Mining RNAseq data reveals dynamic metaboloepigenetic profiles in human, mouse and bovine pre-implantation embryos

Abstract

Metaboloepigenetic regulation has been reported in stem cells, germ cells, and tumor cells. Embryonic metaboloepigenetics, however, have just begun to be described. Here we analyzed RNAseq data to characterize the metaboloepigenetic profiles of human, mouse, and bovine pre-implantation embryos. In embryos, metaboloepigenetic reprogramming was species-specific, varied with the developmental stage and was disrupted with in vitro culture. Metabolic pathways and gene expressions were strongly correlated with early embryo DNA methylation and were changed with in vitro culture. Although the idea that the in vitro environment may influence development is not new, there has been little progress on improving pregnancy rates after decades using in vitro fertilization. Hence, the present data will contribute to understanding how the in vitro manipulation affects the metaboloepigenetic status of early embryos, which can be used to establish culture strategies aimed at improving the in vitro environment and, consequently, pregnancy rates and offspring health.

Keywords: Biological sciences; Endocrinology; Molecular biology; Omics; Transcriptomics.

Graphical abstract

Figure 1

Metaboloepigenetic pathways are species and stage specific General analysis of human (in vitro), mouse (in vivo) and bovine (in vivo) mature oocyte (MII) and embryos (2, 4, 8, 16C, MO and BL), showing proportion of up (PropUp, red) and down (PropDown, green) regulated metabolic and epigenetic pathways (part of Reactome terms “Metabolism” and “Epigenetic regulation of gene expression”) in 2C compared to MII, 4C compared to 2C, 8C compared to 4C, 16C compared to 8C and BL compared to 16C. Differences were calculated using ROAST, and significance determined using a one-sided directional p value < 0.05.

Figure 2

Changes on known metaboloepigenetic pathways are species and stage specific Analysis of human (in vitro), mouse (in vivo) and bovine (in vivo) pre-implantation embryos (2, 4, 8, 16C/MO and BL). Known metaboloepigenetic pathways are depicted alongside each pathway expression pattern among the different pre-implantation stages (ROAST analysis data relative to MII expression) for human (purple), bovine (yellow) and mouse (green). Significant up and down regulated pathways between stages transition (MII-2C, 2C–4C, 4C–8C, 8C–16C/MO and 16C/MO-BL) intra-specie are marked with “∗” (one-sided p value < 0.05).

Figure 3

Metaboloepigenetic control of DNA and histone methylation Analysis of human (purple), mouse (green) and bovine (yellow) in vivo (full lines) and in vitro (dashed lines) pre-implantation stages (MII, 2, 4, 8, 16C/MO and BL). The connection between DNA and histone methylation pathways with the one carbon cycle are depicted alongside selected expression pattern among the different pre-implantation stages for each species of selected genes (mean ± SD). For significant up and down regulated genes between stages and species see Figure S2.

Figure 4

DNA and histone demethylation are controlled by metabolism Connection between metabolism and DNA and histone demethylation of human (purple), mouse (green) and bovine (yellow) in vivo (full lines) and in vitro (dashed lines) pre-implantation stages (MII, 2, 4, 8, 16C/MO and BL). Pathways related to glucose, pyruvate, α-ketoglutarate and glutamine, metabolism and the TCA cycle, that can directly influence DNA and histone demethylation are depicted alongside each gene expression (mean ± SD pattern among the different pre-implantation stages for each species. For significant up and down regulated genes between stages intra-species see Figure S3.

Figure 5

DNA methylation is correlated with metaboloepigenetic pathways and genes Correlation between DNA methylation and metaboloepigenetic genes expression (A) and metaboloepigenetic Reactome pathways (B) for bovine, human and mouse in vivo and in vitro pre-implantation embryos.

Figure 6

In vitro culture influences metaboloepigenetic genes expression (A–D) Embryo General analysis of in vitro bovine and mouse mature oocyte (MII) and embryos (2, 4, 8, 16C, MO and BL) gene expression of metabolism and epigenetic genes. PCA comparing bovine (A) and mouse (B) in vivo and in vitro samples. Metaboloepigenetic genes up (red) and down (green) regulated (adjusted p value < 0.05) comparing in vitro vs in vivo blastocysts from bovine (C) and mouse (D).

Figure 7

Metaboloepigenetic pathways are modified in vitro General analysis of in vitro bovine and mouse mature oocyte (MII) and embryos (2, 4, 8, 16C, MO and BL), showing proportion of up (PropUp, red) and down (PropDown, green) regulated metabolic and epigenetic pathways (part of Reactome terms “Metabolism” and “Epigenetic regulation of gene expression”) in 2C compared to MII (bovine only), 4C compared to 2C, 8C compared to 4C, 16C compared to 8C and BL compared to 16C. Differences on PropUp and PropDown were calculated using ROAST, and significance determined using a the one-sided directional p value < 0.05