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Saenz-de-Juano MD, Silvestrelli G, Ulbrich SE. One-week storage of refrigerated bovine milk does not affect the size, concentration, or molecular properties of extracellular vesicles. J Dairy Sci 2024; 107:1164-1174. [PMID: 37709026 DOI: 10.3168/jds.2023-23726] [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: 05/11/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Milk extracellular vesicles (EV) have gained extensive attention as promising diagnostic and therapeutic tools. Pre-analytical raw milk storage at low temperatures is an ordinary and usually necessary step after sample collection. It is known that direct freezing of unprocessed whole milk contaminates the native pool of milk EV with other cell structures. However, less evidence is available regarding prolonged cooling at 4°C. The current study assessed whether pre-analytical storage of bovine raw milk for several days affected EV isolation and further analysis. To confirm the independence from the health status of the mammary gland, we analyzed milk samples stored at 4°C for 1, 2, 3, and 7 d past collection, respectively, from 2 quarters of the same cow with different somatic cell counts (SCC). Seven days of refrigeration did not change the milk EV size, concentration, or morphology. We did not detect any changes in the EV cargo regarding the amount of protein and RNA, nor in the specific EV markers TSG101, CD9, and CD81 in milk from quarters with high and low SCC. Overall, we observed fewer CD81 and CD9 markers in quarters with high SCC. Moreover, we found no reduction in the mastitis-related miRNA bta-miR-223-3p, suggesting that refrigeration for several days up to 1 wk is a possible storage option compatible with further EV analyses. The findings of this study enhance the confidence that milk EV are highly stable in the raw milk matrix.
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Affiliation(s)
- Mara D Saenz-de-Juano
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, 8092 Zurich, Switzerland
| | - Giulia Silvestrelli
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, 8092 Zurich, Switzerland
| | - Susanne E Ulbrich
- ETH Zurich, Animal Physiology, Institute of Agricultural Sciences, 8092 Zurich, Switzerland.
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2
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Hallberg I, Persson S, Olovsson M, Moberg M, Ranefall P, Laskowski D, Damdimopoulou P, Sirard MA, Rüegg J, Sjunnesson YC. Bovine oocyte exposure to perfluorohexane sulfonate (PFHxS) induces phenotypic, transcriptomic, and DNA methylation changes in resulting embryos in vitro. Reprod Toxicol 2022; 109:19-30. [DOI: 10.1016/j.reprotox.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 10/19/2022]
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3
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Sirard MA. How the environment affects early embryonic development. Reprod Fertil Dev 2021; 34:203-213. [PMID: 35231267 DOI: 10.1071/rd21266] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the field of animal reproduction, the environment associated with gametes and embryos refers to the parents' condition as well as conditions surrounding gametes and embryos in vivo or in vitro . This environment is now known to influence not only the functionality of the early embryo but potentially the future phenotype of the offspring. Using transcriptomic and epigenetic molecular analysis, and the bovine model, recent research has shown that both the female and the male metabolic status, for example age, can affect gene expression and gene programming in the embryo. Evidence demonstrates that milking cows, which are losing weight at the time of conception, generates compromised embryos and offspring with a unique metabolic signature. A similar phenomenon has been associated with different culture conditions and the IVF procedure. The general common consequence of these situations is an embryo behaving on 'economy' mode where translation, cell division and ATP production is reduced, potentially to adapt to the perceived future environment. Few epidemiological studies have been done in bovines to assess if these changes result in a different phenotype and more studies are required to associate specific molecular changes in embryos with visible consequences later in life.
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Affiliation(s)
- Marc-André Sirard
- Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Université Laval, Québec, QC G1V 0A6, Canada
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4
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Zhou Y, Liu S, Hu Y, Fang L, Gao Y, Xia H, Schroeder SG, Rosen BD, Connor EE, Li CJ, Baldwin RL, Cole JB, Van Tassell CP, Yang L, Ma L, Liu GE. Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns. BMC Biol 2020; 18:85. [PMID: 32631327 PMCID: PMC7339546 DOI: 10.1186/s12915-020-00793-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. RESULTS Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. CONCLUSIONS This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Erin E. Connor
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
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5
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Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu GE. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience 2018; 7:4965117. [PMID: 29635292 PMCID: PMC5928411 DOI: 10.1093/gigascience/giy039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements. Conclusions Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
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Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Department of Agriculture, Agriculture Research Service, Madison, WI, 53706, USA
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
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6
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Oxidative stress in sperm affects the epigenetic reprogramming in early embryonic development. Epigenetics Chromatin 2018; 11:60. [PMID: 30333056 PMCID: PMC6192351 DOI: 10.1186/s13072-018-0224-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
Background Reactive oxygen species (ROS)-induced oxidative stress is well known to play a major role in male infertility. Sperm are sensitive to ROS damaging effects because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. However, how oxidative DNA lesions in sperm affect early embryonic development remains elusive. Results Using cattle as model, we show that fertilization using sperm exposed to oxidative stress caused a major developmental arrest at the time of embryonic genome activation. The levels of DNA damage response did not directly correlate with the degree of developmental defects. The early cellular response for DNA damage, γH2AX, is already present at high levels in zygotes that progress normally in development and did not significantly increase at the paternal genome containing oxidative DNA lesions. Moreover, XRCC1, a factor implicated in the last step of base excision repair (BER) pathway, was recruited to the damaged paternal genome, indicating that the maternal BER machinery can repair these DNA lesions induced in sperm. Remarkably, the paternal genome with oxidative DNA lesions showed an impairment of zygotic active DNA demethylation, a process that previous studies linked to BER. Quantitative immunofluorescence analysis and ultrasensitive LC–MS-based measurements revealed that oxidative DNA lesions in sperm impair active DNA demethylation at paternal pronuclei, without affecting 5-hydroxymethylcytosine (5hmC), a 5-methylcytosine modification that has been implicated in paternal active DNA demethylation in mouse zygotes. Thus, other 5hmC-independent processes are implicated in active DNA demethylation in bovine embryos. The recruitment of XRCC1 to damaged paternal pronuclei indicates that oxidative DNA lesions drive BER to repair DNA at the expense of DNA demethylation. Finally, this study highlighted striking differences in DNA methylation dynamics between bovine and mouse zygotes that will facilitate the understanding of the dynamics of DNA methylation in early development. Conclusions The data demonstrate that oxidative stress in sperm has an impact not only on DNA integrity but also on the dynamics of epigenetic reprogramming, which may harm the paternal genetic and epigenetic contribution to the developing embryo and affect embryo development and embryo quality. Electronic supplementary material The online version of this article (10.1186/s13072-018-0224-y) contains supplementary material, which is available to authorized users.
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7
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O'Doherty AM, McGettigan P, Irwin RE, Magee DA, Gagne D, Fournier E, Al-Naib A, Sirard MA, Walsh CP, Robert C, Fair T. Intragenic sequences in the trophectoderm harbour the greatest proportion of methylation errors in day 17 bovine conceptuses generated using assisted reproductive technologies. BMC Genomics 2018; 19:438. [PMID: 29866048 PMCID: PMC5987443 DOI: 10.1186/s12864-018-4818-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/22/2018] [Indexed: 12/31/2022] Open
Abstract
Background Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without consequence as they are often associated with inauspicious pre- and postnatal outcomes including premature birth, intrauterine growth restriction and increased incidence of epigenetic disorders in human and large offspring syndrome in cattle. Here, global DNA methylation profiles in the trophectoderm and embryonic discs of in vitro produced (IVP), superovulation-derived (SOV) and unstimulated, synchronised control day 17 bovine conceptuses (herein referred to as AI) were interrogated using the EmbryoGENE DNA Methylation Array (EDMA). Pyrosequencing was used to validate four loci identified as differentially methylated on the array and to assess the differentially methylated regions (DMRs) of six imprinted genes in these conceptuses. The impact of embryo-production induced DNA methylation aberrations was determined using Ingenuity Pathway Analysis, shedding light on the potential functional consequences of these differences. Results Of the total number of differentially methylated loci identified (3140) 77.3 and 22.7% were attributable to SOV and IVP, respectively. Differential methylation was most prominent at intragenic sequences within the trophectoderm of IVP and SOV-derived conceptuses, almost a third (30.8%) of the differentially methylated loci mapped to intragenic regions. Very few differentially methylated loci were detected in embryonic discs (ED); 0.16 and 4.9% of the differentially methylated loci were located in the ED of SOV-derived and IVP conceptuses, respectively. The overall effects of SOV and IVP on the direction of methylation changes were associated with increased methylation; 70.6% of the differentially methylated loci in SOV-derived conceptuses and 57.9% of the loci in IVP-derived conceptuses were more methylated compared to AI-conceptuses. Ontology analysis of probes associated with intragenic sequences suggests enrichment for terms associated with cancer, cell morphology and growth. Conclusion By examining (1) the effects of superovulation and (2) the effects of an in vitro system (oocyte maturation, fertilisation and embryo culture) we have identified that the assisted reproduction process of superovulation alone has the largest impact on the DNA methylome of subsequent embryos. Electronic supplementary material The online version of this article (10.1186/s12864-018-4818-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alan M O'Doherty
- School of Agriculture and Food Science and Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Paul McGettigan
- School of Agriculture and Food Science and Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland
| | - Rachelle E Irwin
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, UK
| | - David A Magee
- School of Agriculture and Food Science and Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dominic Gagne
- Centre de Recherche en Biologie de la Reproduction (CRBR), Département des Sciences Animales, Université Laval, Québec, Qc, Canada
| | - Eric Fournier
- Centre de Recherche en Biologie de la Reproduction (CRBR), Département des Sciences Animales, Université Laval, Québec, Qc, Canada
| | - Abdullah Al-Naib
- Department of Animal and Poultry Science, School of Agriculture, Virginia Polytechnic Institute and State University, Blacksberg, VA, USA
| | - Marc-André Sirard
- Centre de Recherche en Biologie de la Reproduction (CRBR), Département des Sciences Animales, Université Laval, Québec, Qc, Canada
| | - Colum P Walsh
- Biomedical Sciences Research Institute, University of Ulster, Coleraine, UK
| | - Claude Robert
- Centre de Recherche en Biologie de la Reproduction (CRBR), Département des Sciences Animales, Université Laval, Québec, Qc, Canada
| | - Trudee Fair
- School of Agriculture and Food Science and Lyons Research Farm, University College Dublin, Belfield, Dublin 4, Ireland
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8
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Masala L, Burrai GP, Bellu E, Ariu F, Bogliolo L, Ledda S, Bebbere D. Methylation dynamics during folliculogenesis and early embryo development in sheep. Reproduction 2017; 153:605-619. [PMID: 28250235 DOI: 10.1530/rep-16-0644] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/10/2017] [Accepted: 02/28/2017] [Indexed: 12/27/2022]
Abstract
Genome-wide DNA methylation reprogramming occurs during mammalian gametogenesis and early embryogenesis. Post-fertilization demethylation of paternal and maternal genomes is considered to occur by an active and passive mechanism respectively, in most mammals but sheep; in this species no loss of methylation was observed in either pronucleus. Post-fertilization reprogramming relies on methylating and demethylating enzymes and co-factors that are stored during oocyte growth, concurrently with the re-methylation of the oocyte itself. The crucial remodelling of the oocyte epigenetic baggage often overlaps with potential interfering events such as exposure to assisted reproduction technologies or environmental changes. Here, we report a temporal analysis of methylation dynamics during folliculogenesis and early embryo development in sheep. We characterized global DNA methylation and hydroxymethylation by immunofluorescence and relatively quantified the expression of the enzymes and co-factors mainly responsible for their remodelling (DNA methyltransferases (DNMTs), ten-eleven translocation (TET) proteins and methyl-CpG-binding domain (MBD) proteins). Our results illustrate for the first time the patterns of hydroxymethylation during oocyte growth. We observed different patterns of methylation and hydroxymethylation between the two parental pronuclei, suggesting that male pronucleus undergoes active demethylation also in sheep. Finally, we describe gene-specific accumulation dynamics for methylating and demethylating enzymes during oocyte growth and observe patterns of expression associated with developmental competence in a differential model of oocyte potential. Our work contributes to the understanding of the methylation dynamics during folliculogenesis and early embryo development and improves the overall picture of early rearrangements that will originate the embryo epigenome.
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Affiliation(s)
- Laura Masala
- Department of Veterinary MedicineUniversity of Sassari, Sassari, Italy
| | | | - Emanuela Bellu
- Department of Veterinary MedicineUniversity of Sassari, Sassari, Italy
| | - Federica Ariu
- Department of Veterinary MedicineUniversity of Sassari, Sassari, Italy
| | - Luisa Bogliolo
- Department of Veterinary MedicineUniversity of Sassari, Sassari, Italy
| | - Sergio Ledda
- Department of Veterinary MedicineUniversity of Sassari, Sassari, Italy
| | - Daniela Bebbere
- Department of Veterinary MedicineUniversity of Sassari, Sassari, Italy
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Mendonça ADS, Guimarães ALS, da Silva NMA, Caetano AR, Dode MAN, Franco MM. Characterization of the IGF2 Imprinted Gene Methylation Status in Bovine Oocytes during Folliculogenesis. PLoS One 2015; 10:e0142072. [PMID: 26517264 PMCID: PMC4627647 DOI: 10.1371/journal.pone.0142072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/17/2015] [Indexed: 02/07/2023] Open
Abstract
DNA methylation reprogramming occurs during mammalian gametogenesis and embryogenesis. Sex-specific DNA methylation patterns at specific CpG islands controlling imprinted genes are acquired during this window of development. Characterization of the DNA methylation dynamics of imprinted genes acquired by oocytes during folliculogenesis is essential for understanding the physiological and genetic aspects of female gametogenesis and to determine the parameters for oocyte competence. This knowledge can be used to improve in vitro embryo production (IVP), specifically because oocyte competence is one of the most important aspects determining the success of IVP. Imprinted genes, such as IGF2, play important roles in embryo development, placentation and fetal growth. The aim of this study was to characterize the DNA methylation profile of the CpG island located in IGF2 exon 10 in oocytes during bovine folliculogenesis. The methylation percentages in oocytes from primordial follicles, final secondary follicles, small antral follicles, large antral follicles, MII oocytes and spermatozoa were 73.74 ± 2.88%, 58.70 ± 7.46%, 56.00 ± 5.58%, 65.77 ± 5.10%, 56.35 ± 7.45% and 96.04 ± 0.78%, respectively. Oocytes from primordial follicles showed fewer hypomethylated alleles (15.5%) than MII oocytes (34.6%) (p = 0.039); spermatozoa showed only hypermethylated alleles. Moreover, MII oocytes were less methylated than spermatozoa (p<0.001). Our results showed that the methylation pattern of this region behaves differently between mature oocytes and spermatozoa. However, while this region has a classical imprinted pattern in spermatozoa that is fully methylated, it was variable in mature oocytes, showing hypermethylated and hypomethylated alleles. Furthermore, our results suggest that this CpG island may have received precocious reprogramming, considering that the hypermethylated pattern was already found in growing oocytes from primordial follicles. These results may contribute to our understanding of the reprogramming of imprinted genes during bovine oogenesis.
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Affiliation(s)
- Anelise dos Santos Mendonça
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Ana Luíza Silva Guimarães
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- School of Agriculture and Veterinary Medicine, University of Brasília, Brasília, Distrito Federal, Brazil
| | | | | | - Margot Alves Nunes Dode
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- School of Agriculture and Veterinary Medicine, University of Brasília, Brasília, Distrito Federal, Brazil
| | - Maurício Machaim Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
- * E-mail:
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10
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Tajbakhsh J, Stefanovski D, Tang G, Wawrowsky K, Liu N, Fair JH. Dynamic heterogeneity of DNA methylation and hydroxymethylation in embryonic stem cell populations captured by single-cell 3D high-content analysis. Exp Cell Res 2015; 332:190-201. [PMID: 25700729 DOI: 10.1016/j.yexcr.2015.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/06/2015] [Accepted: 02/07/2015] [Indexed: 12/18/2022]
Abstract
UNLABELLED Cell-surface markers and transcription factors are being used in the assessment of stem cell fate and therapeutic safety, but display significant variability in stem cell cultures. We assessed nuclear patterns of 5-hydroxymethylcytosine (5hmC, associated with pluripotency), a second important epigenetic mark, and its combination with 5-methylcytosine (5mC, associated with differentiation), also in comparison to more established markers of pluripotency (Oct-4) and endodermal differentiation (FoxA2, Sox17) in mouse embryonic stem cells (mESC) over a 10-day differentiation course in vitro: by means of confocal and super-resolution imaging together with 3D high-content analysis, an essential tool in single-cell screening. IN SUMMARY 1) We did not measure any significant correlation of putative markers with global 5mC or 5hmC. 2) While average Oct-4 levels stagnated on a cell-population base (0.015 lnIU/day), Sox17 and FoxA2 increased 22-fold and 3-fold faster, respectively (Sox17: 0.343 lnIU/day; FoxA2: 0.046 lnIU/day). In comparison, global DNA methylation levels increased 4-fold faster (0.068 lnIU/day), and global hydroxymethylation declined at 0.046 lnIU/day, both with a better explanation of the temporal profile. 3) This progression was concomitant with the occurrence of distinct nuclear codistribution patterns that represented a heterogeneous spectrum of states in differentiation; converging to three major coexisting 5mC/5hmC phenotypes by day 10: 5hmC(+)/5mC(-), 5hmC(+)/5mC(+), and 5hmC(-)/5mC(+) cells. 4) Using optical nanoscopy we could delineate the respective topologies of 5mC/5hmC colocalization in subregions of nuclear DNA: in the majority of 5hmC(+)/5mC(+) cells 5hmC and 5mC predominantly occupied mutually exclusive territories resembling euchromatic and heterochromatic regions, respectively. Simultaneously, in a smaller subset of cells we observed a tighter colocalization of the two cytosine variants, presumably delineating chromatin domains in remodeling. We conclude that 1) 5mC emerges as the most differential marker in our model system. 2) However, the combined enrollment of the two DNA modifications provided higher-definition screening and lead to the identification of cell subpopulations based on differential 5hmC/5mC phenotypes corresponding to different 5hmC/5mC ratios. The results encourage: a) assessing the regenerative potential of early-endodermal cells enriched for the three DNA methylation/hydroxymethylation categories, and b) exploring the universality of this type of epigenetic phenotyping across other lineage-specific differentiations.
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Affiliation(s)
- Jian Tajbakhsh
- Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Darko Stefanovski
- Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19348, USA
| | - George Tang
- Chromatin Biology Laboratory, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Kolja Wawrowsky
- Translational Cytomics Group, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Naiyou Liu
- Department of Surgery and UF Health Comprehensive Transplant Center, University of Florida College of Medicine, Gainesville, FL 32608, USA
| | - Jeffrey H Fair
- Department of Surgery and UF Health Comprehensive Transplant Center, University of Florida College of Medicine, Gainesville, FL 32608, USA
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11
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Salvaing J, Li Y, Beaujean N, O'Neill C. Determinants of valid measurements of global changes in 5ʹ-methylcytosine and 5ʹ-hydroxymethylcytosine by immunolocalisation in the early embryo. Reprod Fertil Dev 2015; 27:755-64. [DOI: 10.1071/rd14136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/26/2014] [Indexed: 12/15/2022] Open
Abstract
A classical model of epigenetic reprogramming of methyl-cytosine–phosphate–guanine (CpG) dinucleotides within the genome of the early embryo involves a process of active demethylation of the paternally derived genome immediately following fertilisation, creating marked asymmetry in global cytosine methylation levels in male and female pronuclei, followed by passive demethylation of the maternally derived genome over subsequent cell cycles. This model has dominated thinking in developmental epigenetics over recent decades. Recent re-analyses of the model show that demethylation of the paternally derived genome is more modest than formerly thought and results in overall similar levels of methylation of the paternal and maternal pronuclei in presyngamal zygotes, although there is little evidence for a pervasive process of passive demethylation during the cleavage stage of development. In contrast, the inner cell mass of the blastocyst shows some loss of methylation within specific classes of loci. Improved methods of chemical analysis now allow global base-level analysis of modifications to CpG dinucleotides within the cells of the early embryo, yet the low cost and convenience of the immunolocalisation techniques mean that they still have a valuable place in the analysis of the epigenetics of embryo development. In this review we consider the key strengths and weaknesses of this methodology and some factors required for its valid use and interpretation.
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12
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Dobbs KB, Gagné D, Fournier E, Dufort I, Robert C, Block J, Sirard MA, Bonilla L, Ealy AD, Loureiro B, Hansen PJ. Sexual dimorphism in developmental programming of the bovine preimplantation embryo caused by colony-stimulating factor 2. Biol Reprod 2014; 91:80. [PMID: 25078682 DOI: 10.1095/biolreprod.114.121087] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Physiology of the adult can be modified by alterations in prenatal development driven by the maternal environment. Developmental programming, which can be established before the embryo implants in the uterus, can affect females differently than males. The mechanism by which sex-specific developmental programming is established is not known. Here we present evidence that maternal regulatory signals change female embryos differently than male embryos. In particular, actions of the maternally derived cytokine CSF2 from Day 5 to Day 7 of development affected characteristics of the embryo at Day 15 differently for females than males. CSF2 decreased length and IFNT secretion of female embryos but increased length and IFNT secretion of male embryos. Analysis of a limited number of samples indicated that changes in the transcriptome and methylome caused by CSF2 also differed between female and males. Thus, sex-specific programming by the maternal environment could occur when changes in secretion of maternally derived regulatory molecules alter development of female embryos differently than male embryos.
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Affiliation(s)
- Kyle B Dobbs
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida
| | - Dominic Gagné
- Centre de Recherche en Biologie de la Reproduction, Institut des Nutraceutiques et des Aliments Fonctionnels, Université Laval, Québec, Québec, Canada
| | - Eric Fournier
- Centre de Recherche en Biologie de la Reproduction, Institut des Nutraceutiques et des Aliments Fonctionnels, Université Laval, Québec, Québec, Canada
| | - Isabelle Dufort
- Centre de Recherche en Biologie de la Reproduction, Institut des Nutraceutiques et des Aliments Fonctionnels, Université Laval, Québec, Québec, Canada
| | - Claude Robert
- Centre de Recherche en Biologie de la Reproduction, Institut des Nutraceutiques et des Aliments Fonctionnels, Université Laval, Québec, Québec, Canada
| | - Jeremy Block
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida Ovatech LLC, Gainesville, Florida
| | - Marc-André Sirard
- Centre de Recherche en Biologie de la Reproduction, Institut des Nutraceutiques et des Aliments Fonctionnels, Université Laval, Québec, Québec, Canada
| | - Luciano Bonilla
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida
| | - Alan D Ealy
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Barbara Loureiro
- School of Veterinary Medicine, Universidade Vila Velha, Vila Velha, Espirito Santo, Brazil
| | - Peter J Hansen
- Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program, and Genetics Institute, University of Florida, Gainesville, Florida
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13
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Shojaei Saadi HA, O'Doherty AM, Gagné D, Fournier É, Grant JR, Sirard MA, Robert C. An integrated platform for bovine DNA methylome analysis suitable for small samples. BMC Genomics 2014; 15:451. [PMID: 24912542 PMCID: PMC4092217 DOI: 10.1186/1471-2164-15-451] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/28/2014] [Indexed: 01/16/2023] Open
Abstract
Background Oocytes and early embryos contain minute amounts of DNA, RNA and proteins, making the study of early mammalian development highly challenging. The study of the embryo epigenome, in particular the DNA methylome, has been made accessible thanks to the possibility of amplifying specific sequences according to their initial methylation status. This paper describes a novel platform dedicated to the genome-wide study of bovine DNA methylation, including a complete pipeline for data analysis and visualization. The platform allows processing and integrating of DNA methylome and transcriptome data from the same sample. Procedures were optimized for genome-wide analysis of 10 ng of DNA (10 bovine blastocysts). Bovine sperm and blastocysts were compared as a test of platform capability. Results The hypermethylation of bovine sperm DNA compared to the embryo genome was confirmed. Differentially methylated regions were distributed across various classes of bovine sperm genomic feature including primarily promoter, intronic and exonic regions, non-CpG-island regions (shore, shelf and open-sea) and CpG islands with low-to-intermediate CpG density. The blastocyst genome bore more methylation marks than sperm DNA only in CpG islands with high CpG density. Long-terminal-repeat retrotransposons (LTR), LINE and SINE were more methylated in sperm DNA, as were low-complexity repetitive elements in blastocysts. Conclusions This is the first early embryo compatible genome-wide epigenetics platform for bovine. Such platforms should improve the study of the potential epigenetic risks of assisted reproductive technologies (ART), the establishment sequence of embryonic cell lines and potential deviations in both gene expression and DNA methylation capable of having long-term impact. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-451) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Claude Robert
- Laboratory of Functional Genomics of Early Embryonic Development, Institut des nutraceutiques et des aliments fonctionnels, Faculté des sciences de l'agriculture et de l'alimentation, Pavillon des services, Université Laval, Québec G1V 0A6, Canada.
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14
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Lisanti S, Omar WAW, Tomaszewski B, De Prins S, Jacobs G, Koppen G, Mathers JC, Langie SAS. Comparison of methods for quantification of global DNA methylation in human cells and tissues. PLoS One 2013; 8:e79044. [PMID: 24260150 PMCID: PMC3832524 DOI: 10.1371/journal.pone.0079044] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/26/2013] [Indexed: 12/25/2022] Open
Abstract
DNA methylation is a key epigenetic modification which, in mammals, occurs mainly at CpG dinucleotides. Most of the CpG methylation in the genome is found in repetitive regions, rich in dormant transposons and endogenous retroviruses. Global DNA hypomethylation, which is a common feature of several conditions such as ageing and cancer, can cause the undesirable activation of dormant repeat elements and lead to altered expression of associated genes. DNA hypomethylation can cause genomic instability and may contribute to mutations and chromosomal recombinations. Various approaches for quantification of global DNA methylation are widely used. Several of these approaches measure a surrogate for total genomic methyl cytosine and there is uncertainty about the comparability of these methods. Here we have applied 3 different approaches (luminometric methylation assay, pyrosequencing of the methylation status of the Alu repeat element and of the LINE1 repeat element) for estimating global DNA methylation in the same human cell and tissue samples and have compared these estimates with the "gold standard" of methyl cytosine quantification by HPLC. Next to HPLC, the LINE1 approach shows the smallest variation between samples, followed by Alu. Pearson correlations and Bland-Altman analyses confirmed that global DNA methylation estimates obtained via the LINE1 approach corresponded best with HPLC-based measurements. Although, we did not find compelling evidence that the gold standard measurement by HPLC could be substituted with confidence by any of the surrogate assays for detecting global DNA methylation investigated here, the LINE1 assay seems likely to be an acceptable surrogate in many cases.
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Affiliation(s)
- Sofia Lisanti
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
| | - Wan A. W. Omar
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- Advance Medical and Dental Institute, Universiti Sains Malaysia, Penang, Malaysia
| | - Bartłomiej Tomaszewski
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- Centre for Brain Ageing and Vitality, Institute for Ageing & Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
| | - Sofie De Prins
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Griet Jacobs
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Gudrun Koppen
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - John C. Mathers
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- Centre for Integrated Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- Centre for Brain Ageing and Vitality, Institute for Ageing & Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
| | - Sabine A. S. Langie
- Human Nutrition Research Centre, Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium
- Centre for Brain Ageing and Vitality, Institute for Ageing & Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
- * E-mail:
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