DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

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

Alterations in DNA methylation patterns and gene expression in spermatozoa of subfertile males

“…These correlations are consistent with the results of other authors who existed a wide spread relationships between gene expression and semen parameters (Wagner et al, 2014). On the other hand, this study did not show a correlation between the alteration in sperm DNA methylation level and the expression level of the GAA, UBE2G2 and ALS2CR12 gene, and this agrees with the previous studies that pointed that the DNA methylation at the gene bodies or promoter is directly or indirectly associated with gene expression is not strictly true (Canovas et al, 2017;Gkountela et al, 2015). On the other hand, this study did not show a correlation between the alteration in sperm DNA methylation level and the expression level of the GAA, UBE2G2 and ALS2CR12 gene, and this agrees with the previous studies that pointed that the DNA methylation at the gene bodies or promoter is directly or indirectly associated with gene expression is not strictly true (Canovas et al, 2017;Gkountela et al, 2015).…”

Long term effects of ART: What do animals tell us?

“…After the first wave of epigenome reprogramming that occurs during gametogenesis, a second one takes place in the early embryo during the period spanning from fertilization to implantation. Paternal and maternal genomes brought into a common oocyte cytoplasm by fertilization are first de‐methylated, with different kinetics and by different molecular processes (Canovas et al, ; Salvaing et al, ). The methylation decreases during cleavages and thus over embryonic genome activation, and reaches its lowest level at the blastocyst stage (Guo et al, ; Zhang et al, ).…”

Applications of omics and nanotechnology to improve pig embryo production in vitro

“…The addition of GM‐CSF during culture in vitro increased blastocyst rates and total cell number of IVF and SCNT‐derived embryos. Moreover, when SCNT‐derived porcine embryos cultured with GM‐CSF were transferred to surrogates, they were able to establish pregnancies and resulted in the birth of healthy piglets (Lee et al, ).Recently, in a study conducted by Canovas et al (), porcine genome‐wide analyses by RNA‐Seq and Bisulfite‐Seq were performed to compare gene expression and DNA methylation changes between single in vivo‐derived blastocysts collected by flushing the uteri of animals and single in vitro‐cultured blastocysts without (C‐IVF) or in the presence of natural reproductive fluids (Natur‐IVF). As a result of this supplementation, a higher mean number of cells in Natur‐IVF and in vivo‐derived blastocysts were observed compared to C‐IVF embryos.…”

“…Recently, in a study conducted by Canovas et al (), porcine genome‐wide analyses by RNA‐Seq and Bisulfite‐Seq were performed to compare gene expression and DNA methylation changes between single in vivo‐derived blastocysts collected by flushing the uteri of animals and single in vitro‐cultured blastocysts without (C‐IVF) or in the presence of natural reproductive fluids (Natur‐IVF). As a result of this supplementation, a higher mean number of cells in Natur‐IVF and in vivo‐derived blastocysts were observed compared to C‐IVF embryos.…”

“…Culture with pyruvate and lactate as the primary energy sources has been shown to increase blastocyst rates and total cell numbers, but a bias toward development of male embryos has also been observed (Kim et al, ; Torner, Bussalleu, Briz, Yeste, & Bonet, ; Torner, Bussalleu, Briz, Yeste, & Bonet, ). Currently, two formulations of porcine embryo culture media are predominantly utilized: NCSU‐23 and porcine zygote medium (PZM) variants (Canovas et al, ; Chen et al, ; Petters & Wells, ; Redel et al, ; Spate, Brown, Redel, Whitworth, & Prather, ; Suzuki, Yoshioka, Sakatani, & Takahashi, ; Yoshioka et al, ). NCSU‐23 contains glucose (5.5 mM) and glutamine (1 mM), but certain variants utilize pyruvate (0.5 mM) and lactate (5 mM) for the first 48 hr which is replaced by glucose (5.5 mM) for the remaining duration of culture.…”