Background

Pre-implantation development is a mammalian-specific occurrence, which encompasses the period from fertilization to implantation and involves a number of important events [1]. Understanding pre-implantation development is important, both for basic reproductive biology and for practical applications including regenerative medicine and livestock production. However, due to the scarcity of the materials, both in size (about 0.1 mm diameter) and in quantity (only a few to tens of oocytes from each ovulation) are limited in related research, which has hampered the molecular analysis of human pre-implantation embryos. Thus using the mouse model system has formed the current perfect paradigm about gene expression during pre-implantation development. Recently, more and more global gene expression profiles during mouse pre-implantation development have been examined, two principal transient waves of de novo transcription have been identified [2, 3]. Additionally, several important transcripts have been reported to have the core roles at each developmental stage. For example, H1foo and Msy2 have been reported as the oocyte-specific transcripts, which are not re-expressed later in development, destruction of these maternal mRNAs restricts the length of time that these genes can function [4, 5]; Recent studies have shown that JNK and p38 are involved in cavity formation during pre-implantation development [6, 7]. As the unclear confidence of the previously identified genes, their roles in the regulation of mouse pre-implantation development must be further discussed and the consistence with human must also be considered.

In our study, we employed time course expression datasets of early mouse and human embryo both from the same series. Through our comparative analysis of genome wide temporal gene expression data based on significance analysis and functional annotation, we found that there were many differences in the expression patterns of pre-implantation development between mouse and human, for both the regulatory waves and the identified genes.

Methods

Data collection

We searched GEO [8] for the gene expression profiling studies related to pre-implantation development. Finally, we chose the data set GSE18290 contributed by ** of the human and murine orphan receptors ERRalpha (ESRRA) and ERRbeta (ESRRB) and identification of a novel human ERRalpha-related pseudogene. Genomics. 1997, 45: 320-326. 10.1006/geno.1997.4939." href="/article/10.1186/1477-7827-8-41#ref-CR21" id="ref-link-section-d75648876e930">21]. The second group appears to represent genes that showed a dramatic decrease throughout the stages, abundant in one cell stage but degraded during pre-implantation development, which is cluster 3 (1883 probe sets). The third group is exactly opposite to the second one, it appears to represent genes that showed a dramatic increase throughout the developmental stages, including cluster 5 (690 probe sets). The last group includes cluster 4 (1721 probe sets) and cluster 6 (690 probe sets), the genes here were firstly activated from one cell stage to 8-cell stage, peaked at 8-cell stage but degraded at later stages. In fact, the last group contains Mapk1 and Mapk3, respectively in cluster 4 and cluster 6, which are both well-known genes having central roles in diverse cellular functions [26]. In our study, the profiles of XIST expression in both mouse and human pre-implantation development were known. As a result, the expression of **st was significantly regulated at mouse 2-cell stage and blastocyst, but almost significantly regulated through human pre-implantation development (from 2-cell to blastocyst). On the other hand, in the k-means clustering of significant genes, the mouse **st gene was in Cluster 5 but the human XIST gene was in Cluster 3. The details were shown in Additional file 1 and 2, colored in red. Thus, all of these demonstrate that not as in the mouse, the pattern of human XIST expression is not consistent with a role for early expression in the choice of paternal X inactivation but participates in regulating the whole human early embryo development.

Significantly related GO terms and pathways

We then sought to determine the functions associated with the identified significant genes between each adjacent stage, analysis of over-represented annotations and pathways were performed by using DAVID [14, 15]. If p value was less than 0.01, it was considered as significant GO annotation or pathway. The significant GO terms of over-represented genes were shown in Table 2 and 3 respectively for mouse or human. The significant pathways of over-represented genes were shown in Table 4 and 5 respectively for mouse or human.

Table 2 The over-represented classification of GO annotations for mouse identified genes
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Table 3 The over-represented classification of GO annotations for human identified genes
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Table 4 The over-represented classification of pathways for mouse identified genes
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Table 5 The over-represented classification of pathways for human identified genes
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With comparison to mouse, due to the less different identified genes from one-cell stage to two-cell stage and from two-cell stage to 4-cell stage for human, there were less GO terms during these periods. The GO terms for human focused on such as "cell division", "cellular metabolic process", "primary metabolic process" and "RNA processing". These were all obtained for mouse, except for the GO term "death". Just like to be delayed, most of previous GO terms for mouse were appearing from 4-cell to 8-cell stage for human, such as "macromolecule metabolic process", "macromolecule localization", "establishment of protein localization" and "establishment of RNA localization". These findings support the idea that mid-preimplantation gene activation (MGA) drives the overt morphological changes in the subsequent stages, compaction and bifurcation into two-cell lineages. With the preparation of basic cellular machinery, dramatic biological processes were happening during Human Phase 3 (morula and blastocyst), which is related to the event of implantation.

Briefly, through our pathway analysis, most of the identified pathways were involved in after human 4-cell stage, but the number of identified pathways shared in mouse pre-implantation development. Moreover, many of the features and signaling pathways that are required during human pre-implantation development are also active during tumourigenesis [27]. According to our analysis based on human data, p53 signaling pathway, the pathways of Eenteropathogenic E. coli (EPEC) infection and Enterohemorrhagic E. coli (EHEC) infection were identified separately in 4-cell and 8-cell stages. These pathways were also thought to be related to the formation of cancer and the regulation of human reproduction [28–31]. But these above pathways were not identified from microarray analysis in mouse 4-cell and 8-cell stages. On the contrary, the pathway of oxidative phosphorylation was mostly identified through mouse pre-implantation development, which hardly appeared in human data. The oxidative phosphorylation pathway was reported as one of the obligatory energy metabolism pathways in most species throughout pre-implantation development [32]. And the pathway of Citrate cycle (TCA cycle) was identified after mouse 8-cell stage, which was not identified in human data. It is well know that the mitochondrial TCA cycle is the major source of reducing equivalents in the cytosol so that any change in mitochondrial function in the embryo will be reflected in changes in the intracellular redox state. In the mouse, the metabolic substrates used by the oocyte and early embryo each have a different impact on the intracellular redox state [33]. Surprisingly, the common identified pathway from 4-cell to 8-cell stage between human and mouse was only the Ubiquitin mediated proteolysis pathway, which was reported as an important role in eukaryotic cellular processes [34]. Thus it is advisable to choose the Ubiquitin mediated proteolysis pathway as the candidate pathway for further study on reproductive biology and regenerative medicine using mouse model. Interestingly, some of the known metabolic pathways e.g. biosynthesis of steroids pathway and fatty acid metabolism pathway were shown significant in both human and mouse blastocysts. All of these suggest that unlike in mouse, of which most of pathways found were related to energy, RNA and protein metabolism, the identified pathways in human were mostly disease-related and associated with human pre-implantation embryonic development. By contrast, there are some common metabolic pathways participate in regulating the mammal early embryonic development.

Furthermore, in view of the fact that many researchers working in mice interpret their results in relation to human reproduction, mice and human reproduction differ distinctly in many aspects; e.g. the reproduction in mice is characterized by a very short oestrus cycle and thus, displays a distinctly different endocrine dynamic pattern if compared with humans or domestic animals [35–38]. On the other hand, due to the difference in the inner environment of embryo and the external environment of uterus, there are species differences in the implantation process between mice and human [39–41]. The same applies for the regulatory mechanisms of early embryonic development that can be not simply transferable to the human species.

In sum, pre-implantation development involves a number of biologically significant events, such as compaction and blastocyst formation, which represent morphologically dynamic changes, especially for mouse and human [27]. Although the models of mouse have been well examined, molecular mechanisms regulating the early embryo development of human have been scarcely reported and the credibility of using the mouse model to explain the regulatory mechanism of human pre-implantation development remains unclear. Briefly, in this study, we have shown differences between mouse and human pre-implantation developments both in the global gene expression pattern and the expression changes of individual genes at each stage, including different major transient waves of transcription profiles and some stage-specific genes and pathways. Undeniably, Studies in mice have provided insights into the molecular basis of human pre-implantation development because of their shared features. In both species, early embryo development leads to a complex regulatory mechanism. However, the nature of human embryonic signals that influence uterine functions is more difficult than rodents', especially at the later stages of pre-implantation development (morula and blastocyst). Thus, it limits the availability of adequate amounts of tissues for mouse analysis. Moreover, the quality and quantity of samples chosen in microarray experiments also play essential roles in effecting the accuracy of mouse model, especially the conditions for in vitro maturation and fertilization are crucial for the proper early embryo development and may result in developmental aberrations.

Conclusions

By comparison between mouse and human expression profiles, we have noted that the regulatory mechanism of human pre-implantation development is different from the mouse, and even more complex. Through our analysis, we have found differences between mouse and human transcription profiles both in the global expression pattern of genes and in expression of individual genes within the gene clusters identified and in the significantly related pathways. Not as the fact that 1-cell to 2-cell stage is important for mouse pre-implantation development, the 4-cell stage and 8-cell stage are both essential for human. Unlike in mouse, of which most of pathways found were related to energy, RNA and protein metabolism, the identified pathways in human were mostly disease-related and associated with human pre-implantation embryonic development. Different expression patterns and significantly related biological processes during each stage between mouse and human suggest that a further comparative analysis should be required for applying the result of mouse expression data to human research or therapy, particularly in pre-implantation developments. Our study also provides several potential targets of genes and pathways for studying the regulatory mechanism of human pre-implantation development using mouse model, such as the gene of **st and the Ubiquitin mediated proteolysis pathway.