51
|
Effects of 2,3',4,4'5-pentachlorobiphenyl exposure during pregnancy on epigenetic imprinting and maturation of offspring's oocytes in mice. Arch Toxicol 2019; 93:2575-2592. [PMID: 31388691 DOI: 10.1007/s00204-019-02529-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
Polychlorinated biphenyls (PCBs) are a class of organic pollutants that have been widely found in the environment. The chemical 2,3',4,4'5-pentachlorobiphenyl (PCB118) is an important dioxin-like PCB compound with strong toxicity. PCB118 can accumulate in adipose tissue, serum and milk in mammals, and it is highly enriched in the follicular fluid. In this study, pregnant mice were exposed to 0, 20 and 100 μg/kg/day of PCB118 during pregnancy at the fetal primordial germ cell migration stage. The methylation patterns of the imprinted genes H19, Snrpn, Peg3 and Igf2r as well as the expression levels of Dnmt1, 3a, 3b and 3l, Uhrf1, Tet2 and Tet3 in fully grown germinal vesicle oocytes were measured in offspring. The rates of in vitro maturation, in vitro fertilization, oocyte spindle and chromosomal abnormalities were also calculated. The results showed that prenatal exposure to PCB118 altered the DNA methylation status of differentially methylated regions in some imprinted genes, and the expression levels of Dnmt1, 3a, and 3l, Uhrf1 and Tet3 were also changed. In addition, PCB118 disturbed the maturation process of progeny mouse oocytes in a dose-dependent manner. Therefore, attention should be paid to the potential impacts of PCB118-contaminated dietary intake during pregnancy on the offspring's reproductive health.
Collapse
|
52
|
Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O. Retention of paternal DNA methylome in the developing zebrafish germline. Nat Commun 2019; 10:3054. [PMID: 31296860 PMCID: PMC6624265 DOI: 10.1038/s41467-019-10895-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterise the DNA methylomes of zebrafish PGCs at four developmental stages and identify retention of paternal epigenetic memory, in stark contrast to the findings in mammals. Gene expression profiling of zebrafish PGCs at the same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are independent of DNA methylation-mediated regulation. We identified promoters that are specifically targeted by DNA methylation in somatic and germline tissues during vertebrate embryogenesis and that are frequently misregulated in human cancers. Together, these detailed methylome and transcriptome maps of the zebrafish germline provide insight into vertebrate DNA methylation reprogramming and enhance our understanding of the relationships between germline fate acquisition and oncogenesis.
Collapse
Affiliation(s)
- Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Katsiaryna Tarbashevich
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max-Planck-Institute for Molecular Biomedicine, Roentgenstraße 20, 48149, Münster, Germany
| | - Ryan Lister
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Molecular Medicine Division, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08002, Spain
- ICREA, Barcelona, 08010, Spain
| | - Erez Raz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2010, Australia.
| |
Collapse
|
53
|
Spinelli P, Latchney SE, Reed JM, Fields A, Baier BS, Lu X, McCall MN, Murphy SP, Mak W, Susiarjo M. Identification of the novel Ido1 imprinted locus and its potential epigenetic role in pregnancy loss. Hum Mol Genet 2019; 28:662-674. [PMID: 30403776 DOI: 10.1093/hmg/ddy383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 10/29/2018] [Indexed: 11/14/2022] Open
Abstract
Previous studies show that aberrant tryptophan catabolism reduces maternal immune tolerance and adversely impacts pregnancy outcomes. Tryptophan depletion in pregnancy is facilitated by increased activity of tryptophan-depleting enzymes [i.e. the indolamine-2,3 dioxygenase (IDO)1 and IDO2) in the placenta. In mice, inhibition of IDO1 activity during pregnancy results in fetal loss; however, despite its important role, regulation of Ido1 gene transcription is unknown. The current study shows that the Ido1 and Ido2 genes are imprinted and maternally expressed in mouse placentas. DNA methylation analysis demonstrates that nine CpG sites at the Ido1 promoter constitute a differentially methylated region that is highly methylated in sperm but unmethylated in oocytes. Bisulfite cloning sequencing analysis shows that the paternal allele is hypermethylated while the maternal allele shows low levels of methylation in E9.5 placenta. Further study in E9.5 placentas from the CBA/J X DBA/2 spontaneous abortion mouse model reveals that aberrant methylation of Ido1 is linked to pregnancy loss. DNA methylation analysis in humans shows that IDO1 is hypermethylated in human sperm but partially methylated in placentas, suggesting similar methylation patterns to mouse. Importantly, analysis in euploid placentas from first trimester pregnancy loss reveals that IDO1 methylation significantly differs between the two placenta cohorts, with most CpG sites showing increased percent of methylation in miscarriage placentas. Our study suggests that DNA methylation is linked to regulation of Ido1/IDO1 expression and altered Ido1/IDO1 DNA methylation can adversely influence pregnancy outcomes.
Collapse
Affiliation(s)
- Philip Spinelli
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Sarah E Latchney
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Jasmine M Reed
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ashley Fields
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Brian S Baier
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Xiang Lu
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Shawn P Murphy
- Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, NY, USA
| | - Winifred Mak
- Department of Obstetric Gynecology, Dell Medical School, University of Texas, Austin, TX, USA
| | - Martha Susiarjo
- Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| |
Collapse
|
54
|
SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development. Nat Genet 2019; 51:844-856. [DOI: 10.1038/s41588-019-0398-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/18/2019] [Indexed: 11/09/2022]
|
55
|
Epigenetic changes in mammalian gametes throughout their lifetime: the four seasons metaphor. Chromosoma 2019; 128:423-441. [DOI: 10.1007/s00412-019-00704-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/03/2019] [Accepted: 04/11/2019] [Indexed: 01/22/2023]
|
56
|
Abstract
BACKGROUND Monoallelic expression (MAE) is a frequent genomic phenomenon in normal tissues, however its role in cancer is yet to be fully understood. MAE is defined as the expression of a gene that is restricted to one allele in the presence of a diploid heterozygous genome. Constitutive MAE occurs for imprinted genes, odorant receptors and random X inactivation. Several studies in normal tissues have showed MAE in approximately 5-20% of the cases. However, little information exists on the MAE rate in cancer. In this study we assessed the presence and rate of MAE in melanoma. The genetic basis of melanoma has been studied in depth over the past decades, leading to the identification of mutations/genetic alterations responsible for melanoma development. METHODS To examine the role of MAE in melanoma we used 15 melanoma cell lines and compared their RNA-seq data with genotyping data obtained by the parental TIL (tumor infiltrating lymphocytes). Genotyping was performed using the Illumina HumanOmni1 beadchip. The RNA-seq library preparation and sequencing was performed using the Illumina TruSeq Stranded Total RNA Human Kit and subsequently sequenced using a HiSeq 2500 according to manufacturer's guidelines. By comparing genotyping data with RNA-seq data, we identified SNPs in which DNA genotypes were heterozygous and corresponding RNA genotypes were homozygous. All homozygous DNA genotypes were removed prior to the analysis. To confirm the validity to detect MAE, we examined heterozygous DNA genotypes from X chromosome of female samples as well as for imprinted and olfactory receptor genes and confirmed MAE. RESULTS MAE was detected in all 15 cell lines although to a different rate. When looking at the B-allele frequencies we found a preferential pattern of complete monoallelic expression rather then differential monoallelic expression across the 15 melanoma cell lines. As some samples showed high differences in the homozygous and heterozygous call rate, we looked at the single chromosomes and showed that MAE may be explained by underlying large copy number imbalances in some instances. Interestingly these regions included genes known to play a role in melanoma initiation and progression. Nevertheless, some chromosome regions showed MAE without CN imbalances suggesting that additional mechanisms (including epigenetic silencing) may explain MAE in melanoma. CONCLUSION The biological implications of MAE are yet to be realized. Nevertheless, our findings suggest that MAE is a common phenomenon in melanoma cell lines. Further analyses are currently being undertaken to evaluate whether MAE is gene/pathway specific and to understand whether MAE can be employed by cancers to achieve a more aggressive phenotype.
Collapse
|
57
|
Tucci V, Isles AR, Kelsey G, Ferguson-Smith AC. Genomic Imprinting and Physiological Processes in Mammals. Cell 2019; 176:952-965. [PMID: 30794780 DOI: 10.1016/j.cell.2019.01.043] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 12/22/2022]
Abstract
Complex multicellular organisms, such as mammals, express two complete sets of chromosomes per nucleus, combining the genetic material of both parents. However, epigenetic studies have demonstrated violations to this rule that are necessary for mammalian physiology; the most notable parental allele expression phenomenon is genomic imprinting. With the identification of endogenous imprinted genes, genomic imprinting became well-established as an epigenetic mechanism in which the expression pattern of a parental allele influences phenotypic expression. The expanding study of genomic imprinting is revealing a significant impact on brain functions and associated diseases. Here, we review key milestones in the field of imprinting and discuss mechanisms and systems in which imprinted genes exert a significant role.
Collapse
Affiliation(s)
- Valter Tucci
- Department of Neuroscience and Brain Technologies - Istituto Italiano di Tecnologia, via Morego, 30, 16163, Genova, Italy.
| | - Anthony R Isles
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, CF24 44H, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| |
Collapse
|
58
|
Elli FM, deSanctis L, Maffini MA, Bordogna P, Tessaris D, Pirelli A, Arosio M, Linglart A, Mantovani G. Association of GNAS imprinting defects and deletions of chromosome 2 in two patients: clues explaining phenotypic heterogeneity in pseudohypoparathyroidism type 1B/iPPSD3. Clin Epigenetics 2019; 11:3. [PMID: 30616679 PMCID: PMC6322333 DOI: 10.1186/s13148-018-0607-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/26/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The term pseudohypoparathyroidism (PHP) describes disorders derived from resistance to the parathyroid hormone. Albright hereditary osteodystrophy (AHO) is a disorder with several physical features that can occur alone or in association with PHP. The subtype 1B, classically associated with resistance to PTH and TSH, derives from the epigenetic dysregulation of the GNAS locus. Patients showing features of AHO were described, but no explanation for such phenotypic heterogeneity is available. An AHO-like phenotype was associated with the loss of genetic information stored in chromosome 2q37, making this genomic region an interesting object of study as it could contain modifier genes involved in the development of AHO features in patients with GNAS imprinting defects. The present study aimed to screen a series of 65 patients affected with GNAS imprinting defects, with or without signs of AHO, for the presence of 2q37 deletions in order to find genes involved in the clinical variability. RESULTS The molecular investigations performed on our cohort of patients with GNAS imprinting defects identified two overlapping terminal deletions of the long arm of chromosome 2. The smaller deletion was of approximately 3 Mb and contained 38 genes, one or more of which is potentially involved in the clinical presentation. Patients with the deletions were both affected by a combination of the most pathognomic AHO-like features, brachydactyly, cognitive impairment and/or behavioural defects. Our results support the hypothesis that additional genetic factors besides GNAS methylation defects are involved in the development of a complex phenotype in the subgroup of patients showing signs of AHO. CONCLUSIONS For the first time, the present work describes PHP patients with hormone resistance and AHO signs simultaneously affected by GNAS imprinting defects and 2q37 deletions. Although further studies are needed to confirm the cause of these two rare molecular alterations and to identify candidate genes, this finding provides novel interesting clues for the identification of factors involved in the still unexplained clinical variability observed in PHP1B.
Collapse
Affiliation(s)
- F M Elli
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.
| | - L deSanctis
- Department of Public Health and Paediatric Sciences, University of Torino, Turin, Italy
| | - M A Maffini
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - P Bordogna
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology Unit, Milan, Italy
| | - D Tessaris
- Department of Public Health and Paediatric Sciences, University of Torino, Turin, Italy
| | - A Pirelli
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - M Arosio
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology Unit, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - A Linglart
- APHP, Paediatric Endocrinology and Diabetology for Children, Reference Centre for Rare Disorders of Calcium and Phosphate Metabolism, Platform of Expertise Paris-Sud for Rare Diseases and Filière OSCAR, Bicêtre Paris-Sud Hospital, 94270, Le Kremlin-Bicêtre, France
- APHP, Department of Endocrinology and Diabetology, Reference Centre for Rare Disorders of Calcium and Phosphate Metabolism, 94270, Le Kremlin-Bicêtre, France
| | - G Mantovani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Endocrinology Unit, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| |
Collapse
|
59
|
Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
60
|
Kallimasioti-Pazi EM, Thelakkad Chathoth K, Taylor GC, Meynert A, Ballinger T, Kelder MJE, Lalevée S, Sanli I, Feil R, Wood AJ. Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair. PLoS Biol 2018; 16:e2005595. [PMID: 30540740 PMCID: PMC6306241 DOI: 10.1371/journal.pbio.2005595] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 12/26/2018] [Accepted: 11/21/2018] [Indexed: 11/18/2022] Open
Abstract
Genome editing occurs in the context of chromatin, which is heterogeneous in structure and function across the genome. Chromatin heterogeneity is thought to affect genome editing efficiency, but this has been challenging to quantify due to the presence of confounding variables. Here, we develop a method that exploits the allele-specific chromatin status of imprinted genes in order to address this problem in cycling mouse embryonic stem cells (mESCs). Because maternal and paternal alleles of imprinted genes have identical DNA sequence and are situated in the same nucleus, allele-specific differences in the frequency and spectrum of mutations induced by CRISPR-Cas9 can be unequivocally attributed to epigenetic mechanisms. We found that heterochromatin can impede mutagenesis, but to a degree that depends on other key experimental parameters. Mutagenesis was impeded by up to 7-fold when Cas9 exposure was brief and when intracellular Cas9 expression was low. In contrast, the outcome of mutagenic DNA repair was unaffected by chromatin state, with similar efficiencies of homology-directed repair (HDR) and deletion spectra on maternal and paternal chromosomes. Combined, our data show that heterochromatin imposes a permeable barrier that influences the kinetics, but not the endpoint, of CRISPR-Cas9 genome editing and suggest that therapeutic applications involving low-level Cas9 exposure will be particularly affected by chromatin status.
Collapse
Affiliation(s)
- Eirini M. Kallimasioti-Pazi
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Keerthi Thelakkad Chathoth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Gillian C. Taylor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Meynert
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Tracy Ballinger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Martijn J. E. Kelder
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sébastien Lalevée
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and University of Montpellier, Montpellier, France
| | - Ildem Sanli
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and University of Montpellier, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and University of Montpellier, Montpellier, France
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| |
Collapse
|
61
|
Fontana L, Bedeschi MF, Maitz S, Cereda A, Faré C, Motta S, Seresini A, D'Ursi P, Orro A, Pecile V, Calvello M, Selicorni A, Lalatta F, Milani D, Sirchia SM, Miozzo M, Tabano S. Characterization of multi-locus imprinting disturbances and underlying genetic defects in patients with chromosome 11p15.5 related imprinting disorders. Epigenetics 2018; 13:897-909. [PMID: 30221575 PMCID: PMC6284780 DOI: 10.1080/15592294.2018.1514230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The identification of multilocus imprinting disturbances (MLID) appears fundamental to uncover molecular pathways underlying imprinting disorders (IDs) and to complete clinical diagnosis of patients. However, MLID genetic associated mechanisms remain largely unknown. To characterize MLID in Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes, we profiled by MassARRAY the methylation of 12 imprinted differentially methylated regions (iDMRs) in 21 BWS and 7 SRS patients with chromosome 11p15.5 epimutations. MLID was identified in 50% of BWS and 29% of SRS patients as a maternal hypomethylation syndrome. By next-generation sequencing, we searched for putative MLID-causative mutations in genes involved in methylation establishment/maintenance and found two novel missense mutations possibly causative of MLID: one in NLRP2, affecting ADP binding and protein activity, and one in ZFP42, likely leading to loss of DNA binding specificity. Both variants were paternally inherited. In silico protein modelling allowed to define the functional effect of these mutations. We found that MLID is very frequent in BWS/SRS. In addition, since MLID-BWS patients in our cohort show a peculiar pattern of BWS-associated clinical signs, MLID test could be important for a comprehensive clinical assessment. Finally, we highlighted the possible involvement of ZFP42 variants in MLID development and confirmed NLRP2 as causative locus in BWS-MLID.
Collapse
Affiliation(s)
- L Fontana
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy
| | - M F Bedeschi
- b Clinical Genetics Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Maitz
- c Clinical Pediatric, Genetics Unit , MBBM Foundation, San Gerardo Monza , Monza , Italy
| | - A Cereda
- d Medical Genetics Unit , Papa Giovanni XXIII Hospital , Bergamo , Italy
| | - C Faré
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Motta
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - A Seresini
- f Medical Genetics Laboratory , Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico , Milano , Italy.,g Fondazione Grigioni per il Morbo di Parkinson , Milano , Italy
| | - P D'Ursi
- h Department of Biomedical Sciences National Research Council , Institute for Biomedical Technologies , Segrate , Italy
| | - A Orro
- h Department of Biomedical Sciences National Research Council , Institute for Biomedical Technologies , Segrate , Italy
| | - V Pecile
- i Medical Genetics Division , Institute for maternal and child health IRCCS Burlo Garofolo , Trieste , Italy
| | - M Calvello
- e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy.,j Division of Cancer Prevention and Genetics, IEO , European Institute of Oncology IRCCS , Milano , Italy
| | - A Selicorni
- k UOC Pediatria , ASST Lariana , Como , Italy
| | - F Lalatta
- b Clinical Genetics Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - D Milani
- l Pediatric Highly Intensive Care Unit , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S M Sirchia
- m Medical Genetics, Department of Health Sciences , Università degli Studi di Milano , Milano , Italy
| | - M Miozzo
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy.,e Division of Pathology , Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico , Milano , Italy
| | - S Tabano
- a Laboratory of Molecular Pathology, Department of Pathophysiology and Transplantation , Università degli Studi di Milano , Milano , Italy
| |
Collapse
|
62
|
Beygo J, Mertel C, Kaya S, Gillessen-Kaesbach G, Eggermann T, Horsthemke B, Buiting K. The origin of imprinting defects in Temple syndrome and comparison with other imprinting disorders. Epigenetics 2018; 13:822-828. [PMID: 30227764 DOI: 10.1080/15592294.2018.1514233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Temple syndrome (TS14) is a rare imprinting disorder caused by genetic and epigenetic alterations on chromosome 14q32. A subset of these patients shows an imprinting defect (ID) where the paternal allele harbors a maternal epigenotype thus silencing the paternally expressed genes and leading to an increased expression of the maternally expressed genes. We investigated the grandparental origin of the incorrectly imprinted chromosome 14 in a cohort of 13 TS14 ID patients and their families. In seven families grandmaternal and, in six families, grandpaternal inheritance was observed. These results indicate that the ID occurred after imprint erasure in the paternal germ line. While the complete lack of methylation as observed in the majority of TS14 ID patients may be due to an imprint establishment error in the paternal germ line, cases with methylation mosaicism suggest that in general many IDs (TS14, AS, BWS, and SRS) are in fact of somatic origin in the early or late embryo.
Collapse
Affiliation(s)
- Jasmin Beygo
- a Institut für Humangenetik , Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Claudia Mertel
- a Institut für Humangenetik , Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Sabine Kaya
- a Institut für Humangenetik , Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | | | | | - Bernhard Horsthemke
- a Institut für Humangenetik , Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| | - Karin Buiting
- a Institut für Humangenetik , Universitätsklinikum Essen, Universität Duisburg-Essen , Essen , Germany
| |
Collapse
|
63
|
Khamlichi AA, Feil R. Parallels between Mammalian Mechanisms of Monoallelic Gene Expression. Trends Genet 2018; 34:954-971. [PMID: 30217559 DOI: 10.1016/j.tig.2018.08.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/06/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
Different types of monoallelic gene expression are present in mammals, some of which are highly flexible, whereas others are more rigid. These include allelic exclusion at antigen receptor loci, the expression of olfactory receptor genes, genomic imprinting, X-chromosome inactivation, and random monoallelic expression (MAE). Although these processes play diverse biological roles, and arose through different selective pressures, the underlying epigenetic mechanisms show striking resemblances. Regulatory transcriptional events are important in all systems, particularly in the specification of MAE. Combined with comparative studies between species, this suggests that the different MAE systems found in mammals may have evolved from analogous ancestral processes.
Collapse
Affiliation(s)
- Ahmed Amine Khamlichi
- Institute of Pharmacology and Structural Biology (IPBS), Centre National de la Recherche Scientifique (CNRS) and Paul Sabatier University (UPS), 205 route de Narbonne, 31077 Toulouse, France.
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS and the University of Montpellier, 1919 route de Mende, 34293 Montpellier, France.
| |
Collapse
|
64
|
Yau MYC, Xu L, Huang CL, Wong CM. Long Non-Coding RNAs in Obesity-Induced Cancer. Noncoding RNA 2018; 4:E19. [PMID: 30154386 PMCID: PMC6162378 DOI: 10.3390/ncrna4030019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/22/2018] [Accepted: 08/27/2018] [Indexed: 01/17/2023] Open
Abstract
Many mechanisms of obesity-induced cancers have been proposed. However, it remains unclear whether or not long non-coding RNAs (lncRNAs) play any role in obesity-induced cancers. In this article, we briefly discuss the generally accepted hypotheses explaining the mechanisms of obesity-induced cancers, summarize the latest evidence for the expression of a number of well-known cancer-associated lncRNAs in obese subjects, and propose the potential contribution of lncRNAs to obesity-induced cancers. We hope this review can serve as an inspiration to scientists to further explore the regulatory roles of lncRNAs in the development of obesity-induced cancers. Those findings will be fundamental in the development of effective therapeutics or interventions to combat this life-threatening adverse effect of obesity.
Collapse
Affiliation(s)
- Mabel Yin-Chun Yau
- School of Medical and Health Sciences, Tung Wah College, Hong Kong, China.
| | - Lu Xu
- Department of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Chien-Ling Huang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
| | - Chi-Ming Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
| |
Collapse
|
65
|
Pathak R, Feil R. Environmental effects on chromatin repression at imprinted genes and endogenous retroviruses. Curr Opin Chem Biol 2018; 45:139-147. [DOI: 10.1016/j.cbpa.2018.04.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/05/2018] [Accepted: 04/24/2018] [Indexed: 12/26/2022]
|
66
|
Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Do social insects support Haig's kin theory for the evolution of genomic imprinting? Epigenetics 2018; 12:725-742. [PMID: 28703654 PMCID: PMC5739101 DOI: 10.1080/15592294.2017.1348445] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although numerous imprinted genes have been described in several lineages, the phenomenon of genomic imprinting presents a peculiar evolutionary problem. Several hypotheses have been proposed to explain gene imprinting, the most supported being Haig's kinship theory. This theory explains the observed pattern of imprinting and the resulting phenotypes as a competition for resources between related individuals, but despite its relevance it has not been independently tested. Haig's theory predicts that gene imprinting should be present in eusocial insects in many social scenarios. These lineages are therefore ideal for testing both the theory's predictions and the mechanism of gene imprinting. Here we review the behavioral evidence of genomic imprinting in eusocial insects, the evidence of a mechanism for genomic imprinting and finally we evaluate recent results showing parent of origin allele specific expression in honeybees in the light of Haig's theory.
Collapse
Affiliation(s)
- Mirko Pegoraro
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Hollie Marshall
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Zoë N Lonsdale
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Eamonn B Mallon
- a Department of Genetics and Genome Biology , University of Leicester , UK
| |
Collapse
|
67
|
Rossitto M, Marchive C, Pruvost A, Sellem E, Ghettas A, Badiou S, Sutra T, Poulat F, Philibert P, Boizet-Bonhoure B. Intergenerational effects on mouse sperm quality after in utero exposure to acetaminophen and ibuprofen. FASEB J 2018; 33:339-357. [PMID: 29979629 DOI: 10.1096/fj.201800488rrr] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nonsteroidal antiinflammatory drugs and analgesic drugs, such as N-acetyl- p-aminophenol (APAP; acetaminophen, paracetamol), are widely used by pregnant women. Accumulating evidence has indicated that these molecules can favor genital malformations in newborn boys and reproductive disorders in adults. However, the consequences on postnatal testis development and adult reproductive health after exposure during early embryogenesis are still unknown. Using the mouse model, we show that in utero exposure to therapeutic doses of the widely used APAP-ibuprofen combination during the sex determination period leads to early differentiation and decreased proliferation of male embryonic germ cells, and early 5-methylcytosine and extracellular matrix protein deposition in 13.5 d postcoitum exposed testes. Consequently, in postnatal testes, Sertoli-cell maturation is delayed, the Leydig-cell compartment is hyperplasic, and the spermatogonia A pool is decreased. This results in a reduced production of testosterone and in epididymal sperm parameter defects. We observed a reduced sperm count (19%) in utero-exposed (F0) adult males and also a reduced sperm motility (40%) in their offspring (F1) when both parents were exposed, which leads to subfertility among the 6 mo old F1 animals. Our study suggests that the use of these drugs during the critical period of sex determination affects the germ-line development and leads to adverse effects that could be passed to the offspring.-Rossitto, M., Marchive, C., Pruvost, A., Sellem, E., Ghettas, A., Badiou, S., Sutra, T., Poulat, F., Philibert, P., Boizet-Bonhoure, B. Intergenerational effects on mouse sperm quality after in utero exposure to acetaminophen and ibuprofen.
Collapse
Affiliation(s)
- Moïra Rossitto
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Candice Marchive
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Alain Pruvost
- Service de Pharmacologie et d'Immunoanalyse (SPI), Small Molecules Analysis by Mass Spectrometry (SMArt-MS), Commissariat à l'Energie Atomique (CEA), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Gif sur Yvette, France
| | - Eli Sellem
- Research and Development Department, Allice, Biology of Reproduction, Institut National de la Recherche Agronomique (INRA) Domaine de Vilvert, Jouy en Josas, France
| | - Aurélie Ghettas
- Service de Pharmacologie et d'Immunoanalyse (SPI), Small Molecules Analysis by Mass Spectrometry (SMArt-MS), Commissariat à l'Energie Atomique (CEA), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Gif sur Yvette, France
| | - Stéphanie Badiou
- Département de Biochimie et d'Hormonologie, Hopital Lapeyronie, Centre Hospitalier Universitaire (CHU) de Montpellier; PhyMedExp, INSERM Unité 1046, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 9214, Université de Montpellier, Montpellier, France
| | - Thibault Sutra
- Département de Biochimie et d'Hormonologie, Hopital Lapeyronie, Centre Hospitalier Universitaire (CHU) de Montpellier; PhyMedExp, INSERM Unité 1046, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 9214, Université de Montpellier, Montpellier, France
| | - Francis Poulat
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| | - Pascal Philibert
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France.,Département de Biochimie et d'Hormonologie, Hopital Lapeyronie, Centre Hospitalier Universitaire (CHU) de Montpellier; PhyMedExp, INSERM Unité 1046, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 9214, Université de Montpellier, Montpellier, France
| | - Brigitte Boizet-Bonhoure
- Institute of Human Genetics, Centre National de la Recherche Scientifique (CNRS), University of Montpellier, Montpellier, France
| |
Collapse
|
68
|
Kochmanski JJ, Marchlewicz EH, Cavalcante RG, Perera BPU, Sartor MA, Dolinoy DC. Longitudinal Effects of Developmental Bisphenol A Exposure on Epigenome-Wide DNA Hydroxymethylation at Imprinted Loci in Mouse Blood. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:077006. [PMID: 30044229 PMCID: PMC6108846 DOI: 10.1289/ehp3441] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/04/2018] [Accepted: 06/15/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic machinery plays an important role in genomic imprinting, a developmental process that establishes parent-of-origin-specific monoallelic gene expression. Although a number of studies have investigated the role of 5-methylcytosine in imprinting control, the contribution of 5-hydroxymethylcytosine (5-hmC) to this epigenetic phenomenon remains unclear. OBJECTIVES Using matched mouse blood samples (from mice at 2, 4, and 10 months of age), our objective was to examine the effects of perinatal bisphenol A (BPA) exposure (50 μg/kg diet) on longitudinal 5-hmC patterns at imprinted regions. We also aimed to test the hypothesis that 5-hmC would show defined patterns at imprinted genes that persist across the life course. METHODS Genome-wide 5-hmC levels were measured using hydroxymethylated DNA immunoprecipitation sequencing (HMeDIP-seq). Modeling of differential hydroxymethylation by BPA exposure was performed using a pipeline of bioinformatics tools, including the csaw R package. RESULTS Based on BPA exposure, we identified 5,950 differentially hydroxymethylated regions (DHMRs), including 12 DHMRs that were annotated to murine imprinted genes—Gnas, Grb10, Plagl1, Klf14, Pde10a, Snrpn, Airn, Cmah, Ppp1r9a, Kcnq1, Phactr2, and Pde4d. When visualized, these imprinted gene DHMRs showed clear, consistent patterns of differential 5-hmC by developmental BPA exposure that persisted throughout adulthood. CONCLUSIONS These data show long-term establishment of 5-hmC marks at imprinted loci during development. Further, the effect of perinatal BPA exposure on 5-hmC at specific imprinted loci indicates that developmental exposure to environmental toxicants may alter long-term imprinted gene regulation via an epigenetic mechanism. https://doi.org/10.1289/EHP3441.
Collapse
Affiliation(s)
- Joseph J Kochmanski
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elizabeth H Marchlewicz
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| |
Collapse
|
69
|
Matsuzaki H, Okamura E, Kuramochi D, Ushiki A, Hirakawa K, Fukamizu A, Tanimoto K. Synthetic DNA fragments bearing ICR cis elements become differentially methylated and recapitulate genomic imprinting in transgenic mice. Epigenetics Chromatin 2018; 11:36. [PMID: 29958543 PMCID: PMC6027785 DOI: 10.1186/s13072-018-0207-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/01/2018] [Indexed: 11/24/2022] Open
Abstract
Background Genomic imprinting is governed by allele-specific DNA methylation at imprinting control regions (ICRs), and the mechanism controlling its differential methylation establishment during gametogenesis has been a subject of intensive research interest. However, recent studies have reported that gamete methylation is not restricted at the ICRs, thus highlighting the significance of ICR methylation maintenance during the preimplantation period where genome-wide epigenetic reprogramming takes place. Using transgenic mice (TgM), we previously demonstrated that the H19 ICR possesses autonomous activity to acquire paternal-allele-specific DNA methylation after fertilization. Furthermore, this activity is indispensable for the maintenance of imprinted methylation at the endogenous H19 ICR during the preimplantation period. In addition, we showed that a specific 5′ fragment of the H19 ICR is required for its paternal methylation after fertilization, while CTCF and Sox-Oct motifs are essential for its maternal protection from undesirable methylation after implantation. Results To ask whether specific cis elements are sufficient to reconstitute imprinted methylation status, we employed a TgM co-placement strategy for facilitating detection of postfertilization methylation activity and precise comparison of test sequences. Bacteriophage lambda DNA becomes highly methylated regardless of its parental origin and thus can be used as a neutral sequence bearing no inclination for differential DNA methylation. We previously showed that insertion of only CTCF and Sox-Oct binding motifs from the H19 ICR into a lambda DNA (LCb) decreased its methylation level after both paternal and maternal transmission. We therefore appended a 478-bp 5′ sequence from the H19 ICR into the LCb fragment and found that it acquired paternal-allele-specific methylation, the dynamics of which was identical to that of the H19 ICR, in TgM. Crucially, transgene expression also became imprinted. Although there are potential binding sites for ZFP57 (a candidate protein thought to control the methylation imprint) in the larger H19 ICR, they are not found in the 478-bp fragment, rendering the role of ZFP57 in postfertilization H19 ICR methylation a still open question. Conclusions Our results demonstrate that a differentially methylated region can be reconstituted by combining the activities of specific imprinting elements and that these elements together determine the activity of a genomically imprinted region in vivo. Electronic supplementary material The online version of this article (10.1186/s13072-018-0207-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hitomi Matsuzaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Eiichi Okamura
- Graduate School of Biomedical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Daichi Kuramochi
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Aki Ushiki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan
| | - Katsuhiko Hirakawa
- Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Akiyoshi Fukamizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Keiji Tanimoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan. .,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan.
| |
Collapse
|
70
|
Joh K, Matsuhisa F, Kitajima S, Nishioka K, Higashimoto K, Yatsuki H, Kono T, Koseki H, Soejima H. Growing oocyte-specific transcription-dependent de novo DNA methylation at the imprinted Zrsr1-DMR. Epigenetics Chromatin 2018; 11:28. [PMID: 29875017 PMCID: PMC5989421 DOI: 10.1186/s13072-018-0200-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/31/2018] [Indexed: 12/21/2022] Open
Abstract
Background Zrsr1 is a paternally expressed imprinted gene located in the first intron of Commd1, and the Zrsr1 promoter resides in a differentially methylated region (DMR) that is maternally methylated in the oocyte. However, a mechanism for the establishment of the methylation has remained obscure. Commd1 is transcribed in the opposite direction to Zrsr1 with predominant maternal expression, especially in the adult brain.
Results We found Commed1 transcribed through the DMR in the growing oocyte. Zrsr1-DMR methylation was abolished by the prevention of Commd1 transcription. Furthermore, methylation did not occur at the artificially unmethylated maternal Zrsr1-DMR during embryonic development when transcription through the DMR was restored in the zygote. Loss of methylation at the maternal Zrsr1-DMR resulted in biallelic Zrsr1 expression and reduced the extent of the predominant maternal expression of Commd1. Conclusions These results indicate that the establishment of methylation at Zrsr1-DMR occurs in a transcription-dependent and oocyte-specific manner and caused Zrsr1 imprinting by repressing maternal expression. The predominant maternal expression of Commd1 is likely caused by transcriptional interference by paternal Zrsr1 expression. Electronic supplementary material The online version of this article (10.1186/s13072-018-0200-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
| | - Fumikazu Matsuhisa
- Division of Biological Resources and Development, Analytical Research Center for Experimental Sciences, Saga University, Saga, 849-8501, Japan
| | - Shuji Kitajima
- Division of Biological Resources and Development, Analytical Research Center for Experimental Sciences, Saga University, Saga, 849-8501, Japan
| | - Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Tomohiro Kono
- Laboratory of Animal Developmental Biology, Department of Bioscience, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
| |
Collapse
|
71
|
Heritable, Allele-Specific Chromosomal Looping between Tandem Promoters Specifies Promoter Usage of SHC1. Mol Cell Biol 2018; 38:MCB.00658-17. [PMID: 29440311 DOI: 10.1128/mcb.00658-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 11/20/2022] Open
Abstract
One-half of the genes in the human genome contain alternative promoters, some of which generate products with opposing functions. Aberrant silencing or activation of such alternative promoters is associated with multiple diseases, including cancer, but little is known regarding the molecular mechanisms that control alternative promoter choice. The SHC1 gene encodes p46Shc/p52Shc and p66Shc, proteins oppositely regulating anchorage-independent growth that are produced by transcription initiated from the upstream and downstream tandem promoters of SHC1, respectively. Here we demonstrate that activation of these promoters is mutually exclusive on separate alleles in single primary endothelial cells in a heritable fashion, ensuring expression of both transcripts by the cell. Peripheral blood lymphocytes that do not transcribe p66Shc transcribed p52Shc biallelically. This distinct monoallelic transcription pattern is established by allele-specific chromosomal looping between tandem promoters, which silences the upstream promoter. Our results reveal a new mechanism to control alternative promoter usage through higher-order chromatin structure.
Collapse
|
72
|
Is ZFP57 binding to H19/IGF2:IG-DMR affected in Silver-Russell syndrome? Clin Epigenetics 2018; 10:23. [PMID: 29484033 PMCID: PMC5822596 DOI: 10.1186/s13148-018-0454-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/02/2018] [Indexed: 01/21/2023] Open
Abstract
Background Loss of paternal methylation (LOM) of the H19/IGF2 intergenic differentially methylated region (H19/IGF2:IG-DMR) causes alteration of H19/IGF2 imprinting and Silver-Russell syndrome (SRS). Recently, internal deletions of the H19/IGF2:IG-DMR have been associated with LOM and SRS when present on the paternal chromosome. In contrast, previously described deletions, most of which cause gain of methylation (GOM) and Beckwith-Wiedemann syndrome (BWS) on maternal transmission, were consistently associated with normal methylation and phenotype if paternally inherited. Presentation of the hypothesis The presence of several target sites (ZTSs) and three demonstrated binding regions (BRs) for the imprinting factor ZFP57 in the H19/IGF2:IG-DMR suggest the involvement of this factor in the maintenance of methylation of this locus. By comparing the extension of the H19/IGF2:IG-DMR deletions with the binding profile of ZFP57, we propose that the effect of the deletions on DNA methylation and clinical phenotype is dependent on their interference with ZFP57 binding. Indeed, deletions strongly affecting a ZFP57 BR result in LOM and SRS, while deletions preserving a significant number of ZFPs in each BR do not alter methylation and are associated with normal phenotype. Testing the hypothesis The generation of transgenic mouse lines in which the endogenous H19/IGF2:IG-DMR is replaced by the human orthologous locus including the three ZFP57 BRs or their mutant versions will allow to test the role of ZFP57 binding in imprinted methylation and growth phenotype. Implications of the hypothesis Similarly to what is proposed for maternally inherited BWS mutations and CTCF and OCT4/SOX2 binding, we suggest that deletions of the H19/IGF2:IG-DMR result in SRS with LOM if ZFP57 binding on the paternal chromosome is affected. Electronic supplementary material The online version of this article (10.1186/s13148-018-0454-7) contains supplementary material, which is available to authorized users.
Collapse
|
73
|
Clinical and genetic-epigenetic aspects of recurrent hydatidiform mole: A review of literature. Taiwan J Obstet Gynecol 2018; 57:1-6. [DOI: 10.1016/j.tjog.2017.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2017] [Indexed: 11/19/2022] Open
|
74
|
Saha P, Verma S, Pathak RU, Mishra RK. Long Noncoding RNAs in Mammalian Development and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:155-198. [PMID: 28815540 DOI: 10.1007/978-981-10-5203-3_6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively. These transcripts regulate epigenetic processes and constitute an important layer of regulatory information essential for organismal development and play a causative role in diseases. The noncoding RNA-directed regulatory circuit controls complex characteristics. Sequence variations in noncoding RNAs influence evolution, quantitative traits, and disease susceptibility. This chapter presents an account on a class of such noncoding transcripts that are longer than 200 nucleotides (long noncoding RNA-lncRNA) in mammalian development and diseases.
Collapse
Affiliation(s)
- Parna Saha
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Shreekant Verma
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Rashmi U Pathak
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
| |
Collapse
|
75
|
Takahashi N, Gray D, Strogantsev R, Noon A, Delahaye C, Skarnes WC, Tate PH, Ferguson-Smith AC. ZFP57 and the Targeted Maintenance of Postfertilization Genomic Imprints. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:177-87. [PMID: 27325708 DOI: 10.1101/sqb.2015.80.027466] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications play an important role in modulating genome function. In mammals, inappropriate epigenetic states can cause embryonic lethality and various acquired and inherited diseases; hence, it is important to understand how such states are formed and maintained in particular genomic contexts. Genomic imprinting is a process in which epigenetic states provide a sustained memory of parental origin and cause gene expression/repression from only one of the two parental chromosomes. Genomic imprinting is therefore a valuable model to decipher the principles and processes associated with the targeting and maintenance of epigenetic states in general. Krüppel-associated box zinc finger proteins (KRAB-ZFPs) are proteins that have the potential to mediate this. ZFP57, one of the best characterized proteins in this family, has been shown to target and maintain epigenetic states at imprinting control regions after fertilization. Its role in imprinting through the use of ZFP57 mutants in mouse and the wider implications of KRAB-ZFPs for the targeted maintenance of epigenetic states are discussed here.
Collapse
Affiliation(s)
- Nozomi Takahashi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Dionne Gray
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Angela Noon
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Celia Delahaye
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - William C Skarnes
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Peri H Tate
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | | |
Collapse
|
76
|
Harper JC, Aittomäki K, Borry P, Cornel MC, de Wert G, Dondorp W, Geraedts J, Gianaroli L, Ketterson K, Liebaers I, Lundin K, Mertes H, Morris M, Pennings G, Sermon K, Spits C, Soini S, van Montfoort APA, Veiga A, Vermeesch JR, Viville S, Macek M. Recent developments in genetics and medically assisted reproduction: from research to clinical applications. Eur J Hum Genet 2018; 26:12-33. [PMID: 29199274 PMCID: PMC5839000 DOI: 10.1038/s41431-017-0016-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022] Open
Abstract
Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.
Collapse
Affiliation(s)
- J C Harper
- Institute for Women's Health, University College London, London, UK
| | - K Aittomäki
- Laboratory of Genetics, Helsinki University Hospital, Helsinki, Finland
| | - P Borry
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - M C Cornel
- Department of Clinical Genetics, Section Community Genetics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - G de Wert
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, Maastricht, The Netherlands
| | - W Dondorp
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, Maastricht, The Netherlands
| | - J Geraedts
- Department Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - L Gianaroli
- S.I.S.Me.R. Reproductive Medicine Unit, Bologna, Italy
| | | | - I Liebaers
- Center for Medical Genetics, UZ Brussels, Brussels, Belgium
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - K Lundin
- Reproductive Medicine, Sahlgrenska University Hospital, Göteborg, Sweden
| | - H Mertes
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - M Morris
- Synlab Genetics, Lausanne, Switzerland
| | - G Pennings
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - C Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - S Soini
- Helsinki Biobank, Helsinki University Central Hospital, Helsinki, Finland
| | - A P A van Montfoort
- IVF Laboratory, Department of Obstetrics & Gynaecology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - A Veiga
- Barcelona Stem Cell Bank, Centre of Regenerative Medicine in Barcelona, Hospital Duran i Reynals, Barcelona, Spain
- Reproductive Medicine Service of Dexeus Woman Health, Barcelona, Spain
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Viville
- Institute of Parasitology and Pathology, University of Strasbourg, Strasbourg, France
- Laboratory of Genetic Diagnostics, UF3472-Genetics of Infertility, Nouvel Hôpital Civil, Strasbourg, France
| | - M Macek
- Department of Biology and Medical Genetics, Charles University-2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
| |
Collapse
|
77
|
Harper JC, Aittomäki K, Borry P, Cornel MC, de Wert G, Dondorp W, Geraedts J, Gianaroli L, Ketterson K, Liebaers I, Lundin K, Mertes H, Morris M, Pennings G, Sermon K, Spits C, Soini S, van Montfoort APA, Veiga A, Vermeesch JR, Viville S, Macek M. Recent developments in genetics and medically-assisted reproduction: from research to clinical applications †‡. Hum Reprod Open 2017; 2017:hox015. [PMID: 31486804 PMCID: PMC6276693 DOI: 10.1093/hropen/hox015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022] Open
Abstract
Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively-parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.
Collapse
Affiliation(s)
- J C Harper
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - K Aittomäki
- Laboratory of Genetics, Helsinki University Hospital, PO Box 720, FI-00029, Helsinki, Finland
| | - P Borry
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Kapucijnenvoer 35 - Box 7001. B-3000, Leuven Belgium
| | - M C Cornel
- Department of Clinical Genetics, Amsterdam Public Health Research Institute, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - G de Wert
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, De Byeplein 1, 6229 HA Maastricht, The Netherlands
| | - W Dondorp
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, De Byeplein 1, 6229 HA Maastricht, The Netherlands
| | - J Geraedts
- Department Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - L Gianaroli
- S.I.S.Me.R. Reproductive Medicine Unit, Via Mazzini 12, 40138 Bologna, Italy
| | - K Ketterson
- Althea Science, Inc., 3 Regent St #301, Livingston, NJ 07039, USA
| | - I Liebaers
- Centre for Medical Genetics, UZ Brussel, Laarbeeklaan 101, B-1090 Brussels, Belgium
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - K Lundin
- Reproductive Medicine, Sahlgrenska University Hospital, Blå Stråket 6, 413 45, Göteborg, Sweden
| | - H Mertes
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Belgium
| | - M Morris
- Synlab Genetics, chemin d'Entre-Bois 21, CH-1018, Lausanne, Switzerland
| | - G Pennings
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Belgium
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - C Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - S Soini
- Helsinki Biobank, Helsinki University Central Hospital, Haartmaninkatu 3, PO Box 400, 00029 HUS, Helsinki, Finland
| | - A P A van Montfoort
- IVF laboratory, Department of Obstetrics and Gynaecology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - A Veiga
- Barcelona Stem Cell Bank, Centre of Regenerative Medicine in Barcelona, Hospital Duran i Reynals, Gran Via de l' Hospitalet 199, 08908, Hospitalet de Llobregat, Barcelona, Spain
- Reproductive Medicine Service of Dexeus Woman Health, Gran Via Carles III, 71-75 - 08028 Barcelona, Spain
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium
| | - S Viville
- Institute of Parasitology and Pathology, University of Strasbourg, 3 rue Koberlé, 67000 Strasbourg, France
- Laboratory of Genetic Diagnostics, UF3472-Genetics of Infertility, Nouvel Hôpital Civil, 1 place de l'Hôpital, 67091 Strasbourg cedex, France
| | - M Macek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, Prague CZ-15006, Czech Republic
| |
Collapse
|
78
|
Laqqan M, Tierling S, Alkhaled Y, LoPorto C, Hammadeh ME. Alterations in sperm DNA methylation patterns of oligospermic males. Reprod Biol 2017; 17:396-400. [DOI: 10.1016/j.repbio.2017.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/28/2017] [Accepted: 10/28/2017] [Indexed: 12/12/2022]
|
79
|
Mackay DJ, Temple IK. Human imprinting disorders: Principles, practice, problems and progress. Eur J Med Genet 2017; 60:618-626. [DOI: 10.1016/j.ejmg.2017.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 12/17/2022]
|
80
|
Abstract
Inheritance of DNA methylation states from gametes determines genomic imprinting in mammals. A new study shows that repressive chromatin in oocytes can also confer imprinting.
Collapse
Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| |
Collapse
|
81
|
Pathak R, Feil R. Oocyte-derived histone H3 lysine 27 methylation controls gene expression in the early embryo. Nat Struct Mol Biol 2017; 24:685-686. [DOI: 10.1038/nsmb.3456] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
82
|
Haertle L, Maierhofer A, Böck J, Lehnen H, Böttcher Y, Blüher M, Schorsch M, Potabattula R, El Hajj N, Appenzeller S, Haaf T. Hypermethylation of the non-imprinted maternal MEG3 and paternal MEST alleles is highly variable among normal individuals. PLoS One 2017; 12:e0184030. [PMID: 28854270 PMCID: PMC5576652 DOI: 10.1371/journal.pone.0184030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/16/2017] [Indexed: 01/09/2023] Open
Abstract
Imprinted genes show parent-specific activity (functional haploidy), which makes them particularly vulnerable to epigenetic dysregulation. Here we studied the methylation profiles of oppositely imprinted genes at single DNA molecule resolution by two independent parental allele-specific deep bisulfite sequencing (DBS) techniques. Using Roche (GSJunior) next generation sequencing technology, we analyzed the maternally imprinted MEST promoter and the paternally imprinted MEG3 intergenic (IG) differentially methylated region (DMR) in fetal cord blood, adult blood, and visceral adipose tissue. Epimutations were defined as paternal or maternal alleles with >50% aberrantly (de)methylated CpG sites, showing the wrong methylation imprint. The epimutation rates (range 2–66%) of the paternal MEST and the maternal MEG3 IG DMR allele, which should be completely unmethylated, were significantly higher than those (0–15%) of the maternal MEST and paternal MEG3 alleles, which are expected to be fully methylated. This hypermethylation of the non-imprinted allele (HNA) was independent of parental origin. Very low epimutation rates in sperm suggest that HNA occurred after fertilization. DBS with Illumina (MiSeq) technology confirmed HNA for the MEST promoter and the MEG3 IG DMR, and to a lesser extent, for the paternally imprinted secondary MEG3 promoter and the maternally imprinted PEG3 promoter. HNA leads to biallelic methylation of imprinted genes in a considerable proportion of normal body cells (somatic mosaicism) and is highly variable between individuals. We propose that during development and differentiation maintenance of differential methylation at most imprinting control regions may become to some extent redundant. The accumulation of stochastic and environmentally-induced methylation errors on the non-imprinted allele may increase epigenetic diversity between cells and individuals.
Collapse
Affiliation(s)
- Larissa Haertle
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Julia Böck
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Harald Lehnen
- Department of Gynecology and Obstetrics, Municipal Clinics, Mönchengladbach, Germany
| | - Yvonne Böttcher
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, Leipzig, Germany
- Institute of Clinical Medicine, University of Oslo, Lørenskog, Norway
| | - Matthias Blüher
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, Leipzig, Germany
| | | | - Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Silke Appenzeller
- Core Unit Systems Medicine, Julius Maximilians University, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- * E-mail:
| |
Collapse
|
83
|
Kim J, He H, Kim H. Inversion of the imprinting control region of the Peg3 domain. PLoS One 2017; 12:e0181591. [PMID: 28719641 PMCID: PMC5515438 DOI: 10.1371/journal.pone.0181591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/03/2017] [Indexed: 11/19/2022] Open
Abstract
The imprinting of the mouse Peg3 domain is controlled through a 4-kb genomic region encompassing the bidirectional promoter and 1st exons of Peg3 and Usp29. In the current study, this ICR was inverted to test its orientation dependency for the transcriptional and imprinting control of the Peg3 domain. The inversion resulted in the exchange of promoters and 1st exons between Peg3 and Usp29. Paternal transmission of this inversion caused 10-fold down-regulation of Peg3 and 2-fold up-regulation of Usp29 in neonatal heads, consistent with its original promoter strength in each direction. The paternal transmission also resulted in reduced body size among the animals, which was likely contributed by the dramatic down-regulation of Peg3. Transmission through either allele caused no changes in the DNA methylation and imprinting status of the Peg3 domain except that Zfp264 became bi-allelic through the maternal transmission. Overall, the current study suggests that the orientation of the Peg3-ICR may play no role in its allele-specific DNA methylation, but very critical for the transcriptional regulation of the entire imprinted domain.
Collapse
Affiliation(s)
- Joomyeong Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
- * E-mail:
| | - Hongzhi He
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Hana Kim
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| |
Collapse
|
84
|
Singh VB, Sribenja S, Wilson KE, Attwood KM, Hillman JC, Pathak S, Higgins MJ. Blocked transcription through KvDMR1 results in absence of methylation and gene silencing resembling Beckwith-Wiedemann syndrome. Development 2017; 144:1820-1830. [PMID: 28428215 PMCID: PMC5450836 DOI: 10.1242/dev.145136] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/23/2017] [Indexed: 12/30/2022]
Abstract
The maternally methylated KvDMR1 ICR regulates imprinted expression of a cluster of maternally expressed genes on human chromosome 11p15.5. Disruption of imprinting leads to Beckwith-Wiedemann syndrome (BWS), an overgrowth and cancer predisposition condition. In the majority of individuals with BWS, maternal-specific methylation at KvDMR1 is absent and genes under its control are repressed. We analyzed a mouse model carrying a poly(A) truncation cassette inserted to prevent RNA transcripts from elongation through KvDMR1. Maternal inheritance of this mutation resulted in absence of DNA methylation at KvDMR1, which led to biallelic expression of Kcnq1ot1 and suppression of maternally expressed genes. This study provides further evidence that transcription is required for establishment of methylation at maternal gametic DMRs. More importantly, this mouse model recapitulates the molecular phenotypic characteristics of the most common form of BWS, including loss of methylation at KvDMR1 and biallelic repression of Cdkn1c, suggesting that deficiency of maternal transcription through KvDMR1 may be an underlying cause of some BWS cases.
Collapse
Affiliation(s)
- Vir B Singh
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Sirinapa Sribenja
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Kayla E Wilson
- Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Kristopher M Attwood
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Joanna C Hillman
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Shilpa Pathak
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Michael J Higgins
- Departments of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| |
Collapse
|
85
|
Bouschet T, Dubois E, Reynès C, Kota SK, Rialle S, Maupetit-Méhouas S, Pezet M, Le Digarcher A, Nidelet S, Demolombe V, Cavelier P, Meusnier C, Maurizy C, Sabatier R, Feil R, Arnaud P, Journot L, Varrault A. In Vitro Corticogenesis from Embryonic Stem Cells Recapitulates the In Vivo Epigenetic Control of Imprinted Gene Expression. Cereb Cortex 2017; 27:2418-2433. [PMID: 27095822 DOI: 10.1093/cercor/bhw102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In vitro corticogenesis from embryonic stem cells (ESCs) is an attractive model of cortical development and a promising tool for cortical therapy. It is unknown to which extent epigenetic mechanisms crucial for cortex development and function, such as parental genomic imprinting, are recapitulated by in vitro corticogenesis. Here, using genome-wide transcriptomic and methylation analyses on hybrid mouse tissues and cells, we find a high concordance of imprinting status between in vivo and ESC-derived cortices. Notably, in vitro corticogenesis strictly reproduced the in vivo parent-of-origin-dependent expression of 41 imprinted genes (IGs), including Mest and Cdkn1c known to control corticogenesis. Parent-of-origin-dependent DNA methylation was also conserved at 14 of 18 imprinted differentially methylated regions. The least concordant imprinted locus was Gpr1-Zdbf2, where the aberrant bi-allelic expression of Zdbf2 and Adam23 was concomitant with a gain of methylation on the maternal allele in vitro. Combined, our data argue for a broad conservation of the epigenetic mechanisms at imprinted loci in cortical cells derived from ESCs. We propose that in vitro corticogenesis helps to define the still poorly understood mechanisms that regulate imprinting in the brain and the roles of IGs in cortical development.
Collapse
Affiliation(s)
- Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Emeric Dubois
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Christelle Reynès
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Satya K Kota
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Stéphanie Rialle
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Stéphanie Maupetit-Méhouas
- GReD (Genetics, Reproduction and Development), CNRS UMR6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Mikael Pezet
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Sabine Nidelet
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Vincent Demolombe
- Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Patricia Cavelier
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Céline Meusnier
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Chloé Maurizy
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France.,Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Robert Sabatier
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS UMR 5535, University of Montpellier, Montpellier, France
| | - Philippe Arnaud
- GReD (Genetics, Reproduction and Development), CNRS UMR6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Laurent Journot
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France.,Montpellier GenomiX, BioCampus Montpellier, CNRS UMS3426, INSERM US009, Université de Montpellier, Montpellier, France
| | - Annie Varrault
- Institut de Génomique Fonctionnelle (IGF), CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| |
Collapse
|
86
|
Deng J, Qu X, Lu P, Yang X, Zhu Y, Ji H, Wang Y, Jiang Z, Li X, Zhong Y, Yang H, Pan H, Young WB, Zhu H. Specific and Stable Suppression of HIV Provirus Expression In Vitro by Chimeric Zinc Finger DNA Methyltransferase 1. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 6:233-242. [PMID: 28325289 PMCID: PMC5363508 DOI: 10.1016/j.omtn.2017.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 12/20/2016] [Accepted: 01/09/2017] [Indexed: 12/25/2022]
Abstract
HIV-1 inserts its proviral DNA into the infected host cells, by which HIV proviral DNA can then be duplicated along with each cell division. Thus, provirus cannot be eradicated completely by current antiretroviral therapy. We have developed an innovative strategy to silence the HIV provirus by targeted DNA methylation on the HIV promoter region. We genetically engineered a chimeric DNA methyltransferase 1 composed of designed zinc-finger proteins to become ZF2 DNMT1. After transient transfection of the molecular clone encoding this chimeric protein into HIV-1 infected or latently infected cells, efficient suppression of HIV-1 expression by the methylation of CpG islands in 5′-LTR was observed and quantified. The effective suppression of HIV in latently infected cells by ZF2-DNMT1 is stable and can last through about 40 cell passages. Cytotoxic caused by ZF2-DNMT1 was only observed during cellular proliferation. Taken together, our results demonstrate the potential of this novel approach for anti-HIV-1 therapy.
Collapse
Affiliation(s)
- Junxiao Deng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiying Qu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Panpan Lu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xinyi Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haiyan Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yanan Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhengtao Jiang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xian Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yangcheng Zhong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - He Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hanyu Pan
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Won-Bin Young
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
87
|
Patten MM, Cowley M, Oakey RJ, Feil R. Regulatory links between imprinted genes: evolutionary predictions and consequences. Proc Biol Sci 2017; 283:rspb.2015.2760. [PMID: 26842569 PMCID: PMC4760173 DOI: 10.1098/rspb.2015.2760] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Genomic imprinting is essential for development and growth and plays diverse roles in physiology and behaviour. Imprinted genes have traditionally been studied in isolation or in clusters with respect to cis-acting modes of gene regulation, both from a mechanistic and evolutionary point of view. Recent studies in mammals, however, reveal that imprinted genes are often co-regulated and are part of a gene network involved in the control of cellular proliferation and differentiation. Moreover, a subset of imprinted genes acts in trans on the expression of other imprinted genes. Numerous studies have modulated levels of imprinted gene expression to explore phenotypic and gene regulatory consequences. Increasingly, the applied genome-wide approaches highlight how perturbation of one imprinted gene may affect other maternally or paternally expressed genes. Here, we discuss these novel findings and consider evolutionary theories that offer a rationale for such intricate interactions among imprinted genes. An evolutionary view of these trans-regulatory effects provides a novel interpretation of the logic of gene networks within species and has implications for the origin of reproductive isolation between species.
Collapse
Affiliation(s)
- Manus M Patten
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC 20057, USA
| | - Michael Cowley
- Center for Human Health and the Environment, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Rebecca J Oakey
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK
| | - Robert Feil
- Centre National de Recherche Scientifique (CNRS), Institute of Molecular Genetics (IGMM), 1919 route de Mende, Montpellier 34293, France University of Montpellier, 163 rue Auguste Broussonnet, Montpellier 34090, France Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
88
|
Huang Y, Jiang X, Yu M, Huang R, Yao J, Li M, Zheng F, Yang X. Beneficial effects of diazepin-quinazolin-amine derivative (BIX-01294) on preimplantation development and molecular characteristics of cloned mouse embryos. Reprod Fertil Dev 2017; 29:1260-1269. [DOI: 10.1071/rd15463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 06/04/2016] [Indexed: 12/19/2022] Open
Abstract
Somatic cell nuclear transfer is frequently associated with abnormal epigenetic modifications that may lead to the developmental failure of cloned embryos. BIX-01294 (a diazepine–quinazoline–amine derivative) is a specific inhibitor of the histone methyltransferase G9a. The aim of the present study was to investigate the effects of BIX-01294 on development, dimethylation of histone H3 at lysine 9 (H3K9), DNA methylation and the expression of imprinted genes in cloned mouse preimplantation embryos. There were no significant differences in blastocyst rates of cloned embryos treated with or without 0.1 μM BIX-01294. Relative to clone embryos treated without 0.1 μM BIX-01294, exposure of embryos to BIX-01294 decreased histone H3K9 dimethylation and DNA methylation in cloned embryos to levels that were similar to those of in vivo-fertilised embryos at the 2-cell and blastocyst stages. Cloned embryos had lower expression of octamer-binding transcription factor 4 (Oct4) and small nuclear ribonucleoprotein N (Snrpn), but higher expression of imprinted maternally expressed transcript (non-protein coding) (H19) and growth factor receptor-bound protein 10 (Grb10) compared with in vivo-fertilised counterparts. The addition of 0.1 μM BIX-01294 to the activation and culture medium resulted in lower H19 expression and higher cyclin dependent kinase inhibitor 1C (Cdkn1c) and delta-like 1 homolog (Dlk1) expression, but had no effect on the expression of Oct4, Snrpn and Grb10. The loss of methylation at the Grb10 cytosine–phosphorous–guanine (CpG) islands in cloned embryos was partially corrected by BIX-01294. These results indicate that BIX-01294 treatment of cloned embryos has beneficial effects in terms of correcting abnormal epigenetic modifications, but not on preimplantation development.
Collapse
|
89
|
Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 2016; 41:759-786. [DOI: 10.1007/s12038-016-9650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
90
|
Abstract
In mammals, expression of UBE3A is epigenetically regulated in neurons and expression is restricted to the maternal copy of UBE3A. A recent report claimed that Drosophila melanogaster UBE3A homolog (Dube3a) is preferentially expressed from the maternal allele in fly brain, inferring an imprinting mechanism. However, complex epigenetic regulatory features of the mammalian imprinting center are not present in Drosophila, and allele specific expression of Dube3a has not been documented. We used behavioral and electrophysiological analysis of the Dube3a loss-of-function allele (Dube3a15b) to investigate Dube3a imprinting in fly neurons. We found that motor impairment (climbing ability) and a newly-characterized defect in synaptic transmission are independent of parental inheritance of the Dube3a15b allele. Furthermore, expression analysis of coding single nucleotide polymorphisms (SNPs) in Dube3a did not reveal allele specific expression differences among reciprocal crosses. These data indicate that Dube3a is neither imprinted nor preferentially expressed from the maternal allele in fly neurons.
Collapse
Affiliation(s)
- Kevin A Hope
- a Departments of Neurology , Anatomy and Neurobiology, The University of Tennessee Health Science Center , Memphis , TN , USA
| | - Mark S LeDoux
- a Departments of Neurology , Anatomy and Neurobiology, The University of Tennessee Health Science Center , Memphis , TN , USA
| | - Lawrence T Reiter
- a Departments of Neurology , Anatomy and Neurobiology, The University of Tennessee Health Science Center , Memphis , TN , USA.,b Pediatrics, The University of Tennessee Health Science Center , Memphis , TN , USA
| |
Collapse
|
91
|
Stanurova J, Neureiter A, Hiber M, de Oliveira Kessler H, Stolp K, Goetzke R, Klein D, Bankfalvi A, Klump H, Steenpass L. Angelman syndrome-derived neurons display late onset of paternal UBE3A silencing. Sci Rep 2016; 6:30792. [PMID: 27484051 PMCID: PMC4971516 DOI: 10.1038/srep30792] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/02/2016] [Indexed: 01/21/2023] Open
Abstract
Genomic imprinting is an epigenetic phenomenon resulting in parent-of-origin-specific gene expression that is regulated by a differentially methylated region. Gene mutations or failures in the imprinting process lead to the development of imprinting disorders, such as Angelman syndrome. The symptoms of Angelman syndrome are caused by the absence of functional UBE3A protein in neurons of the brain. To create a human neuronal model for Angelman syndrome, we reprogrammed dermal fibroblasts of a patient carrying a defined three-base pair deletion in UBE3A into induced pluripotent stem cells (iPSCs). In these iPSCs, both parental alleles are present, distinguishable by the mutation, and express UBE3A. Detailed characterization of these iPSCs demonstrated their pluripotency and exceptional stability of the differentially methylated region regulating imprinted UBE3A expression. We observed strong induction of SNHG14 and silencing of paternal UBE3A expression only late during neuronal differentiation, in vitro. This new Angelman syndrome iPSC line allows to study imprinted gene regulation on both parental alleles and to dissect molecular pathways affected by the absence of UBE3A protein.
Collapse
Affiliation(s)
- Jana Stanurova
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Anika Neureiter
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Michaela Hiber
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannah de Oliveira Kessler
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Kristin Stolp
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Roman Goetzke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany
| | - Diana Klein
- Institute for Cell Biology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Agnes Bankfalvi
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147 Essen, Germany
| |
Collapse
|
92
|
Deuve JL, Bonnet-Garnier A, Beaujean N, Avner P, Morey C. Antagonist Xist and Tsix co-transcription during mouse oogenesis and maternal Xist expression during pre-implantation development calls into question the nature of the maternal imprint on the X chromosome. Epigenetics 2016; 10:931-42. [PMID: 26267271 PMCID: PMC4844198 DOI: 10.1080/15592294.2015.1081327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
During the first divisions of the female mouse embryo, the paternal X-chromosome is coated by Xist non-coding RNA and gradually silenced. This imprinted X-inactivation principally results from the apposition, during oocyte growth, of an imprint on the X-inactivation master control region: the X-inactivation center (Xic). This maternal imprint of yet unknown nature is thought to prevent Xist upregulation from the maternal X (XM) during early female development. In order to provide further insight into the XM imprinting mechanism, we applied single-cell approaches to oocytes and pre-implantation embryos at different stages of development to analyze the expression of candidate genes within the Xic. We show that, unlike the situation pertaining in most other cellular contexts, in early-growing oocytes, Xist and Tsix sense and antisense transcription occur simultaneously from the same chromosome. Additionally, during early development, Xist appears to be transiently transcribed from the XM in some blastomeres of late 2-cell embryos concomitant with the general activation of the genome indicating that XM imprinting does not completely suppress maternal Xist transcription during embryo cleavage stages. These unexpected transcriptional regulations of the Xist locus call for a re-evaluation of the early functioning of the maternal imprint on the X-chromosome and suggest that Xist/Tsix antagonist transcriptional activities may participate in imprinting the maternal locus as described at other loci subject to parental imprinting.
Collapse
Affiliation(s)
- Jane Lynda Deuve
- a Laboratoire de Génétique Moléculaire Murine; Institut Pasteur ; Paris , France
| | | | - Nathalie Beaujean
- b INRA; UMR1198 Biologie du Développement et Reproduction ; Jouy-en-Josas , France
| | - Philip Avner
- a Laboratoire de Génétique Moléculaire Murine; Institut Pasteur ; Paris , France
| | - Céline Morey
- a Laboratoire de Génétique Moléculaire Murine; Institut Pasteur ; Paris , France
| |
Collapse
|
93
|
Schneider G, Sellers ZP, Ratajczak MZ. Parentally imprinted genes regulate hematopoiesis-new evidence from the Dlk1-Gtl2 locus. Stem Cell Investig 2016; 3:29. [PMID: 27580759 DOI: 10.21037/sci.2016.06.09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/06/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Gabriela Schneider
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Zachariah Payne Sellers
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA;; Department of Regenerative Medicine, Medical University of Warsaw, Warsaw, Poland
| |
Collapse
|
94
|
Bunkar N, Pathak N, Lohiya NK, Mishra PK. Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med 2016; 43:59-81. [PMID: 27358824 PMCID: PMC4925870 DOI: 10.5653/cerm.2016.43.2.59] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/06/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
It is well established that there is a heritable element of susceptibility to chronic human ailments, yet there is compelling evidence that some components of such heritability are transmitted through non-genetic factors. Due to the complexity of reproductive processes, identifying the inheritance patterns of these factors is not easy. But little doubt exists that besides the genomic backbone, a range of epigenetic cues affect our genetic programme. The inter-generational transmission of epigenetic marks is believed to operate via four principal means that dramatically differ in their information content: DNA methylation, histone modifications, microRNAs and nucleosome positioning. These epigenetic signatures influence the cellular machinery through positive and negative feedback mechanisms either alone or interactively. Understanding how these mechanisms work to activate or deactivate parts of our genetic programme not only on a day-to-day basis but also over generations is an important area of reproductive health research.
Collapse
Affiliation(s)
- Neha Bunkar
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India
| | - Neelam Pathak
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Nirmal Kumar Lohiya
- Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Pradyumna Kumar Mishra
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Department of Molecular Biology, National Institute for Research in Environmental Health (ICMR), Bhopal, India
| |
Collapse
|
95
|
Riso V, Cammisa M, Kukreja H, Anvar Z, Verde G, Sparago A, Acurzio B, Lad S, Lonardo E, Sankar A, Helin K, Feil R, Fico A, Angelini C, Grimaldi G, Riccio A. ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells. Nucleic Acids Res 2016; 44:8165-78. [PMID: 27257070 PMCID: PMC5041456 DOI: 10.1093/nar/gkw505] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/26/2016] [Indexed: 01/14/2023] Open
Abstract
ZFP57 is necessary for maintaining repressive epigenetic modifications at Imprinting control regions (ICRs). In mouse embryonic stem cells (ESCs), ZFP57 binds ICRs (ICRBS) and many other loci (non-ICRBS). To address the role of ZFP57 on all its target sites, we performed high-throughput and multi-locus analyses of inbred and hybrid mouse ESC lines carrying different gene knockouts. By using an allele-specific RNA-seq approach, we demonstrate that ZFP57 loss results in derepression of the imprinted allele of multiple genes in the imprinted clusters. We also find marked epigenetic differences between ICRBS and non-ICRBS suggesting that different cis-acting regulatory functions are repressed by ZFP57 at these two classes of target loci. Overall, these data demonstrate that ZFP57 is pivotal to maintain the allele-specific epigenetic modifications of ICRs that in turn are necessary for maintaining the imprinted expression over long distances. At non-ICRBS, ZFP57 inactivation results in acquisition of epigenetic features that are characteristic of poised enhancers, suggesting that another function of ZFP57 in early embryogenesis is to repress cis-acting regulatory elements whose activity is not yet required.
Collapse
Affiliation(s)
- Vincenzo Riso
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Marco Cammisa
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Harpreet Kukreja
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Zahra Anvar
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Gaetano Verde
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | - Angela Sparago
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Basilia Acurzio
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| | - Shraddha Lad
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | - Enza Lonardo
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | - Aditya Sankar
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark Center for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS, 34293 Montpellier, France University of Montpellier, 34090 Montpellier, France
| | - Annalisa Fico
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo 'Mauro Picone' (IAC), CNR, 80131 Naples, Italy
| | - Giovanna Grimaldi
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Ceinge Biotecnologie Avanzate s.c.a.r.l., 80145 Naples, Italy
| | - Andrea Riccio
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, 81100 Caserta, Italy
| |
Collapse
|
96
|
Voon HPJ, Gibbons RJ. Maintaining memory of silencing at imprinted differentially methylated regions. Cell Mol Life Sci 2016; 73:1871-9. [PMID: 26883803 PMCID: PMC4819931 DOI: 10.1007/s00018-016-2157-6] [Citation(s) in RCA: 16] [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: 12/13/2015] [Accepted: 02/04/2016] [Indexed: 01/09/2023]
Abstract
Imprinted genes are an exceptional cluster of genes which are expressed in a parent-of-origin dependent fashion. This allele-specific expression is dependent on differential DNA methylation which is established in the parental germlines in a sex-specific manner. The DNA methylation imprint is accompanied by heterochromatin modifications which must be continuously maintained through development. This review summarises the factors which are important for protecting the epigenetic modifications at imprinted differentially methylated regions (DMRs), including PGC7, ZFP57 and the ATRX/Daxx/H3.3 complex. We discuss how these factors maintain heterochromatin silencing, not only at imprinted DMRs, but also other heterochromatic regions in the genome.
Collapse
Affiliation(s)
- Hsiao P J Voon
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Richard J Gibbons
- University of Oxford, Oxford, UK.
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK.
| |
Collapse
|
97
|
Canovas S, Ross PJ. Epigenetics in preimplantation mammalian development. Theriogenology 2016; 86:69-79. [PMID: 27165992 DOI: 10.1016/j.theriogenology.2016.04.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 02/27/2016] [Accepted: 03/14/2016] [Indexed: 12/11/2022]
Abstract
Fertilization is a very dynamic period of comprehensive chromatin remodeling, from which two specialized cells result in a totipotent zygote. The formation of a totipotent cell requires extensive epigenetic remodeling that, although independent of modifications in the DNA sequence, still entails a profound cell-fate change, supported by transcriptional profile modifications. As a result of finely tuned interactions between numerous mechanisms, the goal of fertilization is to form a full healthy new individual. To avoid the persistence of alterations in epigenetic marks, the epigenetic information contained in each gamete is reset during early embryogenesis. Covalent modification of DNA by methylation, as well as posttranslational modifications of histone proteins and noncoding RNAs, appears to be the main epigenetic mechanisms that control gene expression. These allow different cells in an organism to express different transcription profiles, despite each cell containing the same DNA sequence. In the context of replacement of spermatic protamine with histones from the oocyte, active cell division, and specification of different lineages, active and passive mechanisms of epigenetic remodeling have been revealed as critical for editing the epigenetic profile of the early embryo. Importantly, redundant factors and mechanisms are likely in place, and only a few have been reported as critical for fertilization or embryo survival by the use of knockout models. The aim of this review is to highlight the main mechanisms of epigenetic remodeling that ensue after fertilization in mammals.
Collapse
Affiliation(s)
- Sebastian Canovas
- LARCEL (Laboratorio Andaluz de Reprogramacion Celular), BIONAND, Centro Andaluz de Nanomedicina y Biotecnologia Campanillas, Malaga, Spain.
| | - Pablo Juan Ross
- Department of Animal Science, University of California, Davis, California, USA.
| |
Collapse
|
98
|
Epigenetic Modifications in Essential Hypertension. Int J Mol Sci 2016; 17:451. [PMID: 27023534 PMCID: PMC4848907 DOI: 10.3390/ijms17040451] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/15/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022] Open
Abstract
Essential hypertension (EH) is a complex, polygenic condition with no single causative agent. Despite advances in our understanding of the pathophysiology of EH, hypertension remains one of the world’s leading public health problems. Furthermore, there is increasing evidence that epigenetic modifications are as important as genetic predisposition in the development of EH. Indeed, a complex and interactive genetic and environmental system exists to determine an individual’s risk of EH. Epigenetics refers to all heritable changes to the regulation of gene expression as well as chromatin remodelling, without involvement of nucleotide sequence changes. Epigenetic modification is recognized as an essential process in biology, but is now being investigated for its role in the development of specific pathologic conditions, including EH. Epigenetic research will provide insights into the pathogenesis of blood pressure regulation that cannot be explained by classic Mendelian inheritance. This review concentrates on epigenetic modifications to DNA structure, including the influence of non-coding RNAs on hypertension development.
Collapse
|
99
|
Wilkins JF, Úbeda F, Van Cleve J. The evolving landscape of imprinted genes in humans and mice: Conflict among alleles, genes, tissues, and kin. Bioessays 2016; 38:482-9. [PMID: 26990753 DOI: 10.1002/bies.201500198] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Three recent genome-wide studies in mice and humans have produced the most definitive map to date of genomic imprinting (gene expression that depends on parental origin) by incorporating multiple tissue types and developmental stages. Here, we explore the results of these studies in light of the kinship theory of genomic imprinting, which predicts that imprinting evolves due to differential genetic relatedness between maternal and paternal relatives. The studies produce a list of imprinted genes with around 120-180 in mice and ~100 in humans. The studies agree on broad patterns across mice and humans including the complex patterns of imprinted expression at loci like Igf2 and Grb10. We discuss how the kinship theory provides a powerful framework for hypotheses that can explain these patterns. Finally, since imprinting is rare in the genome despite predictions from the kinship theory that it might be common, we discuss evolutionary factors that could favor biallelic expression.
Collapse
Affiliation(s)
| | - Francisco Úbeda
- School of Biological Sciences, Royal Holloway, University of London, Egham, UK
| | - Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
100
|
Saenz-de-Juano MD, Billooye K, Smitz J, Anckaert E. The loss of imprinted DNA methylation in mouse blastocysts is inflicted to a similar extent by in vitro follicle culture and ovulation induction. Mol Hum Reprod 2016; 22:427-41. [PMID: 26908643 DOI: 10.1093/molehr/gaw013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/29/2016] [Indexed: 12/24/2022] Open
Abstract
STUDY HYPOTHESIS Does in vitro follicle culture (IFC) have an effect on maintenance of imprinted DNA methylation in preimplantation mouse embryos? STUDY FINDING We report similar alterations in the methylation pattern of H19 imprinted maternally expressed transcript (H19), small nuclear ribonucleoprotein polypeptide N (Snrpn) and mesoderm specific transcript (Mest) imprinted genes in mouse blastocysts obtained after ovulation induction and IFC. Furthermore, we observed no differences in the gene expression of maternal effect proteins related with imprinting maintenance between superovulated in vivo grown or IFC oocytes. WHAT IS KNOWN ALREADY Assisted reproductive technology is associated with adverse post-natal outcomes such as increased risk of premature birth, altered birthweight, congenital anomalies and genomic imprinting syndromes in human and in animal models. Previous studies have shown that ovulation induction allowed normal imprinting establishment in mouse oocytes, but interfered with imprinting maintenance during preimplantation . Normal imprinting establishment was also observed in mouse oocytes derived from a standardized IFC from the early pre-antral follicle stage. STUDY DESIGN, SAMPLES/MATERIALS, METHODS The methylation profiles of differentially methylated regions (DMRs) of three key imprinted genes (H19, Snrpn and Mest) were compared at hatched blastocyst stage between embryos obtained from IFC or superovulated oocytes, each subjected to IVF and preimplantation in vitro culture (IVC); in non-manipulated in vivo produced late blastocyst (control) and in in vivo produced 2-cell embryos that were in vitro cultured until the hatched blastocyst stage (to assess the effect of IVC). Two different mice strains (Mus musculus C57BL/6J X CBA/Ca and Mus musculus B6 (CAST7)) were used to discriminate between maternal and paternal alleles of imprinted genes. Additionally, a limiting-dilution bisulfite-sequencing technique was carried out on individual embryos in order to avoid amplification bias. To assess whether IFC and ovulation induction differentially affect the mRNA expression of imprinting maintenance genes in the oocyte, a comparison of DNA methyltransferase 1 (Dnmt1o), methyl-CpG binding domain protein 3 (MBD3) and developmental pluripotency-associated 3 (Dppa3) was performed by qPCR between in vivo and in vitro grown oocytes at the germinal vesicle and metaphase II (MII) stage. MAIN RESULTS AND THE ROLE OF CHANCE Results showed a loss of global imprinted DNA methylation in all in vitro manipulated embryos, due to an increase in the amount of abnormal alleles (<50% methylated). Importantly, there were no differences in blastocysts obtained from IFC and ovulation induction. Moreover, similar mRNA expression levels for Dnmt1o, MBD3 and Dppa3 genes were observed in IFC and stimulated oocytes. LIMITATIONS, REASONS FOR CAUTION The methylation analysis was restricted to a number of well-selected imprinted genes. Future studies need to determine whether ovulation induction and IFC affect maternal effect factors at the protein level. WIDER IMPLICATIONS OF THE FINDINGS In vitro maturation of oocytes (IVM) is a patient-friendly alternative to conventional ovarian stimulation in PCOS patients. IFC is an emerging technology in human oncofertility. The results of this study show for the first time that in vitro oocyte culture induces no additional epigenetic alterations compared with conventional ovulation induction, at least for imprinted genes at the hatched blastocyst stage. The mouse IFC system can be used to test the sensitivity of the oocyte during its growth and maturation to several nutritional, metabolic and hormonal conditions possibly linked to epigenetic alterations. LARGE SCALE DATA N/A. STUDY FUNDING AND COMPETING INTERESTS This study received funding by Strategic Research Programs-Groeiers (OZR/2014/97), IWT/TBM/110680 and by UZ Brussel Fonds Willy Gepts (WFWG 2013). There is no conflict of interest.
Collapse
Affiliation(s)
- M D Saenz-de-Juano
- Follicle Biology Laboratory, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - K Billooye
- Follicle Biology Laboratory, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - J Smitz
- Follicle Biology Laboratory, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - E Anckaert
- Follicle Biology Laboratory, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| |
Collapse
|