title: Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro.
abstract: Early embryonic loss and altered gene expression in in vitro produced blastocysts are believed to be partly caused by aberrant DNA methylation. However, specific embryonic stage which is sensitive to in vitro culture conditions to alter the DNA methylation profile of the resulting blastocysts remained unclear. Therefore, the aim of this study was to investigate the stage specific effect of in vitro culture environment on the DNA methylation response of the resulting blastocysts. For this, embryos cultured in vitro until zygote (ZY), 4-cell (4C) or 16-cell (16C) were transferred to recipients and the blastocysts were recovery at day 7 of the estrous cycle. Another embryo group was cultured in vitro until blastocyst stage (IVP). Genome-wide DNA methylation profiles of ZY, 4C, 16C and IVP blastocyst groups were then determined with reference to blastocysts developed completely under in vivo condition (VO) using EmbryoGENE DNA Methylation Array. To assess the contribution of methylation changes on gene expression patterns, the DNA methylation data was superimposed to the transcriptome profile data. The degree of DNA methylation dysregulation in the promoter and/or gene body regions of the resulting blastocysts was correlated with successive stages of development the embryos advanced under in vitro culture before transfer to the in vivo condition. Genomic enrichment analysis revealed that in 4C and 16C blastocyst groups, hypermethylated loci were outpacing the hypomethylated ones in intronic, exonic, promoter and proximal promoter regions, whereas the reverse was observed in ZY blastocyst group. However, in the IVP group, as much hypermethylated as hypomethylated probes were detected in gene body and promoter regions. In addition, gene ontology analysis indicated that differentially methylated regions were found to affected several biological functions including ATP binding in the ZY group, programmed cell death in the 4C, glycolysis in 16C and genetic imprinting and chromosome segregation in IVP blastocyst groups. Furthermore, 1.6, 3.4, 3.9 and 9.4% of the differentially methylated regions that were overlapped to the transcriptome profile data were negatively correlated with the gene expression patterns in ZY, 4C, 16C and IVP blastocyst groups, respectively. Therefore, this finding indicated that suboptimal culture condition during preimplantation embryo development induced changes in the DNA methylation landscape of the resulting blastocysts in a stage dependent manner and the altered DNA methylation pattern was only partly explained the observed aberrant gene expression patterns of the blastocysts.
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Dessie
authors.initials: D
authors.lastname: Salilew-Wondim
authors.affiliation: Centre de recherche en biologie de la reproduction, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), Canada G1V 0A6.
authors.forename: Eric
authors.initials: E
authors.lastname: Fournier
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Hoelker
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Saeed-Zidane
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Ernst
authors.initials: E
authors.lastname: Tholen
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Looft
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Christiane
authors.initials: C
authors.lastname: Neuhoff
authors.affiliation: Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, A-1210, Vienna, Austria.
authors.forename: Urban
authors.initials: U
authors.lastname: Besenfelder
authors.affiliation: Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, A-1210, Vienna, Austria.
authors.forename: Vita
authors.initials: V
authors.lastname: Havlicek
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Franca
authors.initials: F
authors.lastname: Rings
authors.affiliation: Centre de recherche en biologie de la reproduction, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), Canada G1V 0A6.
authors.forename: Dominic
authors.initials: D
authors.lastname: Gagné
authors.affiliation: Centre de recherche en biologie de la reproduction, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), Canada G1V 0A6.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Sirard
authors.affiliation: Centre de recherche en biologie de la reproduction, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), Canada G1V 0A6.
authors.forename: Claude
authors.initials: C
authors.lastname: Robert
authors.affiliation: Centre de recherche en biologie de la reproduction, Faculté des sciences de l'agriculture et de l'alimentation, INAF, Pavillon des services, Université Laval (Québec), Canada G1V 0A6.
authors.forename: Habib A
authors.initials: HA
authors.lastname: Shojaei Saadi
authors.affiliation: Department of Animal Production, Faculty of Agriculture, Cairo University, 12613, Giza, Egypt.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Gad
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Karl
authors.initials: K
authors.lastname: Schellander
authors.affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
authors.forename: Dawit
authors.initials: D
authors.lastname: Tesfaye
mesh_terms: D000818:Animals; D001755:Blastocyst / Q000166:cytology*; D002417:Cattle; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D046149:Embryo Culture Techniques; D004624:Embryo Transfer / Q000379:methods; D047108:Embryonic Development / Q000502:physiology*; D005260:Female; D005307:Fertilization in Vitro; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D009865:Oocytes / Q000166:cytology*; D011247:Pregnancy