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Kohlrausch FB, Wang F, McKerrow W, Grivainis M, Fenyo D, Keefe DL. Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos. J Assist Reprod Genet 2024; 41:2257-2269. [PMID: 38951360 PMCID: PMC11405744 DOI: 10.1007/s10815-024-03176-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
PURPOSE Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.
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Affiliation(s)
- Fabiana B Kohlrausch
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil.
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA.
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - Mark Grivainis
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David Fenyo
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
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2
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Dolinko AV, Schultz BM, Ghosh J, Kalliora C, Mainigi M, Coutifaris C, Sapienza C, Senapati S. Disrupted methylation patterns at birth persist in early childhood: a prospective cohort analysis. Clin Epigenetics 2022; 14:129. [PMID: 36243864 PMCID: PMC9568969 DOI: 10.1186/s13148-022-01348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alterations in the epigenome are a risk factor in multiple disease states. We have demonstrated in the past that disruption of the epigenome during early pregnancy or periconception, as demonstrated by altered methylation, may be associated with both assisted reproductive technology and undesirable clinical outcomes at birth, such as low birth weight. We have previously defined this altered methylation, calculated based on statistical upper and lower limits of outlier CpGs compared to the population, as an 'outlier methylation phenotype' (OMP). Our aim in this study was to determine whether children thus identified as possessing an OMP at birth by DNA methylation in cord blood persist as outliers in early childhood based on salivary DNA methylation. RESULTS A total of 31 children were included in the analysis. Among 24 children for whom both cord blood DNA and salivary DNA were available, DNA methylation patterns, analyzed using the Illumina Infinium MethylationEPIC BeadChip (850 K), between cord blood at birth and saliva in childhood at age 6-12 years remain stable (R2 range 0.89-0.97). At birth, three out of 28 children demonstrated an OMP in multiple cord blood datasets and hierarchical clustering. Overall DNA methylation among all three OMP children identified as outliers at birth was remarkably stable (individual R2 0.908, 0.92, 0.915), even when only outlier CpG sites were considered (R2 0.694, 0.738, 0.828). CONCLUSIONS DNA methylation signatures in cord blood remain stable over time as demonstrated by a strong correlation with epigenetic salivary signatures in childhood. Future work is planned to identify whether a clinical phenotype is associated with OMP and, if so, could undesirable clinical outcomes in childhood and adulthood be predicted at birth.
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Affiliation(s)
- Andrey V Dolinko
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Bryant M Schultz
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Charikleia Kalliora
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica Mainigi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Temple University, Philadelphia, PA, USA
| | - Suneeta Senapati
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Pi T, Lang G, Liu B, Shi J. Protective Effects of Dendrobium nobile Lindl. Alkaloids on Alzheimer's Disease-like Symptoms Induced by High-methionine Diet. Curr Neuropharmacol 2022; 20:983-997. [PMID: 34370639 PMCID: PMC9881098 DOI: 10.2174/1570159x19666210809101945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/27/2021] [Accepted: 06/04/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND High methionine-diet (HMD) causes Alzheimer's disease (AD)-like symptoms. Previous studies have shown that Dendrobium nobile Lindle. alkaloids (DNLA) have potential benefits for AD Object: The objective of this study has been to explore whether DNLA can improve AD-like symptoms induced by HMD. METHODS Mice were fed with 2% HMD diet for 11 weeks; the DNLA20 control group (20 mg/kg), DNLA10 group (10 mg/kg), and DNLA20 group (20 mg/kg) were administered DNLA for 3 months. Morris water maze test was used to detect learning and memory ability. Neuron damage was evaluated by HE and Nissl staining. Levels of homocysteine (Hcy), beta-amyloid 1-42 (Aβ1-42), S-adenosine methionine (SAM) and S-adenosine homocysteine (SAH) were detected by ELISA. Immunofluorescence and western blotting (WB) were used to determine the expression of proteins. CPG island methylation levels were accessed by Methylation-specific PCR (MSP) and MethylTarget methylation detection. RESULTS Morris water maze test revealed that DNLA improved learning and memory dysfunction. HE, Nissl, and immunofluorescence staining showed that DNLA alleviated neuron damage and reduced the 5-methylcytosine (5-mC), Aβ1-40) and Aβ1-42) levels. DNLA also decreased the levels of Hcy and Aβ1-42) in the serum, along with decreasing SAM/SAH level in the liver tissue. WB results showed that DNLA down-regulated the expression of amyloid-precursor protein (APP), presenilin-1 (PS1), beta-secretase-1 (BACE1), DNA methyltransferase1 (DNMT1), Aβ1-40) and Aβ1-42) proteins. DNLA also up-regulated the proteins expression of insulin-degrading enzyme (IDE), neprilysin (NEP), DNMT3a and DNMT3b. Meanwhile, DNLA increased CPG island methylation levels of APP and BACE1 genes. CONCLUSION DNLA alleviated AD-like symptoms induced by HMD via the DNA methylation pathway.
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Affiliation(s)
- Tingting Pi
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Guizhou Province, China
| | - Guangping Lang
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Guizhou Province, China
| | - Bo Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Guizhou Province, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Guizhou Province, China,Address correspondence to this author at the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Guizhou Province, China; Tel: +86 851 2864 3666; E-mail:
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4
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Abstract
DNA methylation represents one of the best characterized epigenetic modifications. In particular, global demethylation is a common feature of epigenetic reprogramming to naïve pluripotency in human and mouse pluripotent stem cells. In parallel to the global changes, several locus-specific changes to the DNA methylation landscape occur and also loss of imprinting has been observed in naïve human pluripotent stem cells. The current gold standard to assess and quantitively map DNA methylation is bisulfite sequencing. Various protocols are available for genome-wide bisulfite sequencing and here I describe an optimized method based on Post Bisulfite Adapter Tagging (PBAT) for low amounts of DNA or cells, with as little as 50 cells as minimum requirement, and with the possibility to process a large number of samples in parallel. I outline the basic bioinformatic steps needed to process raw Illumina sequencing data and then describe the inital steps of the analysis of DNA methylation datasets, including an assessment of imprint control regions.
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Affiliation(s)
- Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland. .,Department of Medical & Molecular Genetics, King's College London, London, UK.
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5
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Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
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Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
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6
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Pi T, Liu B, Shi J. Abnormal Homocysteine Metabolism: An Insight of Alzheimer's Disease from DNA Methylation. Behav Neurol 2020; 2020:8438602. [PMID: 32963633 PMCID: PMC7495165 DOI: 10.1155/2020/8438602] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/30/2020] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease in the central nervous system that has complex pathogenesis in the elderly. The current review focuses on the epigenetic mechanisms of AD, according to the latest findings. One of the best-characterized chromatin modifications in epigenetic mechanisms is DNA methylation. Highly replicable data shows that AD occurrence is often accompanied by methylation level changes of the AD-related gene. Homocysteine (Hcy) is not only an intermediate product of one-carbon metabolism but also an important independent risk factor of AD; it can affect the cognitive function of the brain by changing the one-carbon metabolism and interfering with the DNA methylation process, resulting in cerebrovascular disease. In general, Hcy may be an environmental factor that affects AD via the DNA methylation pathway with a series of changes in AD-related substance. This review will concentrate on the relation between DNA methylation and Hcy and try to figure out their rule in the pathophysiology of AD.
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Affiliation(s)
- Tingting Pi
- Department of Pharmacology and the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Bo Liu
- Department of Pharmacology and the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Jingshan Shi
- Department of Pharmacology and the Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
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7
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Mani S, Ghosh J, Coutifaris C, Sapienza C, Mainigi M. Epigenetic changes and assisted reproductive technologies. Epigenetics 2020; 15:12-25. [PMID: 31328632 PMCID: PMC6961665 DOI: 10.1080/15592294.2019.1646572] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/02/2019] [Accepted: 07/16/2019] [Indexed: 02/07/2023] Open
Abstract
Children conceived by Assisted Reproductive Technologies (ART) are at moderately increased risk for a number of undesirable outcomes, including low birth weight. Whether the additional risk is associated with specific procedures used in ART or biological factors that are intrinsic to infertility has been the subject of much debate, as has the mechanism by which ART or infertility might influence this risk. The potential effect of ART clinical and laboratory procedures on the gamete and embryo epigenomes heads the list of mechanistic candidates that might explain the association between ART and undesirable clinical outcomes. The reason for this focus is that the developmental time points at which ART clinical and laboratory procedures are implemented are precisely the time points at which large-scale reorganization of the epigenome takes place during normal development. In this manuscript, we review the many human studies comparing the epigenomes of ART children with children conceived in vivo, as well as assess the potential of individual ART clinical and laboratory procedures to alter the epigenome.
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Affiliation(s)
- Sneha Mani
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayashri Ghosh
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Monica Mainigi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
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8
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Sun W, von Meyenn F, Peleg‐Raibstein D, Wolfrum C. Environmental and Nutritional Effects Regulating Adipose Tissue Function and Metabolism Across Generations. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900275. [PMID: 31179229 PMCID: PMC6548959 DOI: 10.1002/advs.201900275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/21/2019] [Indexed: 05/12/2023]
Abstract
The unabated rise in obesity prevalence during the last 40 years has spurred substantial interest in understanding the reasons for this epidemic. Studies in mice and humans have demonstrated that obesity is a highly heritable disease; however genetic variations within specific populations have so far not been able to explain this phenomenon to its full extent. Recent work has demonstrated that environmental cues can be sensed by an organism to elicit lasting changes, which in turn can affect systemic energy metabolism by different epigenetic mechanisms such as changes in small noncoding RNA expression, DNA methylation patterns, as well as histone modifications. These changes can directly modulate cellular function in response to environmental cues, however research during the last decade has demonstrated that some of these modifications might be transmitted to subsequent generations, thus modulating energy metabolism of the progeny in an inter- as well as transgenerational manner. In this context, adipose tissue has become a focus of research due to its plasticity, which allows the formation of energy storing (white) as well as energy wasting (brown/brite/beige) cells within the same depot. In this Review, the effects of environmental induced obesity with a particular focus on adipose tissue are discussed.
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Affiliation(s)
- Wenfei Sun
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
| | - Ferdinand von Meyenn
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
| | - Daria Peleg‐Raibstein
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
| | - Christian Wolfrum
- Department of Health Science and TechnologiesETH ZürichSchorenstrasse 16SchwerzenbachCH‐8603Switzerland
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9
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Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A. Epigenetic resetting of human pluripotency. Development 2017; 144:2748-2763. [PMID: 28765214 PMCID: PMC5560041 DOI: 10.1242/dev.146811] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 06/09/2017] [Indexed: 12/12/2022]
Abstract
Much attention has focussed on the conversion of human pluripotent stem cells (PSCs) to a more naïve developmental status. Here we provide a method for resetting via transient histone deacetylase inhibition. The protocol is effective across multiple PSC lines and can proceed without karyotype change. Reset cells can be expanded without feeders with a doubling time of around 24 h. WNT inhibition stabilises the resetting process. The transcriptome of reset cells diverges markedly from that of primed PSCs and shares features with human inner cell mass (ICM). Reset cells activate expression of primate-specific transposable elements. DNA methylation is globally reduced to a level equivalent to that in the ICM and is non-random, with gain of methylation at specific loci. Methylation imprints are mostly lost, however. Reset cells can be re-primed to undergo tri-lineage differentiation and germline specification. In female reset cells, appearance of biallelic X-linked gene transcription indicates reactivation of the silenced X chromosome. On reconversion to primed status, XIST-induced silencing restores monoallelic gene expression. The facile and robust conversion routine with accompanying data resources will enable widespread utilisation, interrogation, and refinement of candidate naïve cells.
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Affiliation(s)
- Ge Guo
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | | | - Maria Rostovskaya
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - James Clarke
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Duncan Baker
- Centre for Stem Cell Biology, Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Anna Sahakyan
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Samuel Myers
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Paul Bertone
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Wolf Reik
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Kathrin Plath
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Austin Smith
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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10
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Canovas S, Ivanova E, Romar R, García-Martínez S, Soriano-Úbeda C, García-Vázquez FA, Saadeh H, Andrews S, Kelsey G, Coy P. DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids. eLife 2017; 6. [PMID: 28134613 PMCID: PMC5340525 DOI: 10.7554/elife.23670] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/28/2017] [Indexed: 12/14/2022] Open
Abstract
The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF). Natur-IVF embryos were of higher quality than C-IVF in terms of cell number and hatching ability. RNA-Seq and DNA methylation analyses showed that Natur-IVF embryos have expression and methylation patterns closer to in vivo blastocysts. Genes involved in reprogramming, imprinting and development were affected by culture, with fewer aberrations in Natur-IVF embryos. Methylation analysis detected methylated changes in C-IVF, but not in Natur-IVF, at genes whose methylation could be critical, such as IGF2R and NNAT. DOI:http://dx.doi.org/10.7554/eLife.23670.001 Infertility has become more common in many countries, particularly those where many people delay having children until later in life. To help individuals experiencing infertility conceive a child, scientists have developed treatments called assisted reproductive technologies (or ARTs for short). So far, more than 5 million children have been born with the help of these treatments. Most of the children seem healthy; however, birth defects are more common in ART-conceived babies than those conceived without treatment. The cause of these birth defects is not known, though scientists suspect it may have something to do with techniques used in ART. One possible culprit is the liquid that is used in the laboratory to help the parents’ sperm and egg come together for fertilization. This same liquid is also used to bathe the developing embryo for the first few days after fertilization before it is implanted into its mother’s womb. Some scientists wonder whether adding the fluids normally found in the reproductive tract of their mother to this liquid could reduce defects in children conceived via ART. Now, Canovas et al. have shown that fertilizing and growing pig embryos in liquids supplemented with fluid from the wombs of female pigs results in embryos that are closer to naturally conceived pig embryos than in non-supplemented liquids. In the experiments, naturally conceived embryos were compared to ART embryos exposed to the usual liquids and with ART embryos grown in liquids with fluid collected from the pig’s reproductive tract added. Cutting edge technologies were used to sequence the entire genomes of all of the embryos and compare which genes were active in each case. Canovas et al. also looked at chemical markers on the DNA – called epigenetic changes – that turn on or off the expression of genes without changing the DNA code itself. The analysis showed that ART-conceived embryos grown in the usual liquid had different patterns of gene expression and epigenetic changes compared to naturally conceived embryos. Gene expression and epigenetic changes in the ART embryos grown with the pig reproductive fluid was more similar to the naturally conceived embryos. These findings suggest that abnormal gene expression in the ART-liquid exposed embryos may lead to birth defects, and that using natural reproductive fluids may be safer. To confirm this, scientists will have to implant embryos conceived in these three different conditions into mother pigs and assess the health and gene expression patterns of the resulting piglets. If successful, these new insights might one day lead to improvements in ART techniques used to treat infertility in people. DOI:http://dx.doi.org/10.7554/eLife.23670.002
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Affiliation(s)
- Sebastian Canovas
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Elena Ivanova
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Raquel Romar
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Soledad García-Martínez
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Cristina Soriano-Úbeda
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Francisco A García-Vázquez
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Heba Saadeh
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom.,Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom.,Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
| | - Pilar Coy
- Physiology of Reproduction Group, Departamento de Fisiología, Facultad de Veterinaria, Universidad de Murcia-Campus Mare Nostrum, Murcia, Spain.,Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
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11
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Guo H, Zhu P, Guo F, Li X, Wu X, Fan X, Wen L, Tang F. Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing. Nat Protoc 2015; 10:645-59. [PMID: 25837417 DOI: 10.1038/nprot.2015.039] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The heterogeneity of DNA methylation within a population of cells necessitates DNA methylome profiling at single-cell resolution. Recently, we developed a single-cell reduced-representation bisulfite sequencing (scRRBS) technique in which we modified the original RRBS method by integrating all the experimental steps before PCR amplification into a single-tube reaction. These modifications enable scRRBS to provide digitized methylation information on ∼1 million CpG sites within an individual diploid mouse or human cell at single-base resolution. Compared with the single-cell bisulfite sequencing (scBS) technique, scRRBS covers fewer CpG sites, but it provides better coverage for CpG islands (CGIs), which are likely to be the most informative elements for DNA methylation. The entire procedure takes ∼3 weeks, and it requires strong molecular biology skills.
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Affiliation(s)
- Hongshan Guo
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China
| | - Ping Zhu
- 1] Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China. [2] Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Fan Guo
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China
| | - Xianlong Li
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China
| | - Xinglong Wu
- 1] Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China. [2] Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaoying Fan
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China
| | - Lu Wen
- 1] Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China. [2] Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, China. [3] Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing, China
| | - Fuchou Tang
- 1] Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China. [2] Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, China. [3] Center for Molecular and Translational Medicine, Peking University Health Science Center, Beijing, China
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