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Eidem HR, Ackerman WE, McGary KL, Abbot P, Rokas A. Gestational tissue transcriptomics in term and preterm human pregnancies: a systematic review and meta-analysis. BMC Med Genomics 2015; 8:27. [PMID: 26044726 PMCID: PMC4456776 DOI: 10.1186/s12920-015-0099-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/12/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Preterm birth (PTB), or birth before 37 weeks of gestation, is the leading cause of newborn death worldwide. PTB is a critical area of scientific study not only due to its worldwide toll on human lives and economies, but also due to our limited understanding of its pathogenesis and, therefore, its prevention. This systematic review and meta-analysis synthesizes the landscape of PTB transcriptomics research to further our understanding of the genes and pathways involved in PTB subtypes. METHODS We evaluated published genome-wide pregnancy studies across gestational tissues and pathologies, including those that focus on PTB, by performing a targeted PubMed MeSH search and systematically reviewing all relevant studies. RESULTS Our search yielded 2,361 studies on gestational tissues including placenta, decidua, myometrium, maternal blood, cervix, fetal membranes (chorion and amnion), umbilical cord, fetal blood, and basal plate. Selecting only those original research studies that measured transcription on a genome-wide scale and reported lists of expressed genetic elements identified 93 gene expression, 21 microRNA, and 20 methylation studies. Although 30 % of all PTB cases are due to medical indications, 76 % of the preterm studies focused on them. In contrast, only 18 % of the preterm studies focused on spontaneous onset of labor, which is responsible for 45 % of all PTB cases. Furthermore, only 23 of the 10,993 unique genetic elements reported to be transcriptionally active were recovered 10 or more times in these 134 studies. Meta-analysis of the 93 gene expression studies across 9 distinct gestational tissues and 29 clinical phenotypes showed limited overlap of genes identified as differentially expressed across studies. CONCLUSIONS Overall, profiles of differentially expressed genes were highly heterogeneous both between as well as within clinical subtypes and tissues as well as between studies of the same clinical subtype and tissue. These results suggest that large gaps still exist in the transcriptomic study of specific clinical subtypes as well in the generation of the transcriptional profile of well-studied clinical subtypes; understanding the complex landscape of prematurity will require large-scale, systematic genome-wide analyses of human gestational tissues on both understudied and well-studied subtypes alike.
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Affiliation(s)
- Haley R Eidem
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, USA.
| | - William E Ackerman
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Kriston L McGary
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, USA.
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, USA.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, VU Station B #35-1634, Nashville, TN, 37235, USA.
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Abstract
This review provides an overview of the unique features of DNA methylation in the human placenta. We discuss the importance of understanding placental development, structure, and function in the interpretation of DNA methylation data. Examples are given of how DNA methylation is important in regulating placental-specific gene expression, including monoallelic expression and X-chromosome inactivation in the placenta. We also discuss studies of global DNA methylation changes in the context of placental pathology and environmental exposures.
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Affiliation(s)
- Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - E Magda Price
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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34
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Imprinted genes in myeloid lineage commitment in normal and malignant hematopoiesis. Leukemia 2015; 29:1233-42. [PMID: 25703588 DOI: 10.1038/leu.2015.47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 12/12/2022]
Abstract
Genomic imprinting is characterized by the parent-of-origin monoallelic expression of several diploid genes because of epigenetic regulation. Imprinted genes (IGs) are key factors in development, supporting the ability of a genotype to produce phenotypes in response to environmental stimuli. IGs are highly expressed during prenatal stages but are downregulated after birth. They also affect aspects of life other than growth such as cognition, behavior, adaption to novel environments, social dominance and memory consolidation. Deregulated genomic imprinting leads to developmental disorders and is associated with solid and blood cancer as well. Several data have been published highlighting the involvement of IGs in as early as the very small embryonic-like stem cells stage and further during myeloid lineage commitment in normal and malignant hematopoiesis. Therefore, we have assembled the current knowledge on the topic, based mainly on recent findings, trying not to focus on a particular cluster but rather to have a global view of several different IGs in hematopoiesis.
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Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T. Genome-wide analysis of DNA methylation dynamics during early human development. PLoS Genet 2014; 10:e1004868. [PMID: 25501653 PMCID: PMC4263407 DOI: 10.1371/journal.pgen.1004868] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/02/2014] [Indexed: 12/28/2022] Open
Abstract
DNA methylation is globally reprogrammed during mammalian preimplantation development, which is critical for normal development. Recent reduced representation bisulfite sequencing (RRBS) studies suggest that the methylome dynamics are essentially conserved between human and mouse early embryos. RRBS is known to cover 5–10% of all genomic CpGs, favoring those contained within CpG-rich regions. To obtain an unbiased and more complete representation of the methylome during early human development, we performed whole genome bisulfite sequencing of human gametes and blastocysts that covered>70% of all genomic CpGs. We found that the maternal genome was demethylated to a much lesser extent in human blastocysts than in mouse blastocysts, which could contribute to an increased number of imprinted differentially methylated regions in the human genome. Global demethylation of the paternal genome was confirmed, but SINE-VNTR-Alu elements and some other tandem repeat-containing regions were found to be specifically protected from this global demethylation. Furthermore, centromeric satellite repeats were hypermethylated in human oocytes but not in mouse oocytes, which might be explained by differential expression of de novo DNA methyltransferases. These data highlight both conserved and species-specific regulation of DNA methylation during early mammalian development. Our work provides further information critical for understanding the epigenetic processes underlying differentiation and pluripotency during early human development. DNA methylation reprogramming after fertilization is critical for normal mammalian development. Early embryos are sensitive to environmental stresses and a number of reports have pointed out the increased risk of DNA methylation errors associated with assisted reproduction technologies. Therefore, it is very important to understand normal DNA methylation patterns during early human development. Recent reduced representation bisulfite sequencing studies reported partial methylomes of human gametes and early embryos. To provide a more comprehensive view of DNA methylation dynamics during early human development, we report on whole genome bisulfite sequencing of human gametes and blastocysts. We show that the paternal genome is globally demethylated in blastocysts whereas the maternal genome is demethylated to a much lesser extent. We also reveal unique regulation of imprinted differentially methylated regions, gene bodies and repeat sequences during early human development. Our high-resolution methylome maps are essential to understand epigenetic reprogramming by human oocytes and will aid in the preimplantation epigenetic diagnosis of human embryos.
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Affiliation(s)
- Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- JST, CREST, Saitama, Japan
| | - Hatsune Chiba
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- JST, CREST, Saitama, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- JST, CREST, Saitama, Japan
| | - Hirotaka Hamada
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- JST, CREST, Saitama, Japan
| | - Akiko Sato
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- St. Luke Clinic Laboratory, Oita, Japan
| | | | - Hiroyuki Kikuchi
- Yoshida Ladies Clinic Center for Reproductive Medicine, Sendai, Japan
| | - Hiroaki Yoshida
- Yoshida Ladies Clinic Center for Reproductive Medicine, Sendai, Japan
| | - Atsushi Tanaka
- St. Mother Clinic Laboratory, Kitakyushu, Fukuoka, Japan
| | - Mikita Suyama
- JST, CREST, Saitama, Japan
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Fukuoka, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
- JST, CREST, Saitama, Japan
- * E-mail:
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Chen GG, Diallo AB, Poujol R, Nagy C, Staffa A, Vaillancourt K, Lutz PE, Ota VK, Mash DC, Turecki G, Ernst C. BisQC: an operational pipeline for multiplexed bisulfite sequencing. BMC Genomics 2014; 15:290. [PMID: 24734894 PMCID: PMC4234473 DOI: 10.1186/1471-2164-15-290] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/08/2014] [Indexed: 11/24/2022] Open
Abstract
Background Bisulfite sequencing is the most efficient single nucleotide resolution method for analysis of methylation status at whole genome scale, but improved quality control metrics are needed to better standardize experiments. Results We describe BisQC, a step-by-step method for multiplexed bisulfite-converted DNA library construction, pooling, spike-in content, and bioinformatics. We demonstrate technical improvements for library preparation and bioinformatic analyses that can be done in standard laboratories. We find that decoupling amplification of bisulfite converted (bis) DNA from the indexing reaction is an advantage, specifically in reducing total PCR cycle number and pre-selecting high quality bis-libraries. We also introduce a progressive PCR method for optimal library amplification and size-selection. At the sequencing stage, we thoroughly test the benefits of pooling non-bis DNA library with bis-libraries and find that BisSeq libraries can be pooled with a high proportion of non-bis DNA libraries with minimal impact on BisSeq output. For informatics analysis, we propose a series of optimization steps including the utilization of the mitochondrial genome as a QC standard, and we assess the validity of using duplicate reads for coverage statistics. Conclusion We demonstrate several quality control checkpoints at the library preparation, pre-sequencing, post-sequencing, and post-alignment stages, which should prove useful in determining sample and processing quality. We also determine that including a significant portion of non-bisulfite converted DNA with bisulfite converted DNA has a minimal impact on usable bisulfite read output.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Carl Ernst
- Department of Psychiatry, McGill University, Douglas Hospital Research Institute, Montreal, Quebec, Canada.
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37
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Court F, Tayama C, Romanelli V, Martin-Trujillo A, Iglesias-Platas I, Okamura K, Sugahara N, Simón C, Moore H, Harness JV, Keirstead H, Sanchez-Mut JV, Kaneki E, Lapunzina P, Soejima H, Wake N, Esteller M, Ogata T, Hata K, Nakabayashi K, Monk D. Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment. Genome Res 2014; 24:554-69. [PMID: 24402520 PMCID: PMC3975056 DOI: 10.1101/gr.164913.113] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 12/26/2013] [Indexed: 12/16/2022]
Abstract
Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental disomies, and hydatidiform moles, using a combination of whole-genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent-of-origin methylation, 15 of which are restricted to the placenta. We observe that the extent of imprinted differentially methylated regions (DMRs) is extremely similar between tissues, with the exception of the placenta. This extra-embryonic tissue often adopts a different methylation profile compared to somatic tissues. Further, we profiled all imprinted DMRs in sperm and embryonic stem cells derived from parthenogenetically activated oocytes, individual blastomeres, and blastocysts, in order to identify primary DMRs and reveal the extent of reprogramming during preimplantation development. Intriguingly, we find that in contrast to ubiquitous imprints, the majority of placenta-specific imprinted DMRs are unmethylated in sperm and all human embryonic stem cells. Therefore, placental-specific imprinting provides evidence for an inheritable epigenetic state that is independent of DNA methylation and the existence of a novel imprinting mechanism at these loci.
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Affiliation(s)
- Franck Court
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Valeria Romanelli
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, 08950 Barcelona, Spain
| | - Kohji Okamura
- Department of Systems Biomedicine, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Naoko Sugahara
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI-Universidad de Valencia, INCLIVA, 46980 Paterna, Valencia, Spain
| | - Harry Moore
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Julie V. Harness
- Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA
| | - Hans Keirstead
- Reeve-Irvine Research Centre, Sue and Bill Gross Stem Cell Research Center, Department of Anatomy and Neurobiology, School of Medicine, University of California at Irvine, Irvine, California 92697, USA
| | - Jose Vicente Sanchez-Mut
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
| | - Eisuke Kaneki
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular, CIBERER, IDIPAZ-Hospital Universitario La Paz, Universidad Autónoma de Madrid, 28046 Madrid, Spain
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Norio Wake
- Department of Obstetrics and Gynecology, Graduate School of Medical Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, 08908 Barcelona, Spain
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Novakovic B, Saffery R. Placental pseudo-malignancy from a DNA methylation perspective: unanswered questions and future directions. Front Genet 2013; 4:285. [PMID: 24368911 PMCID: PMC3857887 DOI: 10.3389/fgene.2013.00285] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/26/2013] [Indexed: 11/28/2022] Open
Abstract
The growing fetus is dependent on adequate placental function for delivery of essential nutrients and oxygen, and for waste removal. The placenta also plays an important protective role; shielding the developing baby from the maternal immune system and adverse environmental exposures. Fundamental to these processes is correct invasion of the decidua and remodeling of maternal vasculature, each of which show remarkable parallels to tumorogenesis, with the obvious exception that the former is usually a tightly controlled process. It is not surprising that these physiological similarities are mirrored in gene expression and epigenetic parallels, many not found in any other aspect of human development. In this perspective, we summarize known DNA methylation similarities between placenta and human tumors, and discuss the implications and knowledge gaps associated with these findings. We also speculate on the potential origin of common DNA methylation features in these two disparate aspects of human physiology.
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Affiliation(s)
- Boris Novakovic
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital Parkville, VIC, Australia
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital Parkville, VIC, Australia ; Department of Paediatrics, University of Melbourne Parkville, VIC, Australia
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39
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Novakovic B, Ryan J, Pereira N, Boughton B, Craig JM, Saffery R. Postnatal stability, tissue, and time specific effects of AHRR methylation change in response to maternal smoking in pregnancy. Epigenetics 2013; 9:377-86. [PMID: 24270552 DOI: 10.4161/epi.27248] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intrauterine environment has the potential to "program" the developing fetus in a way that can be potentially deleterious to later health. While in utero environmental/stochastic factors are known to influence DNA methylation profile at birth, it has been difficult to assign specific examples of epigenetic variation to specific environmental exposures. Recently, several studies have linked exposure to smoking with DNA methylation change in the aryl hydrocarbon receptor repressor (AHRR) gene in blood. This includes hypomethylation of AHRR in neonatal blood in response to maternal smoking in pregnancy. The role of AHRR as a negative regulator of pathways involved in pleiotropic responses to environmental contaminants raises the possibility that smoking-induced hypomethylation is an adaptive response to an adverse in utero environmental exposure. However, the tissue specificity of the response to maternal smoking, and the stability of the methylation changes early in life remain to be determined. In this study we analyzed AHRR methylation in three cell types-cord blood mononuclear cells (CBMCs), buccal epithelium, and placenta tissue-from newborn twins of mothers who smoked throughout pregnancy and matched controls. Further, we explored the postnatal stability of this change at 18 months. Our results confirm the previous association between maternal smoking and AHRR methylation in neonatal blood. In addition, this study expands the region of AHRR methylation altered in response to maternal smoking during pregnancy and reveals the tissue-specific nature of epigenetic responses to environmental exposures in utero. Further, the evidence for postnatal stability of smoking-induced epigenetic change supports a role for epigenetics as a mediator of long-term effects of specific in utero exposures in humans. Longitudinal analysis of further specific exposures in larger cohorts is required to examine the extent of this phenomenon in humans.
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Affiliation(s)
- Boris Novakovic
- Cancer, Disease and Developmental Epigenetics; Murdoch Childrens Research Institute; Royal Children's Hospital; Parkville, VIC Australia
| | - Joanne Ryan
- Cancer, Disease and Developmental Epigenetics; Murdoch Childrens Research Institute; Royal Children's Hospital; Parkville, VIC Australia; Department of Paediatrics; University of Melbourne; Parkville, VIC Australia
| | - Natalie Pereira
- Metabolomics Australia; School of Botany; The University of Melbourne; Parkville, VIC Australia
| | - Berin Boughton
- Metabolomics Australia; School of Botany; The University of Melbourne; Parkville, VIC Australia
| | - Jeffrey M Craig
- Department of Paediatrics; University of Melbourne; Parkville, VIC Australia; Early Life Epigenetics; Murdoch Childrens Research Institute; Royal Children's Hospital; Parkville, VIC Australia; Department of Paediatrics; University of Melbourne; Parkville, VIC Australia
| | - Richard Saffery
- Cancer, Disease and Developmental Epigenetics; Murdoch Childrens Research Institute; Royal Children's Hospital; Parkville, VIC Australia; Department of Paediatrics; University of Melbourne; Parkville, VIC Australia
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