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Xiong X, Chen H, Zhang Q, Liu Y, Xu C. Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing. Nucleic Acids Res 2024; 52:e24. [PMID: 38261991 PMCID: PMC10954476 DOI: 10.1093/nar/gkae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.
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Affiliation(s)
- Xiong Xiong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Hengye Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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3
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Chen J, Cheng J, Chen X, Inoue M, Liu Y, Song CX. Whole-genome long-read TAPS deciphers DNA methylation patterns at base resolution using PacBio SMRT sequencing technology. Nucleic Acids Res 2022; 50:e104. [PMID: 35849350 PMCID: PMC9561279 DOI: 10.1093/nar/gkac612] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/07/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Long-read sequencing provides valuable information on difficult-to-map genomic regions, which can complement short-read sequencing to improve genome assembly, yet limited methods are available to accurately detect DNA methylation over long distances at a whole-genome scale. By combining our recently developed TET-assisted pyridine borane sequencing (TAPS) method, which enables direct detection of 5-methylcytosine and 5-hydroxymethylcytosine, with PacBio single-molecule real-time sequencing, we present here whole-genome long-read TAPS (wglrTAPS). To evaluate the performance of wglrTAPS, we applied it to mouse embryonic stem cells as a proof of concept, and an N50 read length of 3.5 kb is achieved. By sequencing wglrTAPS to 8.2× depth, we discovered a significant proportion of CpG sites that were not covered in previous 27.5× short-read TAPS. Our results demonstrate that wglrTAPS facilitates methylation profiling on problematic genomic regions with repetitive elements or structural variations, and also in an allelic manner, all of which are extremely difficult for short-read sequencing methods to resolve. This method therefore enhances applications of third-generation sequencing technologies for DNA epigenetics.
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Affiliation(s)
- Jinfeng Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Jingfei Cheng
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Xiufei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Masato Inoue
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Yibin Liu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
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4
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LIN28 Family in Testis: Control of Cell Renewal, Maturation, Fertility and Aging. Int J Mol Sci 2022; 23:ijms23137245. [PMID: 35806250 PMCID: PMC9266904 DOI: 10.3390/ijms23137245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 12/12/2022] Open
Abstract
Male reproductive development starts early in the embryogenesis with somatic and germ cell differentiation in the testis. The LIN28 family of RNA-binding proteins promoting pluripotency has two members—LIN28A and LIN28B. Their function in the testis has been investigated but many questions about their exact role based on the expression patterns remain unclear. LIN28 expression is detected in the gonocytes and the migrating, mitotically active germ cells of the fetal testis. Postnatal expression of LIN28 A and B showed differential expression, with LIN28A expressed in the undifferentiated spermatogonia and LIN28B in the elongating spermatids and Leydig cells. LIN28 interferes with many signaling pathways, leading to cell proliferation, and it is involved in important testicular physiological processes, such as cell renewal, maturation, fertility, and aging. In addition, aberrant LIN28 expression is associated with testicular cancer and testicular disorders, such as hypogonadotropic hypogonadism and Klinefelter’s syndrome. This comprehensive review encompasses current knowledge of the function of LIN28 paralogs in testis and other tissues and cells because many studies suggest LIN28AB as a promising target for developing novel therapeutic agents.
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5
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Pastor WA, Kwon SY. Distinctive aspects of the placental epigenome and theories as to how they arise. Cell Mol Life Sci 2022; 79:569. [PMID: 36287261 PMCID: PMC9606139 DOI: 10.1007/s00018-022-04568-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 08/18/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022]
Abstract
The placenta has a methylome dramatically unlike that of any somatic cell type. Among other distinctions, it features low global DNA methylation, extensive “partially methylated domains” packed in dense heterochromatin and methylation of hundreds of CpG islands important in somatic development. These features attract interest in part because a substantial fraction of human cancers feature the exact same phenomena, suggesting parallels between epigenome formation in placentation and cancer. Placenta also features an expanded set of imprinted genes, some of which come about by distinctive developmental pathways. Recent discoveries, some from far outside the placental field, shed new light on how the unusual placental epigenetic state may arise. Nonetheless, key questions remain unresolved.
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Affiliation(s)
- William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, QC, H3A 1A3, Canada.
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
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6
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Epigenetic processes during preeclampsia and effects on fetal development and chronic health. Clin Sci (Lond) 2021; 135:2307-2327. [PMID: 34643675 DOI: 10.1042/cs20190070] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/08/2021] [Accepted: 09/29/2021] [Indexed: 01/12/2023]
Abstract
Preeclampsia (PE), the leading cause of maternal and fetal morbidity and mortality, is associated with poor fetal growth, intrauterine growth restriction (IUGR) and low birth weight (LBW). Offspring of women who had PE are at increased risk for cardiovascular (CV) disease later in life. However, the exact etiology of PE is unknown. Moreover, there are no effective interventions to treat PE or alleviate IUGR and the developmental origins of chronic disease in the offspring. The placenta is critical to fetal growth and development. Epigenetic regulatory processes such as histone modifications, microRNAs and DNA methylation play an important role in placental development including contributions to the regulation of trophoblast invasion and remodeling of the spiral arteries. Epigenetic processes that lead to changes in placental gene expression in PE mediate downstream effects that contribute to the development of placenta dysfunction, a critical mediator in the onset of PE, impaired fetal growth and IUGR. Therefore, this review will focus on epigenetic processes that contribute to the pathogenesis of PE and IUGR. Understanding the epigenetic mechanisms that contribute to normal placental development and the initiating events in PE may lead to novel therapeutic targets in PE that improve fetal growth and mitigate increased CV risk in the offspring.
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7
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Anvar Z, Chakchouk I, Demond H, Sharif M, Kelsey G, Van den Veyver IB. DNA Methylation Dynamics in the Female Germline and Maternal-Effect Mutations That Disrupt Genomic Imprinting. Genes (Basel) 2021; 12:genes12081214. [PMID: 34440388 PMCID: PMC8394515 DOI: 10.3390/genes12081214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic imprinting is an epigenetic marking process that results in the monoallelic expression of a subset of genes. Many of these ‘imprinted’ genes in mice and humans are involved in embryonic and extraembryonic growth and development, and some have life-long impacts on metabolism. During mammalian development, the genome undergoes waves of (re)programming of DNA methylation and other epigenetic marks. Disturbances in these events can cause imprinting disorders and compromise development. Multi-locus imprinting disturbance (MLID) is a condition by which imprinting defects touch more than one locus. Although most cases with MLID present with clinical features characteristic of one imprinting disorder. Imprinting defects also occur in ‘molar’ pregnancies-which are characterized by highly compromised embryonic development-and in other forms of reproductive compromise presenting clinically as infertility or early pregnancy loss. Pathogenic variants in some of the genes encoding proteins of the subcortical maternal complex (SCMC), a multi-protein complex in the mammalian oocyte, are responsible for a rare subgroup of moles, biparental complete hydatidiform mole (BiCHM), and other adverse reproductive outcomes which have been associated with altered imprinting status of the oocyte, embryo and/or placenta. The finding that defects in a cytoplasmic protein complex could have severe impacts on genomic methylation at critical times in gamete or early embryo development has wider implications beyond these relatively rare disorders. It signifies a potential for adverse maternal physiology, nutrition, or assisted reproduction to cause epigenetic defects at imprinted or other genes. Here, we review key milestones in DNA methylation patterning in the female germline and the embryo focusing on humans. We provide an overview of recent findings regarding DNA methylation deficits causing BiCHM, MLID, and early embryonic arrest. We also summarize identified SCMC mutations with regard to early embryonic arrest, BiCHM, and MLID.
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Affiliation(s)
- Zahra Anvar
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
| | - Momal Sharif
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
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8
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Juliusdottir T, Steinthorsdottir V, Stefansdottir L, Sveinbjornsson G, Ivarsdottir EV, Thorolfsdottir RB, Sigurdsson JK, Tragante V, Hjorleifsson KE, Helgadottir A, Frigge ML, Thorgeirsson G, Benediktsson R, Sigurdsson EL, Arnar DO, Steingrimsdottir T, Jonsdottir I, Holm H, Gudbjartsson DF, Thorleifsson G, Thorsteinsdottir U, Stefansson K. Distinction between the effects of parental and fetal genomes on fetal growth. Nat Genet 2021; 53:1135-1142. [PMID: 34282336 DOI: 10.1038/s41588-021-00896-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/11/2021] [Indexed: 01/12/2023]
Abstract
Birth weight is a common measure of fetal growth that is associated with a range of health outcomes. It is directly affected by the fetal genome and indirectly by the maternal genome. We performed genome-wide association studies on birth weight in the genomes of the child and parents and further analyzed birth length and ponderal index, yielding a total of 243 fetal growth variants. We clustered those variants based on the effects of transmitted and nontransmitted alleles on birth weight. Out of 141 clustered variants, 22 were consistent with parent-of-origin-specific effects. We further used haplotype-specific polygenic risk scores to directly test the relationship between adult traits and birth weight. Our results indicate that the maternal genome contributes to increased birth weight through blood-glucose-raising alleles while blood-pressure-raising alleles reduce birth weight largely through the fetal genome.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kristjan E Hjorleifsson
- deCODE genetics/Amgen, Reykjavik, Iceland.,Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Gudmundur Thorgeirsson
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Rafn Benediktsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - David O Arnar
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Medicine, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Thora Steingrimsdottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Obstetrics and Gynecology, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Immunology, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen, Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE genetics/Amgen, Reykjavik, Iceland. .,Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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9
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Dini P, Kalbfleisch T, Uribe-Salazar JM, Carossino M, Ali HES, Loux SC, Esteller-Vico A, Norris JK, Anand L, Scoggin KE, Rodriguez Lopez CM, Breen J, Bailey E, Daels P, Ball BA. Parental bias in expression and interaction of genes in the equine placenta. Proc Natl Acad Sci U S A 2021; 118:e2006474118. [PMID: 33853939 PMCID: PMC8072238 DOI: 10.1073/pnas.2006474118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a workflow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.
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Affiliation(s)
- Pouya Dini
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Theodore Kalbfleisch
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202
| | - José M Uribe-Salazar
- Department of Biochemistry and Molecular Medicine, Genome Center, Medical Investigation of Neurodevelopmental Disorders Institute, University of California, Davis, CA 95616
| | - Mariano Carossino
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
- Theriogenology Department, Faculty of Veterinary Medicine, University of Mansoura, 35516, Egypt
| | - Shavahn C Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Alejandro Esteller-Vico
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Jamie K Norris
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Lakshay Anand
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Carlos M Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, University of Kentucky, Lexington, KY 40546
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Ernest Bailey
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503
| | - Peter Daels
- Department of Veterinary Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke 9820, Belgium
| | - Barry A Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40503;
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10
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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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11
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Cinkornpumin JK, Kwon SY, Guo Y, Hossain I, Sirois J, Russett CS, Tseng HW, Okae H, Arima T, Duchaine TF, Liu W, Pastor WA. Naive Human Embryonic Stem Cells Can Give Rise to Cells with a Trophoblast-like Transcriptome and Methylome. Stem Cell Reports 2020; 15:198-213. [PMID: 32619492 PMCID: PMC7363941 DOI: 10.1016/j.stemcr.2020.06.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 01/01/2023] Open
Abstract
Human embryonic stem cells (hESCs) readily differentiate to somatic or germ lineages but have impaired ability to form extra-embryonic lineages such as placenta or yolk sac. Here, we demonstrate that naive hESCs can be converted into cells that exhibit the cellular and molecular phenotypes of human trophoblast stem cells (hTSCs) derived from human placenta or blastocyst. The resulting "transdifferentiated" hTSCs show reactivation of core placental genes, acquisition of a placenta-like methylome, and the ability to differentiate to extravillous trophoblasts and syncytiotrophoblasts. Modest differences are observed between transdifferentiated and placental hTSCs, most notably in the expression of certain imprinted loci. These results suggest that naive hESCs can differentiate to extra-embryonic lineage and demonstrate a new way of modeling human trophoblast specification and placental methylome establishment.
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Affiliation(s)
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Yixin Guo
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Ishtiaque Hossain
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Jacinthe Sirois
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Colleen S Russett
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hsin-Wei Tseng
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Centre, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Centre, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Thomas F Duchaine
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Wanlu Liu
- Department of Orthopedic of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China; Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada.
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12
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Bina M. Discovering candidate imprinted genes and imprinting control regions in the human genome. BMC Genomics 2020; 21:378. [PMID: 32475352 PMCID: PMC7262774 DOI: 10.1186/s12864-020-6688-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genomic imprinting is a process thereby a subset of genes is expressed in a parent-of-origin specific manner. This evolutionary novelty is restricted to mammals and controlled by genomic DNA segments known as Imprinting Control Regions (ICRs) and germline Differentially Methylated Regions (gDMRs). Previously, I showed that in the mouse genome, the fully characterized ICRs/gDMRs often includes clusters of 2 or more of a set of composite-DNA-elements known as ZFBS-morph overlaps. RESULTS Because of the importance of the ICRs to regulating parent-of-origin specific gene expression, I developed a genome-wide strategy for predicting their positions in the human genome. My strategy consists of creating plots to display the density of ZFBS-morph overlaps along the entire chromosomal DNA sequences. In initial evaluations, I found that peaks in these plots pinpointed several of the known ICRs/gDMRs along the DNA in chromosomal bands. I deduced that in density-plots, robust peaks corresponded to actual or candidate ICRs in the DNA. By locating the genes in the vicinity of candidate ICRs, I could discover potential imprinting genes. Additionally, my assessments revealed a connection between several of the potential imprinted genes and human developmental anomalies. Examples include Leber congenital amaurosis 11, Coffin-Siris syndrome, progressive myoclonic epilepsy-10, microcephalic osteodysplastic primordial dwarfism type II, and microphthalmia, cleft lip and palate, and agenesis of the corpus callosum. CONCLUSION With plots displaying the density of ZFBS-morph overlaps, researchers could locate candidate ICRs and imprinted genes. Since the datafiles are available for download and display at the UCSC genome browser, it is possible to examine the plots in the context of Single nucleotide polymorphisms (SNPs) to design experiments to discover novel ICRs and imprinted genes in the human genome.
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Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN, 47907, USA.
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13
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The Role of LIN28- let-7-ARID3B Pathway in Placental Development. Int J Mol Sci 2020; 21:ijms21103637. [PMID: 32455665 PMCID: PMC7279312 DOI: 10.3390/ijms21103637] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Placental disorders are a major cause of pregnancy loss in humans, and 40–60% of embryos are lost between fertilization and birth. Successful embryo implantation and placental development requires rapid proliferation, invasion, and migration of trophoblast cells. In recent years, microRNAs (miRNAs) have emerged as key regulators of molecular pathways involved in trophoblast function. A miRNA binds its target mRNA in the 3ʹ-untranslated region (3ʹ-UTR), causing its degradation or translational repression. Lethal-7 (let-7) miRNAs induce cell differentiation and reduce cell proliferation by targeting proliferation-associated genes. The oncoprotein LIN28 represses the biogenesis of mature let-7 miRNAs. Proliferating cells have high LIN28 and low let-7 miRNAs, whereas differentiating cells have low LIN28 and high let-7 miRNAs. In placenta, low LIN28 and high let-7 miRNAs can lead to reduced proliferation of trophoblast cells, resulting in abnormal placental development. In trophoblast cells, let-7 miRNAs reduce the expression of proliferation factors either directly by binding their mRNA in 3ʹ-UTR or indirectly by targeting the AT-rich interaction domain (ARID)3B complex, a transcription-activating complex comprised of ARID3A, ARID3B, and histone demethylase 4C (KDM4C). In this review, we discuss regulation of trophoblast function by miRNAs, focusing on the role of LIN28-let-7-ARID3B pathway in placental development.
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ZNF597 is a maternally expressed imprinted gene in the Holstein breed. Theriogenology 2020; 143:133-138. [PMID: 31874365 DOI: 10.1016/j.theriogenology.2019.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 11/24/2019] [Accepted: 12/14/2019] [Indexed: 11/22/2022]
Abstract
Genomic imprinting is an epigenetic phenomenon that leads to the preferential expression of genes from either the paternal or maternal allele. Imprinted genes play important roles in mammalian growth and development and a central role in placental function. ZNF597 and NAA60 are two paternally imprinted genes in the human ZNF597-NAA60 imprinted locus, both of which show biallelic expression in the mouse, but their imprinting status in cattle is still unknown. In this study, we examined the allelic expression of ZNF597 and NAA60 in adult bovine placental and somatic tissues. By comparing the mRNA-based genotypes with the genomic DNA-based genotypes, we identified monoallelic expression of ZNF597 in the placenta and in seven other tissues, including the cerebrum, heart, liver, spleen, lung, kidney, and muscle. Nevertheless, analysis revealed biallelic expression of the NAA60 gene in these tissues. Moreover, we tested the imprinting status of ZNF597 and confirmed that the maternal allele is expressed in the bovine placenta. To determine the role of DNA methylation in regulating monoallelic/imprinted expression of bovine ZNF597, the methylation status of two CpG-enriched regions in the bovine ZNF597-NAA60 locus was analyzed using the bisulfite sequencing method. Differentially methylated regions were detected on ten CpG loci in the bovine ZNF597 promoter region. In summary, the bovine ZNF597 gene is a maternally expressed gene, and its expression is regulated by DNA methylation, whereas the NAA60 gene is not imprinted in cattle.
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15
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Freebern E, Santos DJA, Fang L, Jiang J, Parker Gaddis KL, Liu GE, VanRaden PM, Maltecca C, Cole JB, Ma L. GWAS and fine-mapping of livability and six disease traits in Holstein cattle. BMC Genomics 2020; 21:41. [PMID: 31931710 PMCID: PMC6958677 DOI: 10.1186/s12864-020-6461-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multi-tissue transcriptome data. RESULTS We studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, the number of bulls included in the analyses ranged from 11,880 (hypocalcemia) to 24,699 (livability). GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine Major Histocompatibility Complex (MHC) region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression of Group-specific Component (GC) in the liver and association with mastitis as well as the Coiled-Coil Domain Containing 88C (CCDC88C) expression in CD8 cells and association with cow livability. CONCLUSIONS Collectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.
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Affiliation(s)
- Ellen Freebern
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Daniel J. A. Santos
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Lingzhao Fang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | | | - George E. Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Paul M. VanRaden
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, 27695 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
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16
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Farhadova S, Gomez-Velazquez M, Feil R. Stability and Lability of Parental Methylation Imprints in Development and Disease. Genes (Basel) 2019; 10:genes10120999. [PMID: 31810366 PMCID: PMC6947649 DOI: 10.3390/genes10120999] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.
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17
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Submicroscopic aberrations of chromosome 16 in prenatal diagnosis. Mol Cytogenet 2019; 12:36. [PMID: 31391865 PMCID: PMC6681493 DOI: 10.1186/s13039-019-0448-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/10/2019] [Indexed: 12/27/2022] Open
Abstract
Background Nearly 9.89% of chromosome 16 consists of segmental duplications, which makes it prone to non-homologous recombination. The present study aimed to investigate the incidence and perinatal characteristics of submicroscopic chromosome 16 aberrations in prenatal diagnosis. Results A total of 2,414 consecutive fetuses that underwent prenatal chromosomal microarray analysis (CMA) between January 2016 and December 2018 were reviewed. Submicroscopic anomalies of chromosome 16 accounted for 11.1% (15/134) of all submicroscopic anomalies detected in fetuses with normal karyotype, which was larger than the percentage of anomalies in any other chromosome. The 15 submicroscopic anomalies of chromosome 16 were identified in 14 cases; 12 of them had ultrasound abnormalities. They were classified as pathogenic (N = 7), and variants of uncertain significance (N = 8). Seven fetuses with variants of uncertain significance were ended in live-born, and the remaining were end in pregnancy termination. Conclusion Submicroscopic aberrations of chromosome 16 are frequent findings in prenatal diagnosis, which emphasize the challenge of genetic counseling and the value of CMA. Prenatal diagnosis should lead to long-term monitoring of children with such chromosomal abnormalities for better understanding of the phenotype of chromosome 16 microdeletion and microduplication syndromes.
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18
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See GM, Trenhaile-Grannemann MD, Spangler ML, Ciobanu DC, Mote BE. A genome-wide association study for gestation length in swine. Anim Genet 2019; 50:539-542. [PMID: 31297858 DOI: 10.1111/age.12822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2019] [Indexed: 11/26/2022]
Abstract
Selection for increased litter size in swine has potentially resulted in a correlated increase in preweaning mortality. Additional selection criteria should be considered when selecting for increased litter size to account for associated decreases in piglet quality, specifically piglet survival, initial weight and growth. Traits such as gestation length (GL), which have been associated with piglet performance, could be utilized to improve piglet development and survivability. The objective of this study was to conduct a genome-wide association study to identify genomic regions associated with GL in differing parities in swine (n = 831) from the University of Nebraska-Lincoln reproductive longevity project. Gestation length was calculated as the number of days between last insemination administered and farrowing. Sows were genotyped with the Illumina SNP60 BeadArray, and the data were analyzed using Bayesian mixture models for GL at parity 1, 2, 3 and 4 (GL1, GL2, GL3 and GL4 respectively). Means (SD) for GL1-GL4 were 113 (1.4), 114 (1.2), 114 (1.3) and 115 (1.2) respectively. Posterior mean heritability estimates (PSD) for GL1, GL2, GL3 and GL4 were 0.33 (0.06), 0.34 (0.07), 0.32 (0.08) and 0.20 (0.08) respectively. Rank correlations between genomic estimated breeding values between GL1 and GL2, GL3 and GL4 respectively were moderate: 0.67, 0.65 and 0.60. The top SNP (ASGA0017859, SSC4, 7.8 Mb), located in the top common genomic region associated with GL1, GL2 and GL3, was associated with a difference of 1.1 days in GL1 between homozygote genotypes (P < 0.0001). The results of this study suggest that GL is a largely polygenic trait with relatively minor contributions from multiple genomic regions.
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Affiliation(s)
- G M See
- University of Nebraska-Lincoln Department of Animal Science, Lincoln, 68588, Nebraska
| | | | - M L Spangler
- University of Nebraska-Lincoln Department of Animal Science, Lincoln, 68588, Nebraska
| | - D C Ciobanu
- University of Nebraska-Lincoln Department of Animal Science, Lincoln, 68588, Nebraska
| | - B E Mote
- University of Nebraska-Lincoln Department of Animal Science, Lincoln, 68588, Nebraska
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19
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Prata DP, Costa-Neves B, Cosme G, Vassos E. Unravelling the genetic basis of schizophrenia and bipolar disorder with GWAS: A systematic review. J Psychiatr Res 2019; 114:178-207. [PMID: 31096178 DOI: 10.1016/j.jpsychires.2019.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVES To systematically review findings of GWAS in schizophrenia (SZ) and in bipolar disorder (BD); and to interpret findings, with a focus on identifying independent replications. METHOD PubMed search, selection and review of all independent GWAS in SZ or BD, published since March 2011, i.e. studies using non-overlapping samples within each article, between articles, and with those of the previous review (Li et al., 2012). RESULTS From the 22 GWAS included in this review, the genetic associations surviving standard GWAS-significance were for genetic markers in the regions of ACSL3/KCNE4, ADCY2, AMBRA1, ANK3, BRP44, DTL, FBLN1, HHAT, INTS7, LOC392301, LOC645434/NMBR, LOC729457, LRRFIP1, LSM1, MDM1, MHC, MIR2113/POU3F2, NDST3, NKAPL, ODZ4, PGBD1, RENBP, TRANK1, TSPAN18, TWIST2, UGT1A1/HJURP, WHSC1L1/FGFR1 and ZKSCAN4. All genes implicated across both reviews are discussed in terms of their function and implication in neuropsychiatry. CONCLUSION Taking all GWAS to date into account, AMBRA1, ANK3, ARNTL, CDH13, EFHD1 (albeit with different alleles), MHC, PLXNA2 and UGT1A1 have been implicated in either disorder in at least two reportedly non-overlapping samples. Additionally, evidence for a SZ/BD common genetic basis is most strongly supported by the implication of ANK3, NDST3, and PLXNA2.
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Affiliation(s)
- Diana P Prata
- Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciências, Universidade de Lisboa, Portugal; Centre for Neuroimaging Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, SE5 8AF, UK; Instituto Universitário de Lisboa (ISCTE-IUL), Centro de Investigação e Intervenção Social, Lisboa, Portugal.
| | - Bernardo Costa-Neves
- Lisbon Medical School, University of Lisbon, Av. Professor Egas Moniz, 1649-028, Lisbon, Portugal; Centro Hospitalar Psiquiátrico de Lisboa, Av. do Brasil, 53 1749-002, Lisbon, Portugal
| | - Gonçalo Cosme
- Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciências, Universidade de Lisboa, Portugal
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, SE5 8AF, UK
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20
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Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
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Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
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21
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Zhabotynsky V, Inoue K, Magnuson T, Mauro Calabrese J, Sun W. A statistical method for joint estimation of cis-eQTLs and parent-of-origin effects under family trio design. Biometrics 2019; 75:864-874. [PMID: 30666629 DOI: 10.1111/biom.13026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/09/2019] [Indexed: 12/22/2022]
Abstract
RNA sequencing allows one to study allelic imbalance of gene expression, which may be due to genetic factors or genomic imprinting (i.e., higher expression of maternal or paternal allele). It is desirable to model both genetic and parent-of-origin effects simultaneously to avoid confounding and to improve the power to detect either effect. In studies of genetically tractable model organisms, separation of genetic and parent-of-origin effects can be achieved by studying reciprocal cross of two inbred strains. In contrast, this task is much more challenging in outbred populations such as humans. To address this challenge, we propose a new framework to combine experimental strategies and novel statistical methods. Specifically, we propose to study genetic and imprinting effects in family trios with RNA-seq data from the children and genotype data from both parents and children, and quantify genetic effects by cis-eQTLs. Towards this end, we have extended our method that studies the eQTLs of RNA-seq data (Sun, Biometrics 2012, 68(1): 1-11) to model both cis-eQTL and parent-of-origin effects, and evaluated its performance using extensive simulations. Since sample size may be limited in family trios, we have developed a data analysis pipeline that borrows information from external data of unrelated individuals for cis-eQTL mapping. We have also collected RNA-seq data from the children of 30 family trios, applied our method to analyze this dataset, and identified some previously reported imprinted genes as well as some new candidates of imprinted genes.
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Affiliation(s)
- Vasyl Zhabotynsky
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kaoru Inoue
- National Institute for Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Terry Magnuson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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22
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Duan J(E, Zhang M, Flock K, Seesi SA, Mandoiu I, Jones A, Johnson E, Pillai S, Hoffman M, McFadden K, Jiang H, Reed S, Govoni K, Zinn S, Jiang Z, Tian X(C. Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses. Epigenetics 2018; 13:793-807. [PMID: 30051747 PMCID: PMC6224220 DOI: 10.1080/15592294.2018.1503489] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/04/2018] [Accepted: 07/15/2018] [Indexed: 12/27/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date, 263 imprinted genes have been identified among all investigated mammalian species. However, only 21 have been described in sheep, of which 11 are annotated in the current ovine genome. Here, we aim to i) use DNA/RNA high throughput sequencing to identify new monoallelically expressed and imprinted genes in day 135 ovine fetuses and ii) determine whether maternal diet (100%, 60%, or 140% of National Research Council Total Digestible Nutrients) influences expression of imprinted genes. We also reported strategies to solve technical challenges in the data analysis pipeline. We identified 80 monoallelically expressed, 13 new putative imprinted genes, and five known imprinted genes in sheep using the 263 genes stated above as a guide. Sanger sequencing confirmed allelic expression of seven genes, CASD1, COPG2, DIRAS3, INPP5F, PLAGL1, PPP1R9A, and SLC22A18. Among the 13 putative imprinted genes, five were localized in the known sheep imprinting domains of MEST on chromosome 4, DLK1/GTL2 on chromosome 18 and KCNQ1 on chromosome 21, and three were in a novel sheep imprinted cluster on chromosome 4, known in other species as PEG10/SGCE. The expression of DIRAS3, IGF2, PHLDA2, and SLC22A18 was altered by maternal diet, albeit without allelic expression reversal. Together, our results expanded the list of sheep imprinted genes to 34 and demonstrated that while the expression levels of four imprinted genes were changed by maternal diet, the allelic expression patterns were un-changed for all imprinted genes studied.
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Affiliation(s)
| | - Mingyuan Zhang
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kaleigh Flock
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Sahar Al Seesi
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Ion Mandoiu
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Amanda Jones
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Elizabeth Johnson
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Sambhu Pillai
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Maria Hoffman
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Katelyn McFadden
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Sarah Reed
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Kristen Govoni
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Steve Zinn
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Zongliang Jiang
- School of Animal Science, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
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23
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Dunn-Fletcher CE, Muglia LM, Pavlicev M, Wolf G, Sun MA, Hu YC, Huffman E, Tumukuntala S, Thiele K, Mukherjee A, Zoubovsky S, Zhang X, Swaggart KA, Lamm KYB, Jones H, Macfarlan TS, Muglia LJ. Anthropoid primate-specific retroviral element THE1B controls expression of CRH in placenta and alters gestation length. PLoS Biol 2018; 16:e2006337. [PMID: 30231016 PMCID: PMC6166974 DOI: 10.1371/journal.pbio.2006337] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 10/01/2018] [Accepted: 09/10/2018] [Indexed: 01/22/2023] Open
Abstract
Pregnancy and parturition are intricately regulated to ensure successful reproductive outcomes. However, the factors that control gestational length in humans and other anthropoid primates remain poorly defined. Here, we show the endogenous retroviral long terminal repeat transposon-like human element 1B (THE1B) selectively controls placental expression of corticotropin-releasing hormone (CRH) that, in turn, influences gestational length and birth timing. Placental expression of CRH and subsequently prolonged gestational length were found in two independent strains of transgenic mice carrying a 180-kb human bacterial artificial chromosome (BAC) DNA that contained the full length of CRH and extended flanking regions, including THE1B. Restricted deletion of THE1B silenced placental CRH expression and normalized birth timing in these transgenic lines. Furthermore, we revealed an interaction at the 5′ insertion site of THE1B with distal-less homeobox 3 (DLX3), a transcription factor expressed in placenta. Together, these findings suggest that retroviral insertion of THE1B into the anthropoid primate genome may have initiated expression of CRH in placental syncytiotrophoblasts via DLX3 and that this placental CRH is sufficient to alter the timing of birth. The proper timing of delivery is critical during pregnancy; if too early or too late, the baby will be at risk of serious health problems and even death. Corticotropin-releasing hormone (CRH) is a protein that can be detected in maternal blood, and its concentration correlates with the timing of birth. In humans and other anthropoid primates, CRH is made by the placenta, whereas in other mammals, it is produced in a specialized region of the brain. To understand the regulation and evolution of this key protein, we inserted the human CRH gene and nearby regions into the mouse genome, which resulted in human CRH expression in the mouse placenta. Mouse litters that make CRH in their placentas are born later than control mice, showing that CRH can directly affect birth timing. Using our mouse model, we then selectively deleted a remnant of an ancient retrovirus that is normally found in the DNA of anthropoid primates and demonstrated that this specific region controls expression of CRH in the placenta. Deletion of this region also restored normal birth timing in the mice by eliminating CRH production from the placenta. We propose that retroviral regulation of CRH in the placenta may be a mechanism of controlling birth timing in humans and other anthropoid primates.
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Affiliation(s)
- Caitlin E. Dunn-Fletcher
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (CED); (LJM)
| | - Lisa M. Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Mihaela Pavlicev
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ming-An Sun
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Elizabeth Huffman
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Shivani Tumukuntala
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Katri Thiele
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Amrita Mukherjee
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Sandra Zoubovsky
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Xuzhe Zhang
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kayleigh A. Swaggart
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Katherine Y. Bezold Lamm
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Helen Jones
- Division of Pediatric Surgery, Cincinnati Children’s Hospital Medical Center, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Todd S. Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, United States of America
| | - Louis J. Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (CED); (LJM)
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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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Lefebvre T, Roche O, Seegers V, Cherif M, Khiati S, Gueguen N, Desquiret-Dumas V, Geffroy G, Blanchet O, Reynier P, Legendre G, Lenaers G, Procaccio V, Gascoin G. Study of mitochondrial function in placental insufficiency. Placenta 2018; 67:1-7. [PMID: 29941168 DOI: 10.1016/j.placenta.2018.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 01/04/2023]
Abstract
INTRODUCTION It has been suggested that mitochondria play a crucial role in sustaining pregnancy and foetal growth. The aim of the study was to assess the influence of mitochondrial functions and genetics on placental insufficiency diseases. METHODS A total of 115 patients were recruited, subdivided into 74 placenta samples and 41 maternal blood samples: placental insufficiency diseases including intra uterine growth restriction (IUGR) (n = 35), preeclampsia (PE) (n = 13), IUGR associated to PE (PER) (n = 25); and controls (n = 42). Haplogroups were determined for all patients. Eighty-six placenta samples were studied for quantitative and qualitative analyses of mtDNA: IUGR (n = 25), PE (n = 1), PER (n = 18) and controls (n = 42). Sixteen placenta samples were selected for functional analysis: IUGR (n = 6), PER (n = 2) and controls (n = 8). RESULTS Mitochondrial DNA copy numbers and rearrangements and haplogroup distribution were not significantly altered in the patient group. Enzyme activity and expression of respiratory chain complexes were also comparable between both groups. DISCUSSION Our results do not argue in favour of a mitochondrial involvement in placental insufficiency, suggesting that the glycolytic pathway may represent a key energetic source in placental insufficiency diseases.
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Affiliation(s)
- Tiphaine Lefebvre
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France; Department of Reproductive Medicine, CHU Nantes, Nantes, France
| | - Ombeline Roche
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France
| | - Valérie Seegers
- BioInformatics Core Facility, Institut de Cancérologie de l'Ouest, Angers, France
| | - Majida Cherif
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France
| | - Salim Khiati
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France
| | - Naïg Gueguen
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France; Department of Biochemistry and Genetics, CHU Angers, Angers, France
| | - Valérie Desquiret-Dumas
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France; Department of Biochemistry and Genetics, CHU Angers, Angers, France
| | | | - Odile Blanchet
- Centre for Biological Resources, CHU Angers, Angers, France
| | - Pascal Reynier
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France; Department of Biochemistry and Genetics, CHU Angers, Angers, France
| | | | - Guy Lenaers
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France
| | - Vincent Procaccio
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France; Department of Biochemistry and Genetics, CHU Angers, Angers, France
| | - Géraldine Gascoin
- MitoVasc Institute, UMR CNRS 6015, INSERM U1083, Angers, France; Department of Neonatal Medicine, CHU Angers, Angers, France.
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Maternal imprinting on cognition markers of wild type and transgenic Alzheimer's disease model mice. Sci Rep 2018; 8:6434. [PMID: 29691440 PMCID: PMC5915602 DOI: 10.1038/s41598-018-24710-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/09/2018] [Indexed: 12/11/2022] Open
Abstract
The risk of suffering from Alzheimer’s disease (AD) is higher in individuals from AD-affected mothers. The purpose of this investigation was to study whether maternal transmission might produce AD-related alterations in progenies of mice that do not have any genotypic alteration. We used cognitively-intact mothers harbouring in heterozygosity the transgene for overexpressing the Swedish double mutant version of the human amyloid precursor protein (hAβPPswe). The phenotype of the offspring with or without the transgene resulting from crossing young Tg2576 females with wild-type males were compared with those of the offspring resulting from crossing wild-type females with Tg2576 males. The hAβPPswe-bearing offspring from Tg2576 mothers showed an aggravated AD-like phenotype. Remarkably, cognitive, immunohistochemical and some biochemical features displayed by Tg2576 heterozygous mice were also found in wild-type animals generated from Tg2576 females. This suggests the existence of a maternal imprinting in the wild-type offspring that confers a greater facility to launch an AD-like neurodegenerative cascade. Such progeny, lacking any mutant amyloid precursor protein, constitutes a novel model to study maternal transmission of AD and, even more important, to discover early risk markers that predispose to the development of AD.
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27
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Christians JK, Leavey K, Cox BJ. Associations between imprinted gene expression in the placenta, human fetal growth and preeclampsia. Biol Lett 2018; 13:rsbl.2017.0643. [PMID: 29187609 DOI: 10.1098/rsbl.2017.0643] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 11/01/2017] [Indexed: 01/06/2023] Open
Abstract
Genomic imprinting is essential for normal placental and fetal growth. One theory to explain the evolution of imprinting is the kinship theory (KT), which predicts that genes that are paternally expressed will promote fetal growth, whereas maternally expressed genes will suppress growth. We investigated the expression of imprinted genes using microarray measurements of expression in term placentae. Correlations between birthweight and the expression levels of imprinted genes were more significant than for non-imprinted genes, but did not tend to be positive for paternally expressed genes and negative for maternally expressed genes. Imprinted genes were more dysregulated in preeclampsia (a disorder associated with placental insufficiency) than randomly selected genes, and we observed an excess of patterns of dysregulation in preeclampsia that would be expected to reduce nutrient allocation to the fetus, given the predictions of the KT. However, we found no evidence of coordinated regulation among these imprinted genes. A few imprinted genes have previously been shown to be associated with fetal growth and preeclampsia, and our results indicate that this is true for a broader set of imprinted genes.
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Affiliation(s)
- Julian K Christians
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Katherine Leavey
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Brian J Cox
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
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28
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Variant calling from RNA-seq data of the brain transcriptome of pigs and its application for allele-specific expression and imprinting analysis. Gene 2018; 641:367-375. [DOI: 10.1016/j.gene.2017.10.076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 12/21/2022]
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29
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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30
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Fu C, Luo S, Long X, Li Y, She S, Hu X, Mo M, Wang Z, Chen Y, He C, Su J, Zhang Y, Lin F, Xie B, Li Q, Chen S. Mutation screening of the GLIS3 gene in a cohort of 592 Chinese patients with congenital hypothyroidism. Clin Chim Acta 2018; 476:38-43. [DOI: 10.1016/j.cca.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 11/26/2022]
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31
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Two approaches reveal a new paradigm of 'switchable or genetics-influenced allele-specific DNA methylation' with potential in human disease. Cell Discov 2017; 3:17038. [PMID: 29387450 PMCID: PMC5787696 DOI: 10.1038/celldisc.2017.38] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 08/29/2017] [Indexed: 12/11/2022] Open
Abstract
Imprinted genes are vulnerable to environmental influences during early embryonic development, thereby contributing to the onset of disease in adulthood. Monoallelic methylation at several germline imprints has been reported as DNMT1-dependent. However, which of these two epigenetic attributes, DNMT1-dependence or allelic methylation, renders imprinted genes susceptible to environmental stressors has not been determined. Herein, we developed a new approach, referred to as NORED, to identify 2468 DNMT1-dependent DNA methylation patterns in the mouse genome. We further developed an algorithm based on a genetic variation-independent approach (referred to as MethylMosaic) to detect 2487 regions with bimodal methylation patterns. Two approaches identified 207 regions, including known imprinted germline allele-specific methylation patterns (ASMs), that were both NORED and MethylMosaic regions. Examination of methylation in four independent mouse embryonic stem cell lines shows that two regions identified by both NORED and MethylMosaic (Hcn2 and Park7) did not display parent-of-origin-dependent allelic methylation. In these four F1 hybrid cell lines, genetic variation in Cast allele at Hcn2 locus introduces a transcription factor binding site for MTF-1 that may predispose Cast allelic hypomethylation in a reciprocal cross with either C57 or 129 strains. In contrast, each allele of Hcn2 ASM in J1 inbred cell line and Park7 ASM in four F1 hybrid cell lines seems to exhibit similar propensity to be either hypo- or hypermethylated, suggesting a ‘random, switchable’ ASM. Together with published results, our data on ASMs prompted us to propose a hypothesis of regional ‘autosomal chromosome inactivation (ACI)’ that may control a subset of autosomal genes. Therefore, our results open a new avenue to understand monoallelic methylation and provide a rich resource of candidate genes to examine in environmental and nutritional exposure models.
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32
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Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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33
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Griffin NG, Cronin KD, Walley NM, Hulette CM, Grant GA, Mikati MA, LaBreche HG, Rehder CW, Allen AS, Crino PB, Heinzen EL. Somatic uniparental disomy of Chromosome 16p in hemimegalencephaly. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a001735. [PMID: 28864461 PMCID: PMC5593155 DOI: 10.1101/mcs.a001735] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome. Functional studies were performed to evaluate the molecular consequences of candidate disease-causing variants. Both HME patients evaluated were found to have likely disease-causing variants in DNA extracted from brain tissue but not in buccal swab or leukocyte DNA, consistent with a somatic mutational mechanism. In the first case, a previously identified disease-causing somatic single nucleotide in MTOR was identified. In the second case, we detected an overrepresentation of the alleles inherited from the mother on Chromosome 16 in brain tissue DNA only, indicative of somatic uniparental disomy (UPD) of the p-arm of Chromosome 16. Using methylation analyses, an imprinted locus on 16p spanning ZNF597 was identified, which results in increased expression of ZNF597 mRNA and protein in the brain tissue of the second case. Enhanced mTOR signaling was observed in tissue specimens from both patients. We speculate that overexpression of maternally expressed ZNF597 led to aberrant hemispheric development in the patient with somatic UPD of Chromosome 16p possibly through modulation of mTOR signaling.
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Affiliation(s)
- Nicole G Griffin
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA
| | - Kenneth D Cronin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Nicole M Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christine M Hulette
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Neurobiology, Duke University, Durham, North Carolina 27708, USA
| | | | | | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina 27710, USA
| | - Peter B Crino
- Department of Neurology, University of Maryland, School of Medicine, Baltimore, Maryland 21201, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University, New York, New York 10032, USA.,Department of Pathology and Cell Biology, Columbia University, New York, New York 10032, USA
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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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35
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Yingjun X, Zhiyang H, Linhua L, Fangming S, Linhuan H, Jinfeng T, Qianying P, Xiaofang S. Chromosomal uniparental disomy 16 and fetal intrauterine growth restriction. Eur J Obstet Gynecol Reprod Biol 2017; 211:1-7. [DOI: 10.1016/j.ejogrb.2016.12.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/18/2016] [Indexed: 11/28/2022]
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36
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Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genet 2016; 12:e1006427. [PMID: 27835649 PMCID: PMC5106035 DOI: 10.1371/journal.pgen.1006427] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Thousands of regions in gametes have opposing methylation profiles that are largely resolved during the post-fertilization epigenetic reprogramming. However some specific sequences associated with imprinted loci survive this demethylation process. Here we present the data describing the fate of germline-derived methylation in humans. With the exception of a few known paternally methylated germline differentially methylated regions (DMRs) associated with known imprinted domains, we demonstrate that sperm-derived methylation is reprogrammed by the blastocyst stage of development. In contrast a large number of oocyte-derived methylation differences survive to the blastocyst stage and uniquely persist as transiently methylated DMRs only in the placenta. Furthermore, we demonstrate that this phenomenon is exclusive to primates, since no placenta-specific maternal methylation was observed in mouse. Utilizing single cell RNA-seq datasets from human preimplantation embryos we show that following embryonic genome activation the maternally methylated transient DMRs can orchestrate imprinted expression. However despite showing widespread imprinted expression of genes in placenta, allele-specific transcriptional profiling revealed that not all placenta-specific DMRs coordinate imprinted expression and that this maternal methylation may be absent in a minority of samples, suggestive of polymorphic imprinted methylation. Differences in gamete DNA methylation is subject to genome-wide reprogramming during preimplantation development to establish an embryo with an epigenetic state compatible with totipotency. DNA sequences associated with imprinted differentially methylated regions (DMRs) are largely protected from this process, retaining their parent-of-origin epigenetic marks. By comparing the methylation profiles of human oocytes, sperm, blastocysts and various somatic tissues including placenta, we observe hundreds of CpG island sequences that maintain methylation on their maternal allele in blastocysts and placenta indicative of incomplete reprogramming. In some cases this maternal methylation influence transcription of nearby genes, revealing transient imprinting in embryos after genome-activation and in placenta. Strikingly, these placenta-specific DMRs are polymorphic between placenta samples with a minority of samples being robustly unmethylated on both alleles.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Franck Court
- Laboratoire GReD, CNRS, UMR6293, Clermont-Ferrand, France
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Isabel Iglesias-Platas
- Neonatal service, Hospital Sant Joan de Déu, BCNatal Hospital Sant Joan de Déu i Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Maria Eugenia Poo-Llanillo
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institute of Research and Advanced Studies, (ICREA), Passeig de Lluís Companys, Barcelona, Spain
- Centro Nacional de Analisis Genomico (CRG-CNAG), Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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Joshi RS, Garg P, Zaitlen N, Lappalainen T, Watson CT, Azam N, Ho D, Li X, Antonarakis SE, Brunner HG, Buiting K, Cheung SW, Coffee B, Eggermann T, Francis D, Geraedts JP, Gimelli G, Jacobson SG, Le Caignec C, de Leeuw N, Liehr T, Mackay DJ, Montgomery SB, Pagnamenta AT, Papenhausen P, Robinson DO, Ruivenkamp C, Schwartz C, Steiner B, Stevenson DA, Surti U, Wassink T, Sharp AJ. DNA Methylation Profiling of Uniparental Disomy Subjects Provides a Map of Parental Epigenetic Bias in the Human Genome. Am J Hum Genet 2016; 99:555-566. [PMID: 27569549 DOI: 10.1016/j.ajhg.2016.06.032] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 06/30/2016] [Indexed: 02/07/2023] Open
Abstract
Genomic imprinting is a mechanism in which gene expression varies depending on parental origin. Imprinting occurs through differential epigenetic marks on the two parental alleles, with most imprinted loci marked by the presence of differentially methylated regions (DMRs). To identify sites of parental epigenetic bias, here we have profiled DNA methylation patterns in a cohort of 57 individuals with uniparental disomy (UPD) for 19 different chromosomes, defining imprinted DMRs as sites where the maternal and paternal methylation levels diverge significantly from the biparental mean. Using this approach we identified 77 DMRs, including nearly all those described in previous studies, in addition to 34 DMRs not previously reported. These include a DMR at TUBGCP5 within the recurrent 15q11.2 microdeletion region, suggesting potential parent-of-origin effects associated with this genomic disorder. We also observed a modest parental bias in DNA methylation levels at every CpG analyzed across ∼1.9 Mb of the 15q11-q13 Prader-Willi/Angelman syndrome region, demonstrating that the influence of imprinting is not limited to individual regulatory elements such as CpG islands, but can extend across entire chromosomal domains. Using RNA-seq data, we detected signatures consistent with imprinted expression associated with nine novel DMRs. Finally, using a population sample of 4,004 blood methylomes, we define patterns of epigenetic variation at DMRs, identifying rare individuals with global gain or loss of methylation across multiple imprinted loci. Our data provide a detailed map of parental epigenetic bias in the human genome, providing insights into potential parent-of-origin effects.
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Affiliation(s)
- Ricky S Joshi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Noah Zaitlen
- Department of Medicine, UCSF MC2552, 1700 4th Street, Byers Hall Suite 503C, San Francisco, CA 94158, USA
| | - Tuuli Lappalainen
- New York Genome Center, 101 Avenue of the Americas, 7th Floor, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Corey T Watson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nidha Azam
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xin Li
- Departments of Pathology, Genetics and Computer Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 9th Floor, 1 rue Michel-Servet, 1211 Geneva, Switzerland
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Karin Buiting
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstrasse 55, 45122 Essen, Germany
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bradford Coffee
- Emory Genetics Laboratory, Emory University, Atlanta, GA 30033, USA
| | - Thomas Eggermann
- Institute of Human Genetics, University Hospital, RWTH, 52074 Aachen, Germany
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Joep P Geraedts
- Department of Genetics and Cell Biology, Research Institute GROW, Faculty of Health, Medicine and Life Sciences, Maastricht University, PO Box 5800, Maastricht AZ 6202, the Netherlands
| | - Giorgio Gimelli
- Laboratorio di Citogenetica, Istituto G. Gaslini, 16148 Genova, Italy
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, 51 N. 39th Street, Philadelphia, PA 19104, USA
| | - Cedric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Institut de Biologie, 9 quai Moncousu, 44093 Nantes, France; INSERM, UMR 957, Nantes 44035, France; Université de Nantes, Nantes atlantique universités, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Nantes 44035, France
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Deborah J Mackay
- Wessex Regional Genetics Laboratory Salisbury District Hospital, Salisbury, Wiltshire SO2 8BJ, UK
| | - Stephen B Montgomery
- Departments of Pathology, Genetics and Computer Science, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alistair T Pagnamenta
- National Institute for Health Research Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Papenhausen
- Division of Cytogenetics, LabCorp, Center for Molecular Biology and Pathology, Research Triangle Park, NC 27709, USA
| | - David O Robinson
- Wessex Regional Genetics Laboratory Salisbury District Hospital, Salisbury, Wiltshire SO2 8BJ, UK
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Charles Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Bernhard Steiner
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach, Switzerland
| | - David A Stevenson
- Division of Medical Genetics, Lucile Salter Packard Children's Hospital, 300 Pasteur Drive, Boswell Building A097, Stanford, CA 94304, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Thomas Wassink
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Brew O, Sullivan MHF, Woodman A. Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis. PLoS One 2016; 11:e0161504. [PMID: 27560381 PMCID: PMC4999138 DOI: 10.1371/journal.pone.0161504] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/05/2016] [Indexed: 11/19/2022] Open
Abstract
Pre-eclampsia (PE) is a serious multi-factorial disorder of human pregnancy. It is associated with changes in the expression of placental genes. Recent transcription profiling of placental genes with microarray analyses have offered better opportunities to define the molecular pathology of this disorder. However, the extent to which placental gene expression changes in PE is not fully understood. We conducted a systematic review of published PE and normal pregnancy (NP) control placental RNA microarrays to describe the similarities and differences between NP and PE placental gene expression, and examined how these differences could contribute to the molecular pathology of the disease. A total of 167 microarray samples were available for meta-analysis. We found the expression pattern of one group of genes was the same in PE and NP. The review also identified a set of genes (PE unique genes) including a subset, that were significantly (p < 0.05) down-regulated in pre-eclamptic placentae only. Using class prediction analysis, we further identified the expression of 88 genes that were highly associated with PE (p < 0.05), 10 of which (LEP, HTRA4, SPAG4, LHB, TREM1, FSTL3, CGB, INHA, PROCR, and LTF) were significant at p < 0.001. Our review also suggested that about 30% of genes currently being investigated as possibly of importance in PE placenta were not consistently and significantly affected in the PE placentae. We recommend further work to confirm the roles of the PE unique and associated genes, currently not being investigated in the molecular pathology of the disease.
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Affiliation(s)
- O. Brew
- University of West London, Brentford, Middlesex, United Kingdom
| | - M. H. F. Sullivan
- Institute of Reproductive & Developmental Biology, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - A. Woodman
- University of West London, Ealing, London, United Kingdom
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39
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Derakhshan-Horeh M, Abolhassani F, Jafarpour F, Moini A, Karbalaie K, Hosseini SM, Ostadhosseini S, Nasr-Esfahani MH. Methylation Status of H19/IGF2 Differentially Methylated Region in in vitro Human Blastocysts Donated by Healthy Couples. IRANIAN BIOMEDICAL JOURNAL 2016; 21:16-23. [PMID: 27432596 PMCID: PMC5141249 DOI: 10.6091/.21.1.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Imprinted genes are a unique subset of few genes that have been differentially methylated region (DMR) in a parental origin-dependent manner during gametogenesis, and these genes are highly protected during pre-implantation epigenetic reprogramming. Several studies have shown that the particular vulnerability of imprinting genes during suboptimal pre- and peri-conception micro-environments often is occurred by assisted reproduction techniques (ART). This study investigated the methylation status of H19/IGF2 DMR at high-quality expanding/expanded human blastocysts donated by healthy individuals to evaluate the risks linked to ART. METHODS Methylation levels of H19/IGF2 DMR were analyzed by bisulfite conversion and sequencing at 18 CpG sites (CpGs) located in this region. RESULTS The overall percentage of methylated CpGs and the proportion of hyper-methylated clones of H19/IGF2 DMR in analyzed blastocysts were 37.85±4.87% and 43.75±5.1%, respectively. For validation of our technique, the corresponding methylation levels of peripheral human lymphocytes were defined (49.52±1.86% and 50%, respectively). CONCLUSIONS Considering the absence of in vivo- produced human embryos, it is not possible to conclude that the methylation found in H19/IGF2 DMR is actually normal or abnormal. Regarding the possible risks associated with ART, the procedures should be optimized in order to at least reduce some of the epigenetic risks.
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Affiliation(s)
| | - Farid Abolhassani
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farnoosh Jafarpour
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Ashraf Moini
- Department of Endocrinology and Female Infertility, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.,Department of Obstetrics and Gynecology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Karbalaie
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; 6Isfahan Fertility and Infertility Center, Isfahan, Iran
| | - Sayyed Morteza Hosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Somayyeh Ostadhosseini
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, Academic Center for Education, Culture and Research (ACECR), Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; 6Isfahan Fertility and Infertility Center, Isfahan, Iran.,Isfahan Fertility and Infertility Center, Isfahan, Iran
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40
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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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41
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Bak M, Boonen SE, Dahl C, Hahnemann JMD, Mackay DJDG, Tümer Z, Grønskov K, Temple IK, Guldberg P, Tommerup N. Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57. BMC MEDICAL GENETICS 2016; 17:29. [PMID: 27075368 PMCID: PMC4831126 DOI: 10.1186/s12881-016-0292-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 04/08/2016] [Indexed: 12/21/2022]
Abstract
Background Transient neonatal diabetes mellitus 1 (TNDM1) is a rare imprinting disorder characterized by intrautering growth retardation and diabetes mellitus usually presenting within the first six weeks of life and resolves by the age of 18 months. However, patients have an increased risk of developing diabetes mellitus type 2 later in life. Transient neonatal diabetes mellitus 1 is caused by overexpression of the maternally imprinted genes PLAGL1 and HYMAI on chromosome 6q24. One of the mechanisms leading to overexpression of the locus is hypomethylation of the maternal allele of PLAGL1 and HYMAI. A subset of patients with maternal hypomethylation at PLAGL1 have hypomethylation at additional imprinted loci throughout the genome, including GRB10, ZIM2 (PEG3), MEST (PEG1), KCNQ1OT1 and NESPAS (GNAS-AS1). About half of the TNDM1 patients carry mutations in ZFP57, a transcription factor involved in establishment and maintenance of methylation of imprinted loci. Our objective was to investigate whether additional regions are aberrantly methylated in ZFP57 mutation carriers. Methods Genome-wide DNA methylation analysis was performed on four individuals with homozygous or compound heterozygous ZFP57 mutations, three relatives with heterozygous ZFP57 mutations and five controls. Methylation status of selected regions showing aberrant methylation in the patients was verified using bisulfite-sequencing. Results We found large variability among the patients concerning the number and identity of the differentially methylated regions, but more than 60 regions were aberrantly methylated in two or more patients and a novel region within PPP1R13L was found to be hypomethylated in all the patients. The hypomethylated regions in common between the patients are enriched for the ZFP57 DNA binding motif. Conclusions We have expanded the epimutational spectrum of TNDM1 associated with ZFP57 mutations and found one novel region within PPP1R13L which is hypomethylated in all TNDM1 patients included in this study. Functional studies of the locus might provide further insight into the etiology of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0292-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mads Bak
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.
| | - Susanne E Boonen
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark.,Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - Christina Dahl
- Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark
| | - Johanne M D Hahnemann
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - Deborah J D G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.,Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury NHS Foundation Trust, SP2 8BJ, Salisbury, UK
| | - Zeynep Tümer
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark.,Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200N, Copenhagen, Denmark
| | - Karen Grønskov
- Center for Applied Human Molecular Genetics, Kennedy Center, DK-2600, Glostrup, Denmark
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.,Wessex Clinical Genetics Service, Southampton University Hospitals Trust, Southampton, SO16 5YA, UK
| | - Per Guldberg
- Institute of Cancer Biology, Danish Cancer Society, DK-2100, Copenhagen Ø, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, Institute of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, DK-2200, Copenhagen N, Denmark
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42
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Tillo D, Mukherjee S, Vinson C. Inheritance of Cytosine Methylation. J Cell Physiol 2016; 231:2346-52. [DOI: 10.1002/jcp.25350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/19/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Desiree Tillo
- Laboratory of Metabolism; National Cancer Institute; National Institutes of Health; Bethesda Maryland
| | - Sanjit Mukherjee
- Laboratory of Metabolism; National Cancer Institute; National Institutes of Health; Bethesda Maryland
| | - Charles Vinson
- Laboratory of Metabolism; National Cancer Institute; National Institutes of Health; Bethesda Maryland
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43
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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: 77] [Impact Index Per Article: 8.6] [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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44
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The placenta: phenotypic and epigenetic modifications induced by Assisted Reproductive Technologies throughout pregnancy. Clin Epigenetics 2015; 7:87. [PMID: 26300992 PMCID: PMC4546204 DOI: 10.1186/s13148-015-0120-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/02/2015] [Indexed: 02/07/2023] Open
Abstract
Today, there is growing interest in the potential epigenetic risk related to assisted reproductive technologies (ART). Much evidence in the literature supports the hypothesis that adverse pregnancy outcomes linked to ART are associated with abnormal trophoblastic invasion. The aim of this review is to investigate the relationship between epigenetic dysregulation caused by ART and subsequent placental response. The dialogue between the endometrium and the embryo is a crucial step to achieve successful trophoblastic invasion, thus ensuring a non-complicated pregnancy and healthy offspring. However, as described in this review, ART could impair both actors involved in this dialogue. First, ART may induce epigenetic defects in the conceptus by modifying the embryo environment. Second, as a result of hormone treatments, ART may impair endometrial receptivity. In some cases, it results in embryonic growth arrest but, when the development of the embryo continues, the placenta could bring adaptive responses throughout pregnancy. Amongst the different mechanisms, epigenetics, especially thanks to a finely tuned network of imprinted genes stimulated by foetal signals, may modify nutrient transfer, placental growth and vascularization. If these coping mechanisms are overwhelmed, improper maternal-foetal exchanges occur, potentially leading to adverse pregnancy outcomes such as abortion, preeclampsia or intra-uterine growth restriction. But in most cases, successful placental adaptation enables normal progress of the pregnancy. Nevertheless, the risks induced by these modifications during pregnancy are not fully understood. Metabolic diseases later in life could be exacerbated through the memory of epigenetic adaptation mechanisms established during pregnancy. Thus, more research is still needed to better understand abnormal interactions between the embryo and the milieu in artificial conditions. As trophectoderm cells are in direct contact with the environment, they deserve to be studied in more detail. The ultimate goal of these studies will be to render ART protocols safer. Optimization of the environment will be the key to improving the dialogue between the endometrium and embryo, so as to ensure that placentation after ART is similar to that following natural conception.
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45
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Lu R, Smith RM, Seweryn M, Wang D, Hartmann K, Webb A, Sadee W, Rempala GA. Analyzing allele specific RNA expression using mixture models. BMC Genomics 2015; 16:566. [PMID: 26231172 PMCID: PMC4521363 DOI: 10.1186/s12864-015-1749-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/03/2015] [Indexed: 11/10/2022] Open
Abstract
Background Measuring allele-specific RNA expression provides valuable insights into cis-acting genetic and epigenetic regulation of gene expression. Widespread adoption of high-throughput sequencing technologies for studying RNA expression (RNA-Seq) permits measurement of allelic RNA expression imbalance (AEI) at heterozygous single nucleotide polymorphisms (SNPs) across the entire transcriptome, and this approach has become especially popular with the emergence of large databases, such as GTEx. However, the existing binomial-type methods used to model allelic expression from RNA-seq assume a strong negative correlation between reference and variant allele reads, which may not be reasonable biologically. Results Here we propose a new strategy for AEI analysis using RNA-seq data. Under the null hypothesis of no AEI, a group of SNPs (possibly across multiple genes) is considered comparable if their respective total sums of the allelic reads are of similar magnitude. Within each group of “comparable” SNPs, we identify SNPs with AEI signal by fitting a mixture of folded Skellam distributions to the absolute values of read differences. By applying this methodology to RNA-Seq data from human autopsy brain tissues, we identified numerous instances of moderate to strong imbalanced allelic RNA expression at heterozygous SNPs. Findings with SLC1A3 mRNA exhibiting known expression differences are discussed as examples. Conclusion The folded Skellam mixture model searches for SNPs with significant difference between reference and variant allele reads (adjusted for different library sizes), using information from a group of “comparable” SNPs across multiple genes. This model is particularly suitable for performing AEI analysis on genes with few heterozygous SNPs available from RNA-seq, and it can fit over-dispersed read counts without specifying the direction of the correlation between reference and variant alleles. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1749-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rong Lu
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA
| | - Ryan M Smith
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Michal Seweryn
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA.,Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, 43201, USA
| | - Danxin Wang
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Katherine Hartmann
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Amy Webb
- Department of Biomedical Informatics, Program in Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Grzegorz A Rempala
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, 43210, USA. .,Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, 43201, USA.
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Kappil MA, Green BB, Armstrong DA, Sharp AJ, Lambertini L, Marsit CJ, Chen J. Placental expression profile of imprinted genes impacts birth weight. Epigenetics 2015; 10:842-9. [PMID: 26186239 DOI: 10.1080/15592294.2015.1073881] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The importance of imprinted genes in regulating feto-placental development has been long established. However, a comprehensive assessment of the role of placental imprinted gene expression on fetal growth has yet to be conducted. In this study, we examined the association between the placental expression of 108 established and putative imprinted genes and birth weight in 677 term pregnancies, oversampled for small for gestational age (SGA) and large for gestational age (LGA) infants. Using adjusted multinomial regression analyses, a 2-fold increase in the expression of 9 imprinted genes was positively associated with LGA status: BLCAP [odds ratio (OR) = 3.78, 95% confidence interval (CI): 1.83, 7.82], DLK1 [OR = 1.63, 95% CI: 1.27, 2.09], H19 [OR = 2.79, 95% CI: 1.77, 4.42], IGF2 [OR = 1.43, 95% CI:1.31, 2.40], MEG3 [OR = 1.42, 95% CI: 1.19, 1.71], MEST [OR = 4.78, 95% CI: 2.64, 8.65], NNAT [OR = 1.40, 95% CI: 1.05, 1.86], NDN [OR = 2.52, 95% CI: 1.72, 3.68], and PLAGL1 [OR = 1.85, 95% CI: 1.40, 2.44]. For SGA status, a 2-fold increase in MEST expression was associated with decreased risk [OR = 0.31, 95% CI: 0.17, 0.58], while a 2-fold increase in NNAT expression was associated with increased risk [OR = 1.52, 95% CI: 1.1, 2.1]. Following a factor analysis, all genes significantly associated with SGA or LGA status loaded onto 2 of the 8 gene-sets underlying the variability in the dataset. Our comprehensive placental profiling of imprinted genes in a large birth cohort supports the importance of these genes for fetal growth. Given that abnormal birth weight is implicated in numerous diseases and developmental abnormalities, the expression pattern of placental imprinted genes has the potential to be developed as a novel biomarker for postnatal health outcomes.
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Affiliation(s)
- Maya A Kappil
- a Department of Preventive Medicine ; Icahn School of Medicine at Mount Sinai ; New York , NY USA
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47
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Baran Y, Subramaniam M, Biton A, Tukiainen T, Tsang EK, Rivas MA, Pirinen M, Gutierrez-Arcelus M, Smith KS, Kukurba KR, Zhang R, Eng C, Torgerson DG, Urbanek C, Li JB, Rodriguez-Santana JR, Burchard EG, Seibold MA, MacArthur DG, Montgomery SB, Zaitlen NA, Lappalainen T. The landscape of genomic imprinting across diverse adult human tissues. Genome Res 2015; 25:927-36. [PMID: 25953952 PMCID: PMC4484390 DOI: 10.1101/gr.192278.115] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/07/2015] [Indexed: 12/24/2022]
Abstract
Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues.
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Affiliation(s)
- Yael Baran
- The Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Meena Subramaniam
- Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Anne Biton
- Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Emily K Tsang
- Department of Pathology, Stanford University, Stanford, California 94305, USA; Biomedical Informatics Program, Stanford University, Stanford, California 94305, USA
| | - Manuel A Rivas
- Wellcome Trust Center for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, University of Helsinki, 00014 Helsinki, Finland
| | - Maria Gutierrez-Arcelus
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Kevin S Smith
- Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Kim R Kukurba
- Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Rui Zhang
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Dara G Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Cydney Urbanek
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | | | - Esteban G Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Max A Seibold
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado 80206, USA; Department of Pediatrics, National Jewish Health, Denver, Colorado 80206, USA; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Denver, Denver, Colorado 80045, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University, Stanford, California 94305, USA; Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Noah A Zaitlen
- Department of Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, New York 10013, USA; Department of Systems Biology, Columbia University, New York, New York 10032, USA
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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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50
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Transcriptomic analysis of human placenta in intrauterine growth restriction. Pediatr Res 2015; 77:799-807. [PMID: 25734244 DOI: 10.1038/pr.2015.40] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/13/2014] [Indexed: 01/01/2023]
Abstract
BACKGROUND Intrauterine growth restriction (IUGR) is a frequent complication of pregnancy defined as a restriction of fetal growth. The objective of this work was to improve the knowledge on the pathophysiology of IUGR using a genome-wide method of expression analysis. METHODS We analyzed differentially expressed genes in pooled placental tissues from vascular IUGR (four pools of three placentas) and normal pregnancies (four pools of three placentas) using a long nucleotide microarray platform (Nimblegen). We first did a global bioinformatics analysis based only on P value without any a priori. We secondly focused on "target" genes among the most modified ones. Finally, reverse transcription quantitative polymerase chain reaction (RT-qPCR) was performed on an extended panel of tissue samples (n = 62) on selected "target". RESULTS We identified 636 modified genes among which 206 were upregulated (1.5 and higher; P < 0.05). Groups of patients were classified unambiguously. Genes involved in mitochondrial function and oxidative phosphorylation were decreased affecting three out of five complexes of the respiratory chain of the mitochondria, and thus energy production and metabolism. Among the most induced genes, we identified LEP, IGFBP1, and RBP4. CONCLUSION Complementary studies on the role and function of LEP, IGFBP1, and RBP4 in IUGR pathophysiology and also in fetal programming remain necessary.
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