Assessment by differential display-RT-PCR of mRNA transcript transitions and alpha-amanitin sensitivity during bovine preattachment development

Genome distance and phylogenetic inference accommodating gene duplication, loss and new gene input

With the rapid growth of entire genome data, phylogenomics focuses on analyzing evolutionary histories and relationships of species, i.e., the tree of life. For decades it has been realized that the genome-wide phylogenetic inference can be approached based upon the dynamic pattern of gene content (the presence/absence of gene families), or extended gene content (absence, presence as a single-copy, or duplicates). Those methods, conceptually or technically, invoked the birth-and-death process to model the evolutionary process (gene duplication or gene loss. One common drawback is that the mechanism of new gene input, including de novo origin of new genes and the lateral gene transfer, has not been explicitly considered. In this paper, the author developed a new genome distance approach for genome phylogeny inference under the origin-birth-death stochastic process. The model takes gene duplication, gene loss and new gene input into account simultaneously. Computer simulations found that the two-genome approach is statistically difficult to distinguish between two proliferation parameters, i.e., the rate of gene duplication and the rate of new gene input. Nevertheless, it has also demonstrated the statistical feasibility for using the loss-genome distance to infer the genome phylogeny, which can avoid the large sampling problem. The strategy to study the universal tree of life was discussed and exemplified by an example.

Pre-implantation Development of Domestic Animals

During the first days following fertilization, cells of mammalian embryo gradually lose totipotency, acquiring distinct identity. The first three lineages specified in the mammalian embryo are pluripotent epiblast, which later gives rise to the embryo proper, and two extraembryonic lineages, hypoblast (also known as primitive endoderm) and trophectoderm, which form tissues supporting development of the fetus in utero. Most of our knowledge regarding the mechanisms of early lineage specification in mammals comes from studies in the mouse. However, the growing body of evidence points to both similarities and species-specific differences. Understanding molecular and cellular mechanisms of early embryonic development in nonrodent mammals expands our understanding of basic mechanisms of differentiation and is essential for the development of effective protocols for assisted reproduction in agriculture, veterinary medicine, and for biomedical research. This review summarizes the current state of knowledge on key events in epiblast, hypoblast, and trophoblast differentiation in domestic mammals.

Changes in sub-cellular localisation of trophoblast and inner cell mass specific transcription factors during bovine preimplantation development

Background

Preimplantation bovine development is emerging as an attractive experimental model, yet little is known about the mechanisms underlying trophoblast (TE)/inner cell mass (ICM) segregation in cattle. To gain an insight into these processes we have studied protein and mRNA distribution during the crucial stages of bovine development. Protein distribution of lineage specific markers OCT4, NANOG, CDX2 were analysed in 5-cell, 8–16 cell, morula and blastocyst stage embryos. ICM/TE mRNA levels were compared in hatched blastocysts and included: OCT4, NANOG, FN-1, KLF4, c-MYC, REX1, CDX2, KRT-18 and GATA6.

Results

At the mRNA level the observed distribution patterns agree with the mouse model. CDX2 and OCT4 proteins were first detected in 5-cell stage embryos. NANOG appeared at the morula stage and was located in the cytoplasm forming characteristic rings around the nuclei. Changes in sub-cellular localisation of OCT4, NANOG and CDX2 were noted from the 8–16 cell onwards. CDX2 initially co-localised with OCT4, but at the blastocyst stage a clear lineage segregation could be observed. Interestingly, we have observed in a small proportion of embryos (2%) that CDX2 immunolabelling overlapped with mitotic chromosomes.

Conclusions

Cell fate specification in cattle become evident earlier than presently anticipated – around the time of bovine embryonic genome activation. There is an intriguing possibility that for proper lineage determination certain transcription factors (such as CDX2) may need to occupy specific regions of chromatin prior to its activation in the interphase nucleus. Our observation suggests a possible role of CDX2 in the process of epigenetic regulation of embryonic cell fate.

Association of the transcription profile of bovine oocytes and embryos with developmental potential

Although improvements in culture system have enhanced in vitro embryo production, success rates are still not adequate. The reasons for developmental arrest of a part of in vitro produced embryos are unknown, but are connected in part with low cytoplasmic competence of oocytes. The immaturity of cytoplasm can negatively influence fertilization efficiency and subsequent progression through embryonic genome activation (EGA), which are necessary steps in further pre-implantation development. A large number of studies have compared mRNA abundance among oocytes with different developmental competence with the aim to find markers of the normal embryo development. The amount of mitochondrial DNA (mtDNA) and mRNA for mitochondrial transcriptional factors directing oxidative phosphorylation belongs to such promising markers. Nevertheless, recently published studies revealed that the mammalian embryo is able to compensate for a reduced level of mtDNA in oocyte during subsequent pre-implantation development. The search for other molecular markers is in progress. Characterization of oocyte and embryonic mRNA expression patterns during the pre-implantation period, and their relationship to the successful in vitro and in vivo development will be essential for defining the optimized culture conditions or the nuclear transfer protocols. Microarrays technology enables us to reveal the differentially expressed genes during EGA, and to compare the expression profile of in vivo and in vitro produced embryos. Recent evidence indicates that the depletion of the pool of stored maternal mRNAs is critical for subsequent embryo development. All these experiments gradually offer a list of possible candidates for quality and developmental competence markers for mammalian oocytes and pre-implantation embryos.

Gamete/embryo – oviduct interactions: implications onin vitroculture

Fertilization and development of mouse embryos occur in the oviduct. Accumulating data suggested that embryo-maternal communication exists in the preimplantation period, with the female reproductive tract providing the optimal microenvironment conducive to the development of embryos. Signals produced from the developing embryos not only affect their own transport in the oviduct, but the physiology and gene expression patterns of the oviduct. As a step towards understanding the action of embryos on oviductal physiology, both genomics and proteomics approaches are being used to unveil the underlying mechanism of embryo-maternal interaction at the preimplantation stage. Results from recent studies allow us to better understand the roles and the use of oviductal secretory proteins or factors that affect embryo development in vivo and in vitro. It has been shown that in vitro culture alters gene expression of the cultured embryos and may predispose the embryo to certain disease. Therefore, the interaction between gamete/embryo and oviduct in vitro and in vivo, and the long-term effects of embryo culture on foetal development warrant further investigation.

Gene expression during minor genome activation in preimplantation bovine development

The main goal of this study was to identify mRNA transcripts whose content increases during bovine minor embryonic genome activation. We compared the gene expression profile of the bovine 4-cell-stage embryo and MII oocyte using the technique of suppression subtractive hybridization. Differentially expressed amplicons were subcloned, and 60 of them were sequenced. The resulting DNA sequences were compared with GenBank databases using BLAST search. The expression of five differentially expressed genes with an apparent function in cell cycle progression, chromatin remodeling, and splicing or translation initiation was further characterized by a real-time RT-PCR. Centromere protein F, 350/400ka (CENPF), and splicing factor arginine/serine-rich 3 (SRFS3) show an increase in mRNA content during the 2- to 4-cell and late 8-cell stages. For the high mobility group nucleosomal binding domain 2 (HMGN2), the level of mRNA increases in 2- to 4-cell and morula embryos. The transcription of splicing factor SRFS3 is alpha-amanitin sensitive both during 4-cell and late 8-cell stages. The transcription of CENPF and HMGN2 is alpha-amanitin sensitive only at late 8-cell stage and morula, respectively. SRFS3 represents the first described gene with an important function in preimplantation development, which is also expressed during bovine minor genome activation, and it is alpha-amanitin sensitive during this period. All described genes can play an important role in the preimplantation development of bovine embryos.

Spatiotemporal expression of transcriptional regulators in concert with the maternal-to-embryonic transition during bovine in vitro embryogenesis

Cleavage-stage bovine embryos are transcriptionally quiescent until they reach the 8- to 16-cell stage, and thus rely on the reserves provided by the stored maternal mRNAs and proteins found in the oocytes to achieve their first cell divisions. The objective of this study was to characterize the expression and localization of the transcriptional and translational regulators, Y box binding protein 2 (YBX2), TATA box-binding protein (TBP), and activating transcription factor 2 (ATF2), during bovine early embryo development. Germinal vesicle (GV)- and metaphase II (MII)-stage oocytes, as well as 2-, 4-, 8-, 16-cell-stage embryos, morula, and blastocysts, producedin vitrowere analyzed for temporal and spatial protein expression. Using Q-PCR,ATF2mRNA expression was shown to remain constant from the GV-stage oocyte to the four-cell embryo, and then decreased through to the blastocyst stage. By contrast, the protein levels of ATF2 remained constant throughout embryo development and were found in both the cytoplasm and the nucleus. Both TBP and YBX2 showed opposite protein expression patterns, as YBX2 protein levels decreased throughout development, while TBP levels increased through to the blastocyst stage. Immunolocalization studies revealed that TBP protein was localized in the nucleus of 8- to 16-cell-stage embryos, whereas the translational regulator YBX2 was exclusively cytoplasmic and disappeared from the 16-cell stage onward. This study shows that YBX2, TBP, and ATF2 are differentially regulated through embryo development, and provides insight into the molecular events occurring during the activation of the bovine genome during embryo developmentin vitro.

Unveiling the bovine embryo transcriptome during the maternal-to-embryonic transition

Bovine early embryos are transcriptionally inactive and subsist through the initial developmental stages by the consumption of the maternal supplies provided by the oocyte until its own genome activation. In bovine, the activation of transcription occurs during the 8- to 16-cell stages and is associated with a phase called the maternal-to-embryonic transition (MET) where maternal mRNA are replaced by embryonic ones. Although the importance of the MET is well accepted, since its inhibition blocks embryonic development, very little is known about the transcripts expressed at this crucial step in embryogenesis. In this study, we generated and characterized a cDNA library enriched in embryonic transcripts expressed at the MET in bovine. Suppression subtractive hybridization followed by microarray hybridization was used to isolate more than 300 different transcripts overexpressed in untreated late eight-cell embryos compared with those treated with the transcriptional inhibitor, alpha-amanitin. Validation by quantitative RT-PCR of 15 genes from this library revealed that they had remarkable consistency with the microarray data. The transcripts isolated in this cDNA library have an interesting composition in terms of molecular functions; the majority is involved in gene transcription, RNA processing, or protein biosynthesis, and some are potentially involved in the maintenance of pluripotency observed in embryos. This collection of genes associated with the MET is a novel and potent tool that will be helpful in the understanding of particular events such as the reprogramming of somatic cells by nuclear transfer or for the improvement of embryonic culture conditions.

Differential expression of oxygen-regulated genes in bovine blastocysts

Low oxygen conditions (2%) during post-compaction culture of bovine blastocysts improve embryo quality, which is associated with a small yet significant increase in the expression of glucose transporter 1 (GLUT-1), suggesting a role of oxygen in embryo development mediated through oxygen-sensitive gene expression. However, bovine embryos to at least the blastocyst stage lack a key regulator of oxygen-sensitive gene expression, hypoxia-inducible factor 1alpha (HIF1alpha). A second, less well-characterized protein (HIF2alpha) is, however, detectable from the 8-cell stage of development. Here we use differential display to determine additional gene targets in bovine embryos in response to low oxygen conditions. While development to the blastocyst stage was unaffected by the oxygen concentration used during post-compaction culture, differential display identified oxygen-regulation of myotrophin and anaphase promoting complex 1 expression, with significantly lower levels observed following culture under 20% oxygen than 2% oxygen. These results further support the hypothesis that the level of gene expression of specific transcripts by bovine embryos alters in response to changes in the oxygen environment post-compaction. Specifically, we have identified two oxygen-sensitive genes that are potentially regulated by HIF2 in the bovine blastocyst.

Mitogen-activated protein kinase (MAPK) blockade of bovine preimplantation embryogenesis requires inhibition of both p38 and extracellular signal-regulated kinase (ERK) pathways

Blastocyst formation, as a critical period during development, is an effective indicator of embryonic health and reproductive efficiency. Out of a number of mechanisms underlying blastocyst formation, highly conserved mitogen-activated protein kinase (MAPK) signaling has emerged as a major mechanism involved in regulating murine preimplantation embryo development. The objective of our study was to ascertain the role of MAPK signaling in regulating bovine development to the blastocyst stage. Using reverse transcriptase PCR and immunohistochemical staining procedures we have demonstrated that mRNA transcripts and polypeptides encoding p38 MAPK pathway constituents are detectable in preimplantation bovine embryos from the one-cell to the blastocyst stage. Further, the effects on bovine embryo development following inhibition of p38 α/β and extracellular signal-regulated kinase (ERK) signaling by treatment with SB220025 and U0126, respectively, were investigated. Eight-cell bovine embryos (50 per group; three replicates) were placed into treatments consisting of synthetic oviductal fluid (SOF) medium: SOF + SB202474 (inactive analogue), SOF + SB220025, SOF + U0124 (inactive analogue), SOF + U0126, and SOF + SB220025 + U0126. Inhibition of p38 MAPK or ERK signaling individually did not affect development to the blastocyst stage. However, when both pathways were blocked simultaneously there was a significant reduction (P< 0.05) in blastocyst formation, cell number and immunofluorescence of phosphorylated downstream pathway constituents. We have determined that, in variance to what was observed during murine preimplantation development, bovine early embryos progress at normal frequencies to the blastocyst stage in the presence of p38 MAPK inhibitors.

Generation of a bovine oocyte cDNA library and microarray: resources for identification of genes important for follicular development and early embryogenesis

The oocyte is a key regulator of ovarian folliculogenesis and early embryonic development. However, the composition of the oocyte transcriptome and identities and functions of key oocyte-specific genes involved in the above processes are relatively unknown. Using a PCR-based cDNA amplification method (SMART technology), we constructed a bovine oocyte cDNA library. Analysis of 230 expressed sequence tags (ESTs) from this library identified 102 unique sequences. Although some correspond to housekeeping genes (e.g., ribosomal protein L15) and some represent genes previously known to be expressed in oocytes and other tissues, most encode for genes whose expression in mammalian oocytes has not been reported previously (e.g., cocaine- and amphetamine-regulated transcript) or genes of unknown function. Sixteen did not show significant sequence similarity to any entries in the GenBank database and were classified as novel. Using over 2,000 unsequenced, randomly selected cDNA clones from the library, we constructed an oocyte microarray and performed experiments to identify genes preferentially expressed in fetal ovary (an enriched source of oocytes) relative to somatic tissues. Eleven clones were identified by microarray analysis with consistently higher expression in fetal ovaries (collected from animals at days 210-260 of gestation) compared with spleen and liver. DNA sequence analysis of these clones revealed that two correspond to JY-1, a novel bovine oocyte-specific gene. The remaining nine clones represent five identified genes and one additional completely novel gene. Increased abundance of mRNA in fetal ovary for five of the six genes identified was confirmed by real-time PCR. Results demonstrate the potential utility of these unique resources for identification of oocyte-expressed genes potentially important for reproductive function.

Phospholipid transfer protein (PLTP) mRNA expression is stimulated by developing embryos in the oviduct

In mammal, fertilization and early preimplantation embryo development occurs in the oviduct. Evidence is accumulating that the oviductal epithelia secrete various biomolecules to the lumen during the secretory phase of the estrus cycle to enhance embryo development. This secretory activity of the oviduct is under the regulation of steroid hormones. Observations also suggested that the gametes and embryos modulate the physiology and gene-expressing pattern of the oviduct. However, the underlying molecular changes remain elusive. We hypothesize that the developing embryos interact with the surrounding environment and affect the gene expression patterns of the oviduct, thereby modulating the oviductal secretory activity conducive to the preimplantation embryo development. To test this hypothesis, suppression subtractive hybridization (SSH) was used to compare the gene expressions in mouse oviduct containing transferred in vitro cultured preimplantation embryos with that of oviduct containing oocytes during the preimplantation period. We reported here the identification and characterization of phospholipids transfer protein (PLTP), which is highly expressed in the embryo-containing oviduct and localized at the oviductal epithelium by in situ hybridization. PLTP contains signal peptide putative for secretory function. More importantly, PLTP mRNA increases in the oviductal epithelia of pregnant, but not pseudo-pregnant mice when assayed by real-time PCR. Taken together, our data suggested that PLTP may play important role(s) during in vivo preimplantation embryo development. This molecule would be a target to delineate the mechanisms and the roles of oviductal secretory proteins on early embryonic development.

p38 MAPK signaling during murine preimplantation development

Mitogen-activated protein kinase (MAPK) pathways mediate some important cellular processes and are likely to also regulate preimplantation development. The role of p38 MAP kinase signaling during murine preimplantation development was investigated in the present study. p38 MAPK, p38-regulated or -activated kinase (PRAK; MK5), map kinase-activated protein kinase 2 (MK2), and heat shock protein 25 (hsp25) mRNAs and proteins were detected throughout preimplantation development. Two-cell stage embryos cultured in the presence of SB220025 and SB203580 (specific inhibitors of p38 MAPK alpha/beta), progressed to the eight-cell stage with the same frequency as controls; however, treated embryos halted their development at the 8- to 16-cell stage. In addition, embryos treated with p38 MAPK inhibitors displayed a complete loss of MK2 and hsp25 phosphorylation and also a complete loss of filamentous actin as indicated by the absence of rhodamine-phalloidin staining. In these inhibitor-treated groups, the embryos were composed of a mixture of compacting and noncompacting cells, and the embryos were one to two cell divisions behind controls. Treated embryos remained viable as the developmental blockade was rescued by removing embryos from the drug treatment and placing them in drug-free medium until they progressed to the blastocyst stage. This study demonstrates that p38 MAPK activity is required to support development through the murine preimplantation interval.

Global gene expression analysis comparing bovine blastocysts flushed on day 7 or produced in vitro

In vitro produced (IVP) bovine embryos have darker cytoplasm, reduced buoyant density, fragile zonae pellucidae, chromosomal abnormalities, higher pregnancy failure rates, and altered gene expression compared to embryos produced in vivo. Characterization of early deviations in gene expression would enable us to better understand the biology of early embryo development and improve in vitro culture systems. Here we compared gene expression between Day 7 blastocysts generated in TCM199 with 5% FBS and Day 7 in vivo derived blastocysts and using suppression-subtractive hybridization (SSH). Pools of 25 embryos for both driver and tester were used in the RNA extraction process. The subtracted products were cloned and subjected to differential hybridization screening analysis. cDNAs were isolated, single-pass sequenced, and subjected to BLAST search. Of 32 in vivo ESTs (expressed sequence tags) that provided sequence information, 30 matched homologous sequences in GenBank. Of 32 in vitro ESTs, 22 provided specific matches while the remaining ten represented novel transcripts. Two in vivo ESTs, galectin-1 and fibronectin, and one in vitro EST, filamin A, were further characterized using real-time quantitative PCR. To further examine the reproducibility of the SSH data, three different pools of embryos with each pool containing ten embryos produced from each of the following production systems, namely, in vivo, IVP in TCM199 with 5% FBS and CR1aa with 5% FBS were used for real-time reverse transcription-polymerase chain reaction (RT-PCR) confirmation studies. Significant increases in the expression level of galectin-1 and fibronectin were observed in the in vivo derived blastocysts compared to blastocysts produced in TCM199 with 5% FBS and CR1aa cultures. No significant difference in filamin A expression was found between blastocysts produced in vivo and those derived from either of the in vitro production systems. We conclude that these techniques are useful to characterize the transcriptome of the early preattachment embryo and observed deviations in mRNA expression may partially explain the differences in quality between in vivo and IVP embryos.

Quantitative expression analysis of blastocyst-derived gene transcripts in preimplantation developmental stages of in vitro-produced bovine embryos using real-time polymerase chain reaction technology

The main objective of the present study was to analyse the quantitative expression pattern of genes from a subtracted blastocyst transcriptome throughout the preimplantation developmental stages of in vitro-produced bovine oocytes and embryos. For this purpose, Day 5 morula (M) cDNAs were subtracted from Day 7 blastocyst (B) cDNAs (B–M) and used to establish a B–M subtracted cDNA library, as reported previously. From the total generated clones, 19 were analysed quantitatively. The mRNA samples isolated from pools of immature oocytes (n = 150), mature oocytes (n = 150) and two-cell (n = 80), four-cell (n = 40), eight-cell (n = 20), morula (n = 6) and blastocyst (n = 3) embryos were reverse transcribed and subjected to real-time polymerase chain reaction (PCR) using sequence-specific primers and SYBR green as the DNA dye. A relative standard curve method was used to analyse the real-time data taking the morula stage as a calibrator. Applying suppression subtractive hybridisation (SSH), a total of 71 clones, which represent 33 different expressed sequence tags, were generated and available for analysis. Most transcripts were analysed for the first time in bovine embryogenesis. The real-time PCR has validated the results of SSH positively for 84% (16/19) of transcripts, whereas 16% (3/19) showed deviation in the expression pattern from the one seen during SSH. Several transcript-specific expression patterns were observed for genes that play decisive roles in bovine embryogenesis. In addition to identification, accurately quantifying the expression profiles of transcripts during development will pave the way towards understanding the molecular mechanisms of embryogenesis and their potential role in early embryo development. Most importantly, the present study has contributed to the enrichment of bovine embryo gene collection by generating new transcripts involved in bovine embryo development.

Identification and quantification of differentially expressed transcripts in in vitro-produced bovine preimplantation stage embryos

In this study, we used mRNA differential display reverse transcription polymerase chain reaction (DDRT-PCR) to analyze the mRNA expression patterns in in vitro-produced bovine 8-cell, 16-cell, morula, and blastocyst stage embryos and isolate differentially expressed amplicons. Moreover, we have used a fluorescence monitored real time quantitative PCR to quantify and analyze the expression patterns of the target differentially expressed transcripts through out the preimplantation stages from oocytes to blastocyst. For this, total RNA isolated from bovine 8-cell (n = 188), 16-cell (n = 94), morula (n = 35), and blastocyst (n = 15) were reverse transcribed and subjected to DDRT-PCR. Target differentially expressed transcripts were quantified by real time quantitative PCR. The cDNA banding pattern analysis revealed that large number of cDNA bands were conserved at 8-cell and blastocyst stage with a slight decrease at the morula stage. A total of 16 amplicons were cloned and sequenced. All expressed sequence tags (ESTs), except 1C19, showed sequence similarity with known genes or ESTs in GenBank. Sixty-two percent (10/16) of cDNA bands representing differentially expressed genes originated from 8-cell stage and the rest derived from the 16-cell, morula, or blastocyst stage. The quantitative PCR analysis has validated the expression patterns of 75% (12/16) of our transcripts to be in agreement with the results of DDRT-PCR. However, the quantitative PCR results of four transcripts showed a deviation from the pattern seen in DDRT-PCR. In conclusion, we have successfully applied mRNA DDRT-PCR to identify and isolate stage-specific expressed genes in bovine preimplantation embryos. In addition to validating the results of DDRT-PCR, quantitative real time PCR provides quantitative data on the expression of target genes.

Increased messenger RNA for allograft inflammatory factor-1, LERK-5, and a novel gene in 17.5-day relative to 15.5-day bovine embryos

Considerable embryonic loss occurs between Gestation Days 15 and 18 in cattle when critical cellular and molecular events occur, including maternal recognition of pregnancy. To gain insight into these events, mRNA differential display analysis was used to identify eight unique cDNA fragments present in greater abundance in 17.5-day than in 15.5-day bovine embryos. Four cDNA fragments, confirmed to be upregulated in 17.5-day embryos using Northern analysis, were cloned and sequenced. Three cDNA fragments shared sequence identities with known homologs: human allograft inflammatory factor-1 (AIF-1), human LERK-5, and bovine interferon-tau. One novel cDNA fragment did not share sequence identity to previously reported genes, except for a similar DNA sequence in the human genome. AIF-1 mRNA was present in developing placenta through Gestation Day 36, and abundant levels were observed in adult bovine spleen and lung. The novel gene, which we have named periattachment factor (PAF), was not detected in adult tissues using Northern analysis or in conceptuses between Days 30 and 36 of pregnancy. Additional sequence information for bPAF was obtained from a cDNA library constructed from a 25-day bovine embryo. The protein corresponding to the open reading frame has four protein kinase C phosphorylation sites, two casein kinase II phosphorylation sites, a nuclear targeting sequence, but no obvious DNA or RNA binding motifs. Abundant expression of this gene during a narrow but critical window of embryonic development makes it worthy of further study.

Gene expression and chromatin structure in the pre-implantation embryo

The pre-implantation period of mammalian development includes the formation of the zygote, the activation of the embryonic genome (EGA), and the beginning of cellular differentiation. During this period, protamines are replaced by histones, the methylated haploid parental genomes undergo demethylation following formation of the diploid zygote, and maternal control of development is succeeded by zygotic control. Superimposed on this activation of the embryonic genome is the formation of a chromatin-mediated transcriptionally repressive state requiring enhancers for efficient gene expression. The development of this transcriptionally repressive state most likely occurs at the level of chromatin structure, because inducing histone hyperacetylation relieves the requirements for enhancers. Characterization of zygotic mRNA expression patterns during the pre-implantation period and their relationship to successful development in vitro and in vivo will be essential for defining optimized culture conditions and nuclear transfer protocols. The focus of this review is to summarize recent advances in this field and to discuss their implications for developmental biology.

Molecular characterization of genomic activities at the onset of zygotic transcription in mammals

In rabbit embryos, zygotic transcripts are required for the development of the embryo only from the 8- to 16-cell stage onward, more than 44 h after fertilization (i.e., zygotic gene activation; ZGA). In order to characterize the first zygotic transcripts expressed in this species we used a suppression subtractive hybridization approach to isolate RNA that was present after the major transcriptional activation (morula stage), but absent at the 1-cell stage as maternal transcripts. One hundred fourteen differentially expressed inserts were selected and sequenced. A statistical analysis of expression patterns throughout the preimplantation period of development shows that genes transcribed from ZGA onward follow different patterns of expression. Considering their early post-ZGA behavior, we describe at least two main patterns: a gradual increase from ZGA onward, and a sharp increase in expression at ZGA followed by a marked decrease at the morula stage. Our data show that both ZGA and some early post-ZGA events are involved in the establishment of specific patterns of embryonic gene expression.

Rac-1 and IQGAP are potential regulators of E-cadherin–catenin interactions during murine preimplantation development

Adherens junction formation is fundamental for compaction and trophectoderm differentiation during mammalian preimplantation development. We recently isolated an IQGAP-2 cDNA from a differential display-polymerase chain reaction screen of bovine preimplantation developmental stages. IQGAP-1 and -2 proteins mediate E-cadherin-based cell-to-cell adhesion through interactions with beta-catenin and the Rho GTPases, rac1 and cdc42. Our study demonstrates IQGAP-1,-2, rac-1 and cdc42 mRNAs are present throughout murine preimplantation development. IQGAP-1 and rac-1 protein distribution changes from predominantly plasma membrane associated to predominantly cytoplasmic as the embryo progresses through cleavage divisions and compaction to the blastocyst stage.

Analysis of gene expression in the bovine blastocyst produced in vitro using suppression-subtractive hybridization

Successful embryonic development is dependent on time and location-specific expression of appropriate genes. Unfortunately, information on stage-specific gene expression during early embryonic development in the bovine is lacking. In the present study, we compared gene expression between in vitro-produced Day 7-8 intact blastocysts (driver) and Day 9-10 hatched blastocysts (tester) using suppression-subtractive hybridization. Pools of 30 embryos for both driver and tester were used in the RNA extraction process. From limited amounts of starting material ( approximately 400 ng of total RNA), a reverse transcription-polymerase chain reaction (PCR) procedure was used to amplify the mRNA and generate sufficient cDNA to conduct suppression-subtractive hybridization. The subtracted cDNA products were cloned, and 126 cDNAs representing expressed mRNAs were isolated, sized, single-pass sequenced, and compared to known sequences in GenBank. Ninety-two clones provided sequence information for further analysis. Among these, 31 exhibited high homology to known genes. Three, 26S proteasomal ATPase (PSMC3), casein kinase 2 alpha subunit (CK2), and phosphoglycerate kinase (PGK) were selected and further characterized using real-time quantitative PCR to assess their differential expression in hatched blastocysts. Overall, a 1.3-, 1.6-, and 1.5-fold increase in expression level was observed in hatched blastocysts compared with intact blastocyst for PSMC3, CK2, and PGK, respectively. These results show that construction of subtracted cDNA libraries from small numbers of embryos is feasible and can provide information on gene expression patterns during preattachment embryogenesis.

Developmental, qualitative, and ultrastructural differences between ovine and bovine embryos produced in vivo or in vitro

The objective of this study was to compare bovine and ovine oocytes in terms of (1) developmental rates following maturation, fertilization, and culture in vitro, (2) the quality of blastocysts produced in vitro, assessed in terms of their ability to undergo cryopreservation, and (3) the ultrastructural morphology of these blastocysts. In vitro blastocysts were produced following oocyte maturation/fertilization and culture of presumptive zygotes in synthetic oviduct fluid. In vivo blastocysts were used as a control from both species. In Experiment 1, the cleavage rate of bovine oocytes was significantly higher than that of ovine oocytes (78.3% vs. 58.0%, respectively, P < 0.001). The overall blastocyst yield was similar for both species (28.7% vs. 29.0%). However, when corrected for cleavage rate, significantly more ovine oocytes reached the blastocyst stage at all time-points (36.6% vs. 50.0% on day 8, for bovine and ovine, respectively, P < 0.001). Following vitrification, there was no difference in survival between in vivo produced bovine and ovine blastocysts (72 hr: 85.7% vs. 75.0%). However, IVP ovine blastocysts survived at significantly higher rates than IVP bovine blastocysts at all time points (72 hr: 47.4% vs. 18.1%, P < 0.001). At the ultrastructural level, compared with their in vivo counterparts, IVP blastocysts were characterized by a lack of desmosomal junctions, a reduction in the microvilli population, an increase in the average number of lipid droplets and increased debris in the perivitelline space and intercellular cavities. These differences were more marked in bovine IVP blastocysts, which also displayed electron-lucent mitochondria and large intercellular cavities. These observations may in part explain the species differences observed in terms of cryotolerance. In conclusion, the quality of ovine blastocysts was significantly higher than their bovine counterparts produced under identical in vitro conditions suggesting inherent species differences between these two groups affecting embryo quality.

Analysis of differential messenger RNA expression between bovine blastocysts produced in different culture systems: implications for blastocyst quality

Using reverse transcriptase-amplified fragment length polymorphism (RT-AFLP) analysis of differential mRNA expression and semiquantitative reverse transcriptase-polymerase chain reaction, we compared mRNA expression in bovine blastocysts from 4 sources, known to differ in quality in terms of their ability to withstand cryopreservation: 1) in vitro culture in synthetic oviduct fluid of in vitro-matured (IVM)/in vitro fertilized (IVF) zygotes; 2) in vitro culture in TCM-199 supplemented with granulosa cells (coculture) of IVM/IVF zygotes; 3) in vivo culture in the ewe oviduct of IVM/IVF zygotes; or 4) superovulation, artificial insemination, and nonsurgical embryo recovery. Total mRNA was isolated from pools of blastocysts and reverse transcription was performed. Triplicate reactions from each sample were displayed, and only consistent banding variations were recorded. Using AFLP-differential display assay, we found that cDNA banding patterns are highly conserved between the 4 groups of blastocysts studied; however, there was a difference of 7% in bands either missing or expressed across the groups. Fifty bands were reamplified, and a sequence comparison search revealed similarity of 14 isolated fragments to ribosomal and mitochondrial genes, 16 matched to described cDNA, and 20 corresponded to unknown sequences that may represent novel genes. The study of 7 differentially expressed mRNAs known to be involved in developmental process in the embryo suggests roles for apoptosis, oxidative stress, gap junctions, and differentiation in the determination of embryo quality. The aberrant transcription patterns detected in in vitro-produced bovine embryos compared with those produced in vivo may explain their reduced quality in terms of viability after cryopreservation.

Expression of 3 beta-hydroxysteroid dehydrogenase in early bovine embryo development

We analyzed the presence of 3 beta-Hydroxysteroid Dehydrogenase/Delta(5-->4)-isomerase enzyme (3 beta-HSD) activity, a key enzyme of the steroid metabolic pathway, the mRNA of this enzyme, and the steroid metabolism in in vitro produced bovine embryos. 3 beta-HSD activity was detected in in vitro matured oocytes (74.4 +/- 1.4%), 1-cell (72.9 +/- 6.1%), 2-cell (61.8 +/- 7.4%), 8-cell (50 +/- 5%), morulae (50.8 +/- 2.6%), blastocysts (94.4 +/- 3%), and hatched blastocysts (100 +/- 0%) meanwhile the 4-cell stage showed a significant reduction (16.7 +/- 4.7%). When total embryonic RNA of different stages was subjected to RT-PCR assays, the mRNA of 3 beta-HSD was found to be present in all developmental stages of in vitro produced bovine embryos, from the oocyte to the blastocyst, with a marked decrease at the 4-cell stage. To determine whether the temporal pattern of enzyme activity was dependent on the maternal to zygotic transition, embryos were incubated in the presence of a transcription inhibitor, alpha-amanitin. The reappearance of the enzyme activity after the 4-cell stage was blocked in alpha-amanitin treated embryos, indicating the requirement of embryonic transcription. On the other hand, the embryonic steroid metabolism was tested by incubating blastocyst with tritiated pregnenolone. Analysis of the metabolites by TLC indicated the production of a compound with a mobility identical to progesterone. These results described the expression of the 3 beta-HSD and the activity of this metabolic enzyme in bovine oocytes and preimplantation embryos, suggesting that steroids may act as autocrine effectors on preimplantation embryo development.

Consequences of bovine oocyte maturation, fertilization or early embryo development in vitro versus in vivo: implications for blastocyst yield and blastocyst quality

The aim of this study is to examine the effect of bovine oocyte maturation, fertilization or culture in vivo or in vitro on the proportion of oocytes reaching the blastocyst stage, and on blastocyst quality as measured by survival following vitrification. In Experiment 1, 4 groups of oocytes were used: (1) immature oocytes from 2-6 mm follicles; (2) immature oocytes from > 6 mm follicles; (3) immature oocytes recovered in vivo just before the LH surge; and (4) in vivo matured oocytes. Significantly more blastocysts developed from oocytes matured in vivo than those recovered just before the LH surge or than oocytes from 2-6 mm follicles. Results from > 6 mm follicles were intermediate. All blastocysts had low survival following vitrification. In Experiment 2, in vivo matured oocytes were either (1) fertilized in vitro or (2) fertilized in vivo by artificial insemination and the resulting presumptive zygotes recovered on day 1. Both groups were then cultured in vitro. In vivo fertilized oocytes had a significantly higher blastocyst yield than those fertilized in vitro. Blastocyst quality was similar between the groups. Both groups had low survival following vitrification. In Experiment 3a, presumptive zygotes produced by in vitro maturation (IVM)/fertilization (IVF) were cultured either in vitro in synthetic oviduct fluid, or in vivo in the ewe oviduct. In Experiment 3b, in vivo matured/in vivo fertilized zygotes were either surgically recovered on day 1 and cultured in vitro in synthetic oviduct fluid, or were nonsurgically recovered on day 7. There was no difference in blastocyst yields between groups of zygotes originating from the same source (in vivo or in vitro fertilization) irrespective of whether culture took place in vivo or in vitro. However, there was a dramatic effect on blastocyst quality with those blastocysts produced following in vivo culture surviving vitrification at significantly higher rates than their in vitro cultured counterparts. Collectively, these results indicate that the intrinsic quality of the oocyte is the main factor affecting blastocyst yields, while the conditions of embryo culture have a crucial role in determining blastocyst quality.

Transcriptional activity in in vivo developed early cleavage stage bovine embryos

Bovine embryos developed in vivo from the first to the fourth post-fertilization cell cycles were processed for ultrastructural autoradiography after incubation with 3H-uridine for 10 h. We wished to detect and localize transcriptional activity. During the first (1-cell stage) and second (2-cell stage) cell cycles we observed electron-dense fibrillar spheres (nucleolus precursor bodies) and fibrillo-granular complexes in the nuclei. During these cell cycles, autoradiographic labeling was observed in heterochromatic areas and at the periphery of the fibrillo-granular complexes. During the third cell cycle (4-cell stage) the electron dense fibrillar spheres exhibited vacuolization. Autoradiographic labeling was found in heterochromatic areas and in the vacuoles of the fibrillar spheres. During the fourth cell cycle (8-cell stage), the electron dense fibrillar spheres exhibited both a large eccentric vacuole and peripheral smaller vacuoles. Autoradiographic labeling was found in heterochromatic areas throughout the nucleus and over the substance of the vacuolated fibrillar spheres, especially where chromatin penetrated into them and where presumptive fibrillar centers were formed. In conclusion, a low level of transcription can be detected in in vivo developed bovine embryos as early as the one-cell stage. Moreover, nuclear entities that probably prepare for nucleolus formation during the fourth cell cycle, display a progressive autoradiographic labeling that signals a possible initiation of transcription of the ribosomal RNA genes during the third cell cycle.

Comparison by restriction fragment differential display RT-PCR of gene expression pattern in bovine oocytes matured in the presence or absence of fetal calf serum

A novel restriction fragment differential display (RFDD) RT-PCR has been used to compare patterns of mRNA expression in bovine oocytes matured in vitro in the presence (10%) or absence of fetal calf serum (FCS). Total RNA extracted from matured and denuded oocytes was processed using display Profile kit (Display System Biotech). RFDD RT-PCR products were separated on 6% polyacrylamide gel and analyzed using a Storm 860 scanner. Selected bands representing potentially differentially expressed fragments were excised from the gel and re-amplified. Re-amplified fragments with size matched to the original fragment were cloned into the TA vector and sequenced. Initially, 10 and 15 differentially expressed fragments were isolated from oocytes matured in the presence and absence of FCS, respectively. Eight out of 10 and 10 out of 15 fragments were re-amplified successfully as evidenced by size similarity to the original fragments. Finally, the size of six inserts sequenced from each group matched the size of corresponding original as well as re-amplified fragments. Sequence comparison search revealed similarity of some isolated fragments to 18s ribosomal RNA, bovine apolipoprotein A-I, bovine mitochondrion DNA, human CGI-79 mRNA, human Ab1-interactor protein, and bovine satellite DNA. The other sequenced fragments may represent novel genes. We showed that RFDD RT-PCR can be effectively applied to contrast gene expression pattern in bovine oocytes and that presence or absence of FCS during maturation interval affects gene expression pattern in matured bovine oocytes.

Onset of zygotic transcription and maternal transcript legacy in the rabbit embryo

Onset of zygotic transcription is progressive from the one-cell stage onward in the rabbit embryo. Maternal transcripts remain fairly stable until the 8-16 cell stage when major transcriptional activation of the zygotic genome takes place. To understand the mechanisms of the maternal-to-zygotic transition in the genetic information governing development, we asked whether a progressive synthesis of zygotic transcripts takes over the maternal molecules, or whether the synthesis of zygotic transcripts is very abrupt and independent of the persistence of the maternal counterparts. To answer this question, we set up mRNA differential display experiments comparing the mRNA content of rabbit embryos at different stages during the preimplantation period. We isolated eight zygotic transcripts whose synthesis is abruptly turned on at the 8-16 cell stage. These transcripts are involved in general cellular metabolism and their maternal counterparts are still present up to the four-cell and even the 8-16 cell stage. This identification of early zygotic transcripts suggests that global long range modifications of chromatin structure result in a rapid increase in transcription rates during the major transcriptional activation of the zygotic genome.

mRNAs encoding aquaporins are present during murine preimplantation development

The present study was conducted to investigate the mechanisms underlying fluid movement across the trophectoderm during blastocyst formation by determining whether aquaporins (AQPs) are expressed during early mammalian development. AQPs belong to a family of major intrinsic membrane proteins and function as molecular water channels that allow water to flow rapidly across plasma membranes in the direction of osmotic gradients. Ten different AQPs have been identified to date. Murine preimplantation stage embryos were flushed from the oviducts and uteri of superovulated CD1 mice. Reverse transcription-polymerase chain reaction (RT-PCR) methods employing primer sets designed to amplify conserved sequences of AQPs (1-9) were applied to murine embryo cDNA samples. PCR reactions were conducted for up to 40 cycles involving denaturation of DNA hybrids at 95 degrees C, primer annealing at 52-60 degrees C and extension at 72 degrees C. PCR products were separated on 2% agarose gels and were stained with ethidium bromide. AQP PCR product identity was confirmed by sequence analysis. mRNAs encoding AQPs 1, 3, 5, 6, 7, and 9 were detected in murine embryos from the one-cell stage up to the blastocyst stage. AQP 8 mRNAs were not detected in early cleavage stages but were present in morula and blastocyst stage embryos. The results were confirmed in experimental replicates applied to separate embryo pools of each embryo stage. These results demonstrate that transcripts encoding seven AQP gene products are detectable during murine preimplantation development. These findings predict that AQPs may function as conduits for trophectoderm fluid transport during blastocyst formation.