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Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro.

Salilew-Wondim D, Fournier E, Hoelker M, Saeed-Zidane M, Tholen E, Looft C, Neuhoff C, Besenfelder U, Havlicek V, Rings F, Gagné D, Sirard MA, Robert C, A Shojaei Saadi H, Gad A, Schellander K, Tesfaye D - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.

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.

No MeSH data available.


Related in: MedlinePlus

Venn diagram depicting differentially methylated genomic regions specific in ZY, 4C, 16C or IVP blastocyst group or genomic regions stably hypermethylated or hypomethylated in two or more blastocyst groups.Symbols, ↑ and ↓ indicate hypermethylation and hypomethylation, respectively. DMRs = the number of differentially methylated regions. The gene lists under the column target genes indicate only representative ones.
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pone.0140467.g003: Venn diagram depicting differentially methylated genomic regions specific in ZY, 4C, 16C or IVP blastocyst group or genomic regions stably hypermethylated or hypomethylated in two or more blastocyst groups.Symbols, ↑ and ↓ indicate hypermethylation and hypomethylation, respectively. DMRs = the number of differentially methylated regions. The gene lists under the column target genes indicate only representative ones.

Mentions: In order to get insight into the genomic loci that were differentially methylated in a stable or stage dependent manner, we looked into the DMRs that were specific to each blastocyst group and the DMRs that were common in two or more blastocyst groups. Hypermethylated or hypomethylated genomic loci which appeared in two or more blastocyst groups were considered as “stably” differentially methylated regions. Accordingly, a total of 137, 624, 1180, and 3086 DMRs were found to be specific to only ZY, 4C, 16C and IVP blastocyst groups, respectively, whereas 115, 350, 65 and 348 DMRs in ZY, 4C, 16C and IVP blastocyst groups, respectively were stably differentially methylated in two or more blastocyst groups (Fig 3). Moreover, differentially methylated genomic loci specific to each group were increased depending on stages of the embryos while stably differentially methylated genomic loci didn’t exhibit that trend. Among stably hypermethylated or hypomethylated genomic loci, 45 DMRs were identified in ZY, 4C and IVP groups, but these genomic loci were not significantly differentially methylated in the 16C blastocyst group (Fig 3, S3 Table). Furthermore, we look into a stage wise comparisons from ZY to IVP, it was evidenced that the ZY blastocyst group had relatively higher DMRs in common with 4C group than it did with other blastocyst groups (Fig 3, S3 Table). On the other hand, the 4C blastocysts shared relatively higher number of DMRs (n = 290; 29.7% of the total) with IVP blastocyst group and thus compared to other groups, in terms of common DMRs, the 4C blastocyst group was quite closer to the IVP blastocyst group (Fig 3, S5 Table) followed by ZY group. However, the 16C blastocyst group, which the EGA is believed to occur in vitro, shared only 3% of the DMRs (45/1245) with IVP blastocyst group (Fig 3).


Genome-Wide DNA Methylation Patterns of Bovine Blastocysts Developed In Vivo from Embryos Completed Different Stages of Development In Vitro.

Salilew-Wondim D, Fournier E, Hoelker M, Saeed-Zidane M, Tholen E, Looft C, Neuhoff C, Besenfelder U, Havlicek V, Rings F, Gagné D, Sirard MA, Robert C, A Shojaei Saadi H, Gad A, Schellander K, Tesfaye D - PLoS ONE (2015)

Venn diagram depicting differentially methylated genomic regions specific in ZY, 4C, 16C or IVP blastocyst group or genomic regions stably hypermethylated or hypomethylated in two or more blastocyst groups.Symbols, ↑ and ↓ indicate hypermethylation and hypomethylation, respectively. DMRs = the number of differentially methylated regions. The gene lists under the column target genes indicate only representative ones.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4633222&req=5

pone.0140467.g003: Venn diagram depicting differentially methylated genomic regions specific in ZY, 4C, 16C or IVP blastocyst group or genomic regions stably hypermethylated or hypomethylated in two or more blastocyst groups.Symbols, ↑ and ↓ indicate hypermethylation and hypomethylation, respectively. DMRs = the number of differentially methylated regions. The gene lists under the column target genes indicate only representative ones.
Mentions: In order to get insight into the genomic loci that were differentially methylated in a stable or stage dependent manner, we looked into the DMRs that were specific to each blastocyst group and the DMRs that were common in two or more blastocyst groups. Hypermethylated or hypomethylated genomic loci which appeared in two or more blastocyst groups were considered as “stably” differentially methylated regions. Accordingly, a total of 137, 624, 1180, and 3086 DMRs were found to be specific to only ZY, 4C, 16C and IVP blastocyst groups, respectively, whereas 115, 350, 65 and 348 DMRs in ZY, 4C, 16C and IVP blastocyst groups, respectively were stably differentially methylated in two or more blastocyst groups (Fig 3). Moreover, differentially methylated genomic loci specific to each group were increased depending on stages of the embryos while stably differentially methylated genomic loci didn’t exhibit that trend. Among stably hypermethylated or hypomethylated genomic loci, 45 DMRs were identified in ZY, 4C and IVP groups, but these genomic loci were not significantly differentially methylated in the 16C blastocyst group (Fig 3, S3 Table). Furthermore, we look into a stage wise comparisons from ZY to IVP, it was evidenced that the ZY blastocyst group had relatively higher DMRs in common with 4C group than it did with other blastocyst groups (Fig 3, S3 Table). On the other hand, the 4C blastocysts shared relatively higher number of DMRs (n = 290; 29.7% of the total) with IVP blastocyst group and thus compared to other groups, in terms of common DMRs, the 4C blastocyst group was quite closer to the IVP blastocyst group (Fig 3, S5 Table) followed by ZY group. However, the 16C blastocyst group, which the EGA is believed to occur in vitro, shared only 3% of the DMRs (45/1245) with IVP blastocyst group (Fig 3).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.

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.

No MeSH data available.


Related in: MedlinePlus