Genes Preferentially Expressed in Bovine Oocytes Revealed by Subtractive and Suppressive Hybridization1

Bioinformatic analysis of the clinicopathological and prognostic significance of oocyte-arresting BTG4 mRNA expression in gynecological cancers

BTG4 arrests the cell cycle and suppresses oocyte and embryonic development. We performed a bioinformatic analysis of BTG4 expression. BTG4 expression was downregulated in breast cancer compared with normal tissues (p < .05), but the opposite was observed in cervical, endometrial and ovarian cancers (p < .05). BTG4 methylation was negatively correlated with its mRNA expression in breast, cervical and endometrial cancers (p < .05). BTG4 mRNA expression was negatively correlated with T staging and distant metastasis of breast cancer; and with tumor invasion, clinical stage, low weight and BMI, low histological grade and no diabetes in endometrial cancer but positively with T stage and non-keratinizing squamous carcinoma in endometrial cancer. BTG4 expression was negatively correlated with the survival of ovarian cancer patients (p < .05), but positively for breast, cervical and endometrial cancers (p < .05). BTG4 expression is thus a potential marker reflecting the carcinogenesis, aggressiveness and prognosis in gynecological cancers.Impact StatementWhat is already known on this subject? Previous studies have revealed the structure and location of BTG4. BTG4 inhibit cell proliferative, promote apoptosis, induce G1 cell cycle arrest. BTG4 promotes the development of mouse embryos from cell stage 1 to 2. The methylation and biological function of BTG4 were clarified in gastric and/or colorectal cancer cells.What do the results of this study add? BTG4 is found to closely link to reflect the carcinogenesis, histogenesis, aggressive behaviors and prognosis of gynecological cancers, and involved in ligand-receptor interaction, microtubule motor activity, dynein light chain binding, cilium organization, assembly, and movement in endometrial and ovarian cancers.What are the implications of these finding for clinical practice and/or further research? Aberrant BTG4 mRNA expression can be employed as a marker of the tumorigenesis, histogenesis, aggressiveness and prognosis of gynecological cancers in the future practice and guide the investigation of BTG4-related signal pathways.

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

BACKGROUND

Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group.

RESULTS

After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations.

CONCLUSIONS

Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

A Comparative Analysis of Oocyte Development in Mammals

Sexual reproduction requires the fertilization of a female gamete after it has undergone optimal development. Various aspects of oocyte development and many molecular actors in this process are shared among mammals, but phylogeny and experimental data reveal species specificities. In this chapter, we will present these common and distinctive features with a focus on three points: the shaping of the oocyte transcriptome from evolutionarily conserved and rapidly evolving genes, the control of folliculogenesis and ovulation rate by oocyte-secreted Growth and Differentiation Factor 9 and Bone Morphogenetic Protein 15, and the importance of lipid metabolism.

From clinics to (cow)mics: a reproductive journey

This manuscript describes the different topics I have been involved in the fields of reproductive physiology and embryo biotechnologies with attempts to address practical issues raised mainly by the breeding industry. The journey started with phenotyping work in the field of reproductive physio-pathology. Other issues were related to the optimization of reproductive biotechnologies to favorize genetic selection. The implementation of genomic selection raised opportunities to develop the use embryo biotechnologies and showed the interest of combining them in the case of embryo genotyping. There is still a need to refine phenotyping for reproductive traits especially for the identification of markers of uterine dysfunction. It is believed that new knowledge generated by combining different molecular approaches will be the source of applications that may benefit AI practice and embryo technologies.

Characterization of SCF-Complex during Bovine Preimplantation Development

The degradation of maternal proteins is one of the most important events during early development, and it is presumed to be essential for embryonic genome activation (EGA), but the precise mechanism is still not known. It is thought that a large proportion of the degradation of maternal proteins is mediated by the ubiquitin-proteolytic system. In this study we focused on the expression of the Skp1-Cullin1-F-box (SCF) complex, a modular RING-type E3 ubiquitin-ligase, during bovine preimplantation development. The complex consists of three invariable components—Cul1, Skp1, Rbx1 and F-box protein, which determines the substrate specificity. The protein level and mRNA expression of all three invariable members were determined. Cul1 and Skp1 mRNA synthesis was activated at early embryonic stages, at the 4c and early 8c stage, respectively, which suggests that these transcripts are necessary for preparing the embryo for EGA. CUL1 protein level increased from MII to the morula stage, with a significant difference between MII and L8c, and between MII and the morula. The CUL1 protein was localized primarily to nuclei and to a lesser extent to the cytoplasm, with a lower signal in the inner cell mass (ICM) compared to the trophectoderm (TE) at the blastocyst stage. The level of SKP1 protein significantly increased from MII oocytes to 4c embryos, but then significantly decreased again. The localization of the SKP1 protein was analysed throughout the cell and similarly to CUL1 at the blastocyst stage, the staining was less intensive in the ICM. There were no statistical differences in RBX1 protein level and localization. The active SCF-complex, which is determined by the interaction of Cul1 and Skp1, was found throughout the whole embryo during preimplantation development, but there was a difference at the blastocyst stage, which exhibits a much stronger signal in the TE than in the ICM. These results suggest that all these genes could play an important role during preimplantation development. This paper reveals comprehensive expression profile, the basic but important knowledge necessary for further studying.

Microarray Analyses Reveal Marked Differences in Growth Factor and Receptor Expression Between 8-Cell Human Embryos and Pluripotent Stem Cells

Previous microarray analyses of RNAs from 8-cell (8C) human embryos revealed a lack of cell cycle checkpoints and overexpression of core circadian oscillators and cell cycle drivers relative to pluripotent human stem cells [human embryonic stem cells/induced pluripotent stem (hES/iPS)] and fibroblasts, suggesting growth factor independence during early cleavage stages. To explore this possibility, we queried our combined microarray database for expression of 487 growth factors and receptors. Fifty-one gene elements were overdetected on the 8C arrays relative to hES/iPS cells, including 14 detected at least 80-fold higher, which annotated to multiple pathways: six cytokine family (CSF1R, IL2RG, IL3RA, IL4, IL17B, IL23R), four transforming growth factor beta (TGFB) family (BMP6, BMP15, GDF9, ENG), one fibroblast growth factor (FGF) family [FGF14(FH4)], one epidermal growth factor member (GAB1), plus CD36, and CLEC10A. 8C-specific gene elements were enriched (73%) for reported circadian-controlled genes in mouse tissues. High-level detection of CSF1R, ENG, IL23R, and IL3RA specifically on the 8C arrays suggests the embryo plays an active role in blocking immune rejection and is poised for trophectoderm development; robust detection of NRG1, GAB1, -2, GRB7, and FGF14(FHF4) indicates novel roles in early development in addition to their known roles in later development. Forty-four gene elements were underdetected on the 8C arrays, including 11 at least 80-fold under the pluripotent cells: two cytokines (IFITM1, TNFRSF8), five TGFBs (BMP7, LEFTY1, LEFTY2, TDGF1, TDGF3), two FGFs (FGF2, FGF receptor 1), plus ING5, and WNT6. The microarray detection patterns suggest that hES/iPS cells exhibit suppressed circadian competence, underexpression of early differentiation markers, and more robust expression of generic pluripotency genes, in keeping with an artificial state of continual uncommitted cell division. In contrast, gene expression patterns of the 8C embryo suggest that it is an independent circadian rhythm-competent equivalence group poised to signal its environment, defend against maternal immune rejection, and begin the rapid commitment events of early embryogenesis.

Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth

Background

The successful achievement of early ovarian folliculogenesis is important for fertility and reproductive life span. This complex biological process requires the appropriate expression of numerous genes at each developmental stage, in each follicular compartment. Relatively little is known at present about the molecular mechanisms that drive this process, and most gene expression studies have been performed in rodents and without considering the different follicular compartments.

Results

We used RNA-seq technology to explore the sheep transcriptome during early ovarian follicular development in the two main compartments: oocytes and granulosa cells. We documented the differential expression of 3,015 genes during this phase and described the gene expression dynamic specific to these compartments. We showed that important steps occurred during primary/secondary transition in sheep. We also described the in vivo molecular course of a number of pathways. In oocytes, these pathways documented the chronology of the acquisition of meiotic competence, migration and cellular organization, while in granulosa cells they concerned adhesion, the formation of cytoplasmic projections and steroid synthesis. This study proposes the involvement in this process of several members of the integrin and BMP families. The expression of genes such as Kruppel-like factor 9 (KLF9) and BMP binding endothelial regulator (BMPER) was highlighted for the first time during early follicular development, and their proteins were also predicted to be involved in gene regulation. Finally, we selected a data set of 24 biomarkers that enabled the discrimination of early follicular stages and thus offer a molecular signature of early follicular growth. This set of biomarkers includes known genes such as SPO11 meiotic protein covalently bound to DSB (SPO11), bone morphogenetic protein 15 (BMP15) and WEE1 homolog 2 (S. pombe)(WEE2) which play critical roles in follicular development but other biomarkers are also likely to play significant roles in this process.

Conclusions

To our knowledge, this is the first in vivo spatio-temporal exploration of transcriptomes derived from early follicles in sheep.

Breast-cancer anti-estrogen resistance 4 (BCAR4) encodes a novel maternal-effect protein in bovine and is expressed in the oocyte of humans and other non-rodent mammals

STUDY QUESTION

Does BCAR4 have a role in mammalian embryo development?

SUMMARY ANSWER

Expression, localization and functional data support that BCAR4 is a maternal-effect protein in non-rodent mammals.

WHAT IS KNOWN ALREADY

BCAR4 was previously identified as an oocyte-specific gene in cattle, and as a marker of certain breast tumors in humans.

STUDY DESIGN, SIZE, DURATION

Human oocytes were obtained from patients undergoing IVF, but had failed to mature after ovarian stimulation. Dog oocytes were obtained from ovariectomized bitches. Pig, horse and bovine ovaries were obtained from commercial slaughterhouses for extraction of immature oocyte-cumulus complexes. In vivo matured bovine matured oocytes were obtained after ovulation induction and ovulation inducing treatment of Montbeliard heifers.

MATERIALS, SETTING AND METHODS

Expression at the RNA level was analyzed by reverse transcription coupled to polymerase chain reaction. Western blot and immunolabeling coupled to confocal or electronic microscopy were used to analyze bovine protein expression and intracellular localization. For the functional approach, short-interfering RNA were microinjected into mature bovine oocytes, followed by IVF; cleavage and embryo development were recorded.

MAIN RESULTS AND THE ROLE OF CHANCE

The BCAR4 gene is conserved in mammalian species from various orders and has been lost in rodents after divergence with lagomorphs. The transcript is expressed in the oocytes of humans and domestic species. We bring the first experimental evidence of the BCAR4 protein in mammals. In cattle, the protein is not detected in immature oocytes but starts to be synthesized during maturation, increases in the zygote and persists until the morula stage. The protein is detected throughout the cytoplasm in mature oocytes, concentrates in and around the pronuclei in the zygote, and appears to shuttle in and out of the nuclei starting in the 2-cell embryo; BCAR4 is also present at the junctions between blastomeres from 2-cell to morula. In our functional approach, targeting the BCAR4 transcript by small-interfering RNA significantly compromised development to the morula or/and blastocyst stages (P < 0.05, logistic regression).

LIMITATIONS, REASONS FOR CAUTION

As indicated above, protein expression and function were investigated in cattle and mostly in vitro matured oocytes were used.

WIDER IMPLICATIONS OF THE FINDINGS

This study provides a novel candidate gene whose mutation or deregulation may underlie certain cases of unexplained female infertility.

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.

Effect of ovarian stimulation on oocyte gene expression in cattle

The objective was to analyze the impact of follicle stimulating hormone (FSH, ovarian stimulation) on the transcriptome of in vivo bovine oocytes three times around the luteinizing hormone (LH) surge. In vivo bovine oocytes were collected 2 h pre-LH surge, 6 h post-LH surge, and 22 h post-LH surge in both naturally ovulating and superovulated animals. To assess potential changes in gene levels, samples were hybridized using a custom bovine microarray. Two series of hybridizations were performed: the first comparing natural vs. stimulated cycles, the second according to time of collection. Among the potential candidates, 13 genes were selected according to their degree of differential expression and their potential link to oocyte competence. Measurements of their relative mRNA levels was made using QPCR. Gene candidates BTG4 (P = 0.0006), PTTG1 (P = 0.0027), PAPOLA (P = 0.0245), and LEO1 (P = 0.0393) had higher mRNA levels in oocytes treated with FSH for all collection times when compared to oocytes produced through the natural cycle. Among our selected candidates, only one gene, GDF9 (P = 0.0261), was present at a higher level in oocytes collected at -2 h and 6 h than 22 h post-LH for all treatments, regardless of the presence of FSH. Although the number of genes influenced by ovarian stimulation seemed low, the observed differences occurred at a time of minimal transcriptional activity and supported the potential impact on the future embryo. These impacts could have been epigenetic in nature, as embryo quality was not reported to be different from stimulated animals.

In vitro maturation supplements affect developmental competence of bovine cumulus-oocyte complexes and embryo quality after vitrification

Oocyte quality affects subsequent embryo development and quality. We examined the impact of bovine oocyte in vitro maturation (IVM) conditions on subsequent embryo yield, quality and cryosurvival. Cumulus-oocyte complexes (COCs) were sampled for cytological and gene expression analysis after IVM in TCM199 supplemented with 10% fetal bovine serum (FBS), 4 mg/ml of fatty-acid-free bovine serum albumin (FAFBSA), 4 mg/ml of polyvinylpyrrolidone (PVP), FAFBSA with epidermal growth factor (EGF, 100 ng/ml) and insulin-like growth factor 1 (IGF-I, 100 ng/ml) (FAFBSAGF), PVP with EGF and IGF-I (PVPGF) or PVP with single strength BME and MEM amino acids (PVPAA). The remaining COCs were fertilized. On day 7 (IVF=day 0) quality 1 blastocysts were vitrified or analyzed for glucose transporter 1 (Glut-1) expression levels. The remaining blastocysts (days 7-9) were evaluated for morphology and total cell counts. After warming, survival and hatching rates were evaluated followed by total cell counts and Glut-1 expression levels. Only PVPGF IVM resulted in embryo production rates comparable to those recorded with FBS IVM. Growth factors with FAFBSA and amino acids with PVP reduced embryo production rates whereas the effect of the growth factors with PVP was negligible. Insulin-like growth factor 2 binding protein 3 (IGF2BP3) and beta cell translocation gene 4 (BTG4) were revealed as potential candidates for oocyte developmental competence, and secreted protein, acidic and rich in cysteine (SPARC) for cumulus cell expansion. There were no differences among treatments in hatching rates of vitrified embryos after warming. However, total cell numbers and Glut-1 expression levels at 72 h were affected.

Expression of maternal transcripts during bovine oocyte in vitro maturation is affected by donor age

The primary objective of this study was to compare expression of maternal transcripts in bovine oocyte populations with differential developmental competence: oocytes from prepubertal and pubertal animals; and oocytes from small (3-4 mm) and large (6-10 mm) follicles from pubertal animals. All transcripts were examined in oocytes prior to and after in vitro maturation (IVM). Genes were selected based on their known maternal effect in mouse (ZAR1, STELLA, HSF1, MATER/NLRP5 and its paralogue NLRP9), or their identification as markers of oocyte maturation, either involved in redox metabolism (PRDX1, PRDX2) or meiotic progression (AURKA). Total or polyadenylated forms of the transcripts were followed by reverse transcription coupled to real-time PCR. Six polyadenylated transcripts were found significantly reduced after maturation irrespective of donor age or follicle diameter (p<0.05). Within these six polyadenylated transcripts, ZAR1, NLRP9, HSF1, PRDX1 and PRDX2 were significantly reduced in oocytes from prepubertal animals compared to adult animals (p<0.05). A younger age was also associated with lower abundance (total form) of PRDX2/PRDX1 irrespective of maturation. Total HSF1, PRDX1 and polyadenylated NLRP9 showed a tendency (p values from 0.053 to 0.08) for a higher detection in oocytes from small follicles, thus encouraging further investigation of the follicle diameter model. However, at the present time, follicle size did not significantly affect expression of transcripts examined. In conclusion, this study demonstrates differences in the maternal store of RNA and its regulation during IVM which is dependent on donor age.

Transcriptomic analysis of in vivo and in vitro produced bovine embryos revealed a developmental change in cullin 1 expression during maternal-to-embryonic transition

Pre-implantation embryos derived by in vitro fertilization differ in their developmental potential from embryos obtained in vivo. In order to characterize changes in gene expression profiles caused by in vitro culture environment, we employed microarray constructed from bovine oocyte and preimplantation embryo-specific cDNAs (BlueChip, Université Laval, Québec). The analysis revealed changes in the level of 134 transcripts between in vitro derived (cultured in COOK BVC/BVB media) and in vivo derived 4-cell stage embryos and 97 transcripts were differentially expressed between 8-cell stage in vitro and in vivo embryos. The expression profiles of 7 selected transcripts (BUB3, CUL1, FBL, NOLC1, PCAF, GABPA and CNOT4) were studied in detail. We have identified a switch from Cullin 1-like transcript variant 1 to Cullin 1 transcript variant 3 (UniGene IDs BT.36789 and BT.6490, respectively) expressions around the time of bovine major gene activation (8-cell stage). New fibrillarin protein was detected by immunofluorescence already in early 8-cell stage and this detection correlated with increased level of fibrillarin mRNA. The qRT-PCR analysis revealed significant differences in the level of BUB3, NOLC1, PCAF, GABPA and CNOT4 gene transcripts between in vivo derived (IVD) and in vitro produced (IVP) embryos in late 8-cell stage. The combination of these genes represents a suitable tool for addressing questions concerning normal IVD embryo development and can be potentially useful as a marker of embryo quality in future attempts to optimize in vitro culture conditions.

Identification of early transcripts related to male development in chicken embryos

Early transcripts related to male development in chicken embryos and their expression profiles were examined. A total of 89 and 127 candidate male development transcripts that represented 83 known and 119 unknown non-redundant sequences, respectively, were characterized in an embryonic day 3 (E3; Hamburger and Hamilton Stage 20: HH20) male-subtract-female complementary DNA library. Of 35 selected transcripts, quantitative reverse transcription-polymerase chain reaction validated that the expression levels of 25 transcripts were higher in male E3 whole embryos than in females (P < 0.05). Twelve of these transcripts mapped to the Z chromosome. At 72 wk of age, 20 and 4 transcripts were expressed at higher levels in the testes and brains of male than in the ovaries and brains of female chickens (P < 0.05), respectively. Whole mount and frozen cross-section in situ hybridization, as well as Western blotting analysis further corroborated that riboflavin kinase (RFK), WD repeat domain 36 (WDR36), and EY505808 transcripts; RFK and WDR36 protein products were predominantly expressed in E7 male gonads. Treatment with an aromatase inhibitor formestane at E4 affected the expression levels at E7 of the coatomer protein complex (subunit beta 1), solute carrier family 35 member F1, LOC427316 and EY505812 transcripts across both sexes (P < 0.05), similar to what was observed for the doublesex and mab-3 related transcription factor 1 gene. The interaction effects of sex by formestane treatment were observed in 15 candidate male development transcripts (P < 0.05). Taken together, we identified a panel of potentially candidate male development transcripts during early chicken embryogenesis; some might be regulated by sex hormones.

Regulation of bovine oocyte-specific transcripts during in vitro oocyte maturation and after maternal-embryonic transition analyzed using a transcriptomic approach

Oocyte/embryo genomics in mammals faces specific challenges due to limited biological material, to the comparison of models with different total RNA contents, and to expression of a specific set of genes often absent from commercially available microarrays. Here, we report experimental validation of a RNA amplification protocol for bovine oocytes and blastocysts. Using real-time PCR, we have confirmed that the profile of both abundant and scarce polyadenylated transcripts was conserved after RNA amplification. Next, amplified probes generated from immature oocytes, in vitro matured oocytes, and in vitro produced hatched blastocysts were hybridized onto a macroarray that included oocyte-specific genes. Following an original approach, we have compared two normalization procedures, based on the median signal or an exogenous standard. We have evidenced the expected difference in sets of differential genes depending on the normalization procedure. Using a 1.5-fold threshold, no transcript was found to be upregulated when data were normalized to an exogenous standard, which reflects the absence of transcription during in vitro oocyte maturation. In blastocysts, the majority of oocyte-preferentially expressed genes were not activated, as previously observed in mouse. Finally, microarray data were validated by real-time PCR on a random subset of genes. Our study sheds new light on and complements previous transcriptomic analyses of bovine oocyte to embryo transition using commercial platforms.

Revealing the bovine embryo transcript profiles during early in vivo embryonic development

Gene expression profiling is proving to be a powerful approach for the identification of molecular mechanisms underlying complex cellular functions such as the dynamic early embryonic development. The objective of this study was to perform a transcript abundance profiling analysis of bovine early embryonic developmentin vivousing a bovine developmental array. The molecular description of the first week of life at the mRNA level is particularly challenging when considering the important fluctuations in RNA content that occur between developmental stages. Accounting for the different intrinsic RNA content between developmental stages was achieved by restricting the reaction time during the global amplification steps and by using spiked controls and reference samples. Analysis based on intensity values revealed that most of the transcripts on the array were present at some point duringin vivobovine early embryonic development, while the varying number of genes detected in each developmental stage confirmed the dynamic profile of gene expression occurring during embryonic development. Pair-wise comparison of gene expression showed a marked difference between oocytes and blastocysts profiles, and principal component analysis revealed that the majority of the transcripts could be regrouped into three main clusters representing distinct RNA abundance profiles. Overall, these data provide a detailed temporal profile of the abundance of mRNAs revealing the richness of signaling processes in early mammalian development. Results presented here provide better knowledge of bovinein vivoembryonic development and contribute to the progression of our current knowledge regarding the first week of life in mammals.

Oocyte-specific genes: role in fertility and infertility

Genetic determinations of oocyte and ovarian follicle growth are still not well understood. Genes specifically expressed on oocytes seem to play an important role in these processes. Oocyte-specific genes are also involved in ovulation and early embryogenesis processes. Studies on the identification and characterization of new oocyte-specific genes can help in our understanding of cardinal fertility and infertility mechanisms. They can also be candidate genes for reproductive disorders such as polycystic ovary syndrome, premature ovarian failure and infertility. Infertility is an important worldwide problem affecting around 15% of couples. Approximately 20% of infertility is referred as idiopathic infertility. Studies on these genes could improve the diagnostic and therapeutic procedures of human infertility.

Factors affecting oocyte quality: who is driving the follicle?

Mammalian ovaries contain a large stock of oocytes enclosed in primordial follicles. Ovarian cyclic activity induces some of these follicles to initiate growth towards a possible ovulation. However, most of these follicles terminate their growth at any moment and degenerate through atresia. In growing follicles, only a subset of oocytes are capable to support meiosis, fertilization and early embryo development to the blastocyst stage, as shown through embryo in vitro production experiments. This proportion of competent oocytes is increasing along with follicular size. Growing lines of evidence suggest that oocyte competence relies on the storage of gene products (messenger RNA or protein) that will be determinant to support early stages of embryo development, before full activation of embryonic genome. Given these facts, the question is: are these gene products stored in oocytes during late folliculogenesis, allowing an increasing proportion of them to become competent? Alternatively, these transcripts may be stored during early folliculogenesis as the oocyte grows and displays high transcription activity. Several arguments support this latter hypothesis and are discussed in this review: (i) many attempts at prolonged culture of oocytes from antral follicles have failed to increase developmental competence, suggesting that developmental competence may be acquired before antral formation; (ii) the recent discovery of oocyte secreted factors and of their ability to regulate many parameters of surrounding somatic cells, possibly influencing the fate of follicles between ovulation or atresia, suggests a central role of oocyte quality in the success of folliculogenesis. Finally, in addition to their role in interfollicular regulation of ovulation rate, late folliculogenesis regulation and atresia could also be seen as a selective process aimed at the elimination through follicular atresia of oocytes that did not succeed to store proper gene products set during their growth.

In silico identification and molecular characterization of genes predominantly expressed in the fish oocyte

Background

In fish, molecular mechanisms that control follicle-enclosed oocyte progression throughout oogenesis and oocyte developmental competence acquisition remain poorly understood. Existing data in mammals have indicated that the so called "oocyte-specific" genes play an important role in oogenesis, fertilization, and early embryo development. In teleost species, very little is known about "oocyte-specific" genes. The present study therefore aimed at identifying and characterizing oocyte-specific genes in fish.

Results

Using digital differential display PCR, mouse ESTs exhibiting an oocyte-predominant expression were identified. Those murine ESTs were subsequently used to identify cognate rainbow trout (Oncorhynchus mykiss) ESTs using a reciprocal Blast search strategy. In the present study we report the identification of five previously uncharacterized rainbow trout cDNAs exhibiting a oocyte-specific, oocyte-predominant, or gonad-specific expression: zygote arrest 1 (zar1), v-mos Moloney murine sarcoma viral oncogene-like protein (mos), B-cell translocation gene (btg3), growth differentiation factor 9 (gdf9), and mutS homolog 4 (msh4). The orthology relationship of each of these genes with vertebrate counterparts was verified by phylogenetic analysis. Among those five genes, three had never been characterized in any fish species. In addition, we report the oocyte-predominant expression of btg3 for the first time in any vertebrate species. Finally, those five genes are present in unfertilized eggs as maternally-inherited mRNAs thus suggesting that they could participate in ovarian folliculogenesis as well as early embryonic development.

Conclusion

The expression patterns of zar1, mos, btg3, gdf9 and msh4 in rainbow trout and the functions of their orthologs in higher vertebrates strongly suggest that they might play an important role in follicle-enclosed oocyte development, meiosis control and early embryonic development in fish. Future investigations are however required to unravel the participation of those strong candidates in the molecular processes that control folliculogenesis and/or oocyte developmental competence in fish.

Protein expression profile of the mouse metaphase-II oocyte

The mature oocyte contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins have yet to be characterized. In this study, two-dimensional electrophoresis (2-DE) of mouse metaphase-II (MII) oocyte proteins, stained with silver staining or Pro-Q Diamond dye, was performed to describe the proteome and phosphoproteome of the mouse oocyte derived from ICR mice. A total of 869 selected protein spots, corresponding to 380 unique proteins, were identified successfully by mass spectrometry, in which 90 protein spots representing 53 unique proteins have been stained with Pro-Q Diamond, indicating that they are in phosphorylated forms. All identified proteins were bioinformatically annotated in detail and compared with the embryonic stem cell (ESC) proteome. A proteome reference database for the mouse oocyte was established from the protein data generated in this study, which can be accessed over the Internet ( http://reprod.njmu.edu.cn/2d). This database is the most detailed mouse oocyte proteomic database to date. It should be valuable in expanding our knowledge of the regulation of signaling in oogenesis, fertilization, and embryo development, while revealing potential mechanisms for epigenetic reprogramming.

Identification of novel and known ovary-specific genes including ZP2, in a marsupial, the stripe-faced dunnart

During the early stages of oogenesis, oocyte-specific factors, synthesized by and stored within the oocyte, play critical roles during oogenesis, folliculogenesis, fertilization and early embryonic development in the mouse. The identification of marsupial maternal factors, expressed specifically in the ovary or oocyte, may provide an insight into the conserved evolutionary mechanisms that drive mammalian oocyte development to cleavage stages. In this study, 10 clones including dunnart ZP2 and c-mos, isolated by cDNA representational difference analysis, were validated by RT-PCR for ovary-specific expression. This novel combination of techniques to isolate ovary-specific genes has identified three novel genes with ovary-specific expression. Both dunnart ZP2 and c-mos exhibited ovary-specific expression, making this study the first isolation of c-mos in a marsupial species. Dunnart ZP2 expression was examined in detail by in situ hybridization and results indicate oocyte-specific expression of dunnart ZP2 in the cytoplasm of oocytes of primordial, primary and secondary follicles with expression being highest in oocytes of primary follicles. ZP2 was not expressed in granulosa cells of any follicles.

Search for the genes involved in oocyte maturation and early embryo development in the hen

Background

The initial stages of development depend on mRNA and proteins accumulated in the oocyte, and during these stages, certain genes are essential for fertilization, first cleavage and embryonic genome activation. The aim of this study was first to search for avian oocyte-specific genes using an in silico and a microarray approaches, then to investigate the temporal and spatial dynamics of the expression of some of these genes during follicular maturation and early embryogenesis.

Results

The in silico approach allowed us to identify 18 chicken homologs of mouse potential oocyte genes found by digital differential display. Using the chicken Affymetrix microarray, we identified 461 genes overexpressed in granulosa cells (GCs) and 250 genes overexpressed in the germinal disc (GD) of the hen oocyte. Six genes were identified using both in silico and microarray approaches. Based on GO annotations, GC and GD genes were differentially involved in biological processes, reflecting different physiological destinations of these two cell layers. Finally we studied the spatial and temporal dynamics of the expression of 21 chicken genes. According to their expression patterns all these genes are involved in different stages of final follicular maturation and/or early embryogenesis in the chicken. Among them, 8 genes (btg4, chkmos, wee, zpA, dazL, cvh, zar1 and ktfn) were preferentially expressed in the maturing occyte and cvh, zar1 and ktfn were also highly expressed in the early embryo.

Conclusion

We showed that in silico and Affymetrix microarray approaches were relevant and complementary in order to find new avian genes potentially involved in oocyte maturation and/or early embryo development, and allowed the discovery of new potential chicken mature oocyte and chicken granulosa cell markers for future studies. Moreover, detailed study of the expression of some of these genes revealed promising candidates for maternal effect genes in the chicken. Finally, the finding concerning the different state of rRNA compared to that of mRNA during the postovulatory period shed light on some mechanisms through which oocyte to embryo transition occurs in the hen.

Spatio-Temporal Expression Patterns of Aurora Kinases A, B, and C and Cytoplasmic Polyadenylation-Element-Binding Protein in Bovine Oocytes During Meiotic Maturation1

Maturation of immature bovine oocytes requires cytoplasmic polyadenylation and synthesis of a number of proteins involved in meiotic progression and metaphase-II arrest. Aurora serine-threonine kinases--localized in centrosomes, chromosomes, and midbody--regulate chromosome segregation and cytokinesis in somatic cells. In frog and mouse oocytes, Aurora A regulates polyadenylation-dependent translation of several mRNAs such as MOS and CCNB1, presumably by phosphorylating CPEB, and Aurora B phosphorylates histone H3 during meiosis. We analyzed the expression of three Aurora kinase genes--AURKA, AURKB, and AURKC--in bovine oocytes during meiosis by reverse transcription followed by quantitative real-time PCR and immunodetection. Aurora A was the most abundant form in oocytes, both at mRNA and protein levels. AURKA protein progressively accumulated in the oocyte cytoplasm during antral follicle growth and in vitro maturation. AURKB associated with metaphase chromosomes. AURKB, AURKC, and Thr-phosphorylated AURKA were detected at a contractile ring/midbody during the first polar body extrusion. CPEB, localized in oocyte cytoplasm, was hyperphosphorylated during prophase/metaphase-I transition. Most CPEB degraded in metaphase-II oocytes and remnants remained localized in a contractile ring. Roscovitine, U0126, and metformin inhibited meiotic divisions; they all induced a decrease of CCNB1 and phospho-MAPK3/1 levels and prevented CPEB degradation. However, only metformin depleted AURKA. The Aurora kinase inhibitor VX680 at 100 nmol/L did not inhibit meiosis but led to multinuclear oocytes due to the failure of the polar body extrusion. Thus, in bovine oocyte meiosis, massive destruction of CPEB accompanies metaphase-I/II transition, and Aurora kinases participate in regulating segregation of the chromosomes, maintenance of metaphase-II, and formation of the first polar body.

Opportunities and challenges in applying genomics to the study of oogenesis and folliculogenesis in farm animals

Ovarian oogenesis and folliculogenesis are complex and coordinated biological processes which require a series of events that induce morphological and functional changes within the follicle, leading to cell differentiation and oocyte development. In this context, the challenge of the researchers is to describe the dynamics of gene expression in the different compartments and their interactions during the follicular programme. In recent years, high-throughput arrays have become a powerful tool with which to compare the whole population of transcripts in a single experiment. Here, we review the challenges of applying genomics to this model in farm animal species. The first limitation lies in limited the availability of biological material, which makes the study of the follicle compartments (oocyte, granulosa cells and thecal cells) or early embryo much more difficult. The concept of observing all transcripts at once is very attractive but despite progress in sequencing, the genome annotation remains very incomplete in non-model species. Particularly, oogenesis and early embryo development relate to the high proportion of unknown expressed sequence tags. Then, it is important to consider post-transcriptional and translational regulation to understand the role of these genes. Ultimately, these new inferred insights will still have to be validated by functional approaches. In addition toin vitroorex vivofunctional approaches, both ‘natural mutant’ ewe models and RNA interference represent, at the moment, the best hope for functional genomics. Advances in our understanding of reproductive physiology should be facilitated by gene expression data exchange and translation into a better understanding of the underlying biological phenomena.

Differential regulation of abundance and deadenylation of maternal transcripts during bovine oocyte maturation in vitro and in vivo

Background

In bovine maturing oocytes and cleavage stage embryos, gene expression is mostly controlled at the post-transcriptional level, through degradation and deadenylation/polyadenylation. We have investigated how post transcriptional control of maternal transcripts was affected during in vitro and in vivo maturation, as a model of differential developmental competence.

Results

Using real time PCR, we have analyzed variation of maternal transcripts, in terms of abundance and polyadenylation, during in vitro or in vivo oocyte maturation and in vitro embryo development. Four genes are characterized here for the first time in bovine: ring finger protein 18 (RNF18) and breast cancer anti-estrogen resistance 4 (BCAR4), whose oocyte preferential expression was not previously reported in any species, as well as Maternal embryonic leucine zipper kinase (MELK) and STELLA. We included three known oocyte marker genes (Maternal antigen that embryos require (MATER), Zygote arrest 1 (ZAR1), NACHT, leucine rich repeat and PYD containing 9 (NALP9)). In addition, we selected transcripts previously identified as differentially regulated during maturation, peroxiredoxin 1 and 2 (PRDX1, PRDX2), inhibitor of DNA binding 2 and 3 (ID2, ID3), cyclin B1 (CCNB1), cell division cycle 2 (CDC2), as well as Aurora A (AURKA). Most transcripts underwent a moderate degradation during maturation. But they displayed sharply contrasted deadenylation patterns that account for variations observed previously by DNA array and correlated with the presence of a putative cytoplasmic polyadenylation element in their 3' untranslated region. Similar variations in abundance and polyadenylation status were observed during in vitro maturation or in vivo maturation, except for PRDX1, that appears as a marker of in vivo maturation. Throughout in vitro development, oocyte restricted transcripts were progressively degraded until the morula stage, except for MELK ; and the corresponding genes remained silent after major embryonic genome activation.

Conclusion

Altogether, our data emphasize the extent of post-transcriptional regulation during oocyte maturation. They do not evidence a general alteration of this phenomenon after in vitro maturation as compared to in vivo maturation, but indicate that some individual messenger RNA can be affected.

Conserved molecular portraits of bovine and human blastocysts as a consequence of the transition from maternal to embryonic control of gene expression

The present study investigated mRNA expression profiles of bovine oocytes and blastocysts by using a cross-species hybridization approach employing an array consisting of 15,529 human cDNAs as probe, thus enabling the identification of conserved genes during human and bovine preimplantation development. Our analysis revealed 419 genes that were expressed in both oocytes and blastocysts. The expression of 1,324 genes was detected exclusively in the blastocyst, in contrast to 164 in the oocyte including a significant number of novel genes. Genes indicative for transcriptional and translational control (ELAVL4, TACC3) were overexpressed in the oocyte, whereas cellular trafficking (SLC2A14, SLC1A3), proteasome (PSMA1, PSMB3), cell cycle (BUB3, CCNE1, GSPT1), and protein modification and turnover (TNK1, UBE3A) genes were found to be overexpressed in blastocysts. Transcripts implicated in chromatin remodeling were found in both oocytes (NASP, SMARCA2) and blastocysts (H2AFY, HDAC7A). The trophectodermal markers PSG2 and KRT18 were enriched 5- and 50-fold in the blastocyst. Pathway analysis revealed differential expression of genes involved in 107 distinct signaling and metabolic pathways. For example, phosphatidylinositol signaling and gluconeogenesis were prominent pathways identified in the blastocyst. Expression patterns in bovine and human blastocysts were to a large extent identical. This analysis compared the transcriptomes of bovine oocytes and blastocysts and provides a solid foundation for future studies on the first major differentiation events in blastocysts and identification of a set of markers indicative for regular mammalian development.

Application of DNA array technology to mammalian embryos

Early embryogenesis depends on a tightly choreographed succession of gene expression patterns which define normal development. Fertilization and the first zygotic cleavage involve major changes to paternal and maternal chromatin and translation of maternal RNAs which have been sequestered in the oocyte during oogenesis. At a critical species-specific point known as the major onset of embryonic expression, there is a dramatic increase in expression from the new diploid genome. The advent of array technology has, for the first time, made possible to determine the transcriptional profile of all approximately 20,000 mammalian genes during embryogenesis, although the small amount of mRNA in a single embryo necessitates either pooling large numbers of embryos or a global amplification procedure to give sufficient labeled RNA for analysis. Following array hybridization, various bioinformatic tools must be employed to determine the expression level for each gene, often based on multiple oligonucleotide probes and complex background estimation protocols. The grouped analysis of clusters of genes which represent specific biological pathways provides the key to understanding embryonic development, embryonic stem cell proliferation and the reprogramming of gene expression after somatic cloning. Arrays are being developed to address specific biological questions related to embryonic development including DNA methylation and microRNA expression. Array technology in its various facets is an important diagnostic tool for the early detection of developmental aberrations; for improving the safety of assisted reproduction technologies for man; and for improving the efficiency of producing cloned and/or transgenic farm animals. This review discusses current approaches and limitations of DNA microarray technology with emphasis on bovine embryos.

Identification of a putative oocyte-specific small nuclear ribonucleoprotein polypeptide C in gibel carp

Previous studies have demonstrated that germinal vesicle of amphibian oocyte contains small nuclear ribonucleoprotein polypeptide C (SNRPC). In this study, a putative member of SNRPC was identified from Carassius auratus gibelio oocyte cDNA library. Its full-length cDNA has an open reading frame of 201 nt for encoding a peptide of 66 aa, a short 5'-UTR of 19 nt and a long 3'-UTR of 347 nt including a polyadenylation signal and poly- (A) tail, and the deduced amino acid sequence has 47% identity with the C-terminal of the zebrafish small nuclear ribonucleoprotein polypeptide C. Western blot analysis revealed its oocyte-specific expression. Immunofluorescence localization indicated that its gene product localized to numerous nucleoli within the oocytes and showed dynamic changes with the nucleoli during oocyte maturation. RT-PCR and Western blot analysis further revealed its constant presence in the oocytes and in the embryos until hatching. The data suggested that the newly identified CagOSNRPC might be a nucleolar protein.

Identification of transcripts related to high egg production in the chicken hypothalamus and pituitary gland

To identify transcripts related to high egg production expressed specifically in the hypothalamus and pituitary gland of the chicken, two subtracted cDNA libraries were constructed. Two divergently selected strains of Taiwan Country Chickens (TCCs), B (sire line) and L2 (dam line) were used; they had originated from a single population and were further subjected (since 1982) to selection for egg production to 40 wk of age and body weight/comb size, respectively. A total of 324 and 370 clones were identified from the L2-B (L2-subtract-B) and the B-L2 subtracted cDNA libraries, respectively. After sequencing and annotation, 175 and 136 transcripts that represented 53 known and 65 unknown non-redundant sequences were characterized in the L2-B subtracted cDNA library. Quantitative reverse-transcription (RT)-PCR was used to screen the mRNA expression levels of 32 randomly selected transcripts in another 78 laying hens from five different strains. These strains included the two original strains (B and L2) used to construct the subtracted cDNA libraries and an additional three commercial strains, i.e., Black- and Red-feather TCCs and Single-Comb White Leghorn (WL) layer. The mRNA expression levels of 16 transcripts were significantly higher in the L2 than in the B strain, whereas the mRNA expression levels of nine transcripts, BDH, NCAM1, PCDHA@, PGDS, PLAG1, PRL, SAR1A, SCG2 and STMN2, were significantly higher in two high egg production strains, L2 and Single-Comb WL; this indicated their usefulness as molecular markers of high egg production.

An annotated cDNA library of juvenile Euprymna scolopes with and without colonization by the symbiont Vibrio fischeri

BACKGROUND

Biologists are becoming increasingly aware that the interaction of animals, including humans, with their coevolved bacterial partners is essential for health. This growing awareness has been a driving force for the development of models for the study of beneficial animal-bacterial interactions. In the squid-vibrio model, symbiotic Vibrio fischeri induce dramatic developmental changes in the light organ of host Euprymna scolopes over the first hours to days of their partnership. We report here the creation of a juvenile light-organ specific EST database.

RESULTS

We generated eleven cDNA libraries from the light organ of E. scolopes at developmentally significant time points with and without colonization by V. fischeri. Single pass 3' sequencing efforts generated 42,564 expressed sequence tags (ESTs) of which 35,421 passed our quality criteria and were then clustered via the UIcluster program into 13,962 nonredundant sequences. The cDNA clones representing these nonredundant sequences were sequenced from the 5' end of the vector and 58% of these resulting sequences overlapped significantly with the associated 3' sequence to generate 8,067 contigs with an average sequence length of 1,065 bp. All sequences were annotated with BLASTX (E-value < -03) and Gene Ontology (GO).

CONCLUSION

Both the number of ESTs generated from each library and GO categorizations are reflective of the activity state of the light organ during these early stages of symbiosis. Future analyses of the sequences identified in these libraries promise to provide valuable information not only about pathways involved in colonization and early development of the squid light organ, but also about pathways conserved in response to bacterial colonization across the animal kingdom.

Zygote arrest 1 gene in pig, cattle and human: evidence of different transcript variants in male and female germ cells

BACKGROUND

Zygote arrest 1 (ZAR1) is one of the few known oocyte-specific maternal-effect genes essential for the beginning of embryo development discovered in mice. This gene is evolutionary conserved in vertebrates and ZAR1 protein is characterized by the presence of atypical plant homeobox zing finger domain, suggesting its role in transcription regulation. This work was aimed at the study of this gene, which could be one of the key regulators of successful preimplantation development of domestic animals, in pig and cattle, as compared with human.

METHODS

Screenings of somatic cell hybrid panels and in silico research were performed to characterize ZAR1 chromosome localization and sequences. Rapid amplification of cDNA ends was used to obtain full-length cDNAs. Spatio-temporal mRNA expression patterns were studied using Northern blot, reverse transcription coupled to polymerase chain reaction and in situ hybridization.

RESULTS

We demonstrated that ZAR1 is a single copy gene, positioned on chromosome 8 in pig and 6 in cattle, and several variants of correspondent cDNA were cloned from oocytes. Sequence analysis of ZAR1 cDNAs evidenced numerous short inverted repeats within the coding sequences and putative Pumilio-binding and embryo-deadenylation elements within the 3'-untranslated regions, indicating the potential regulation ways. We showed that ZAR1 expressed exclusively in oocytes in pig ovary, persisted during first cleavages in embryos developed in vivo and declined sharply in morulae and blastocysts. ZAR1 mRNA was also detected in testis, and, at lower level, in hypothalamus and pituitary in both species. For the first time, ZAR1 was localized in testicular germ cells, notably in round spermatids. In addition, in pig, cattle and human only shorter ZAR1 transcript variants resulting from alternative splicing were found in testis as compared to oocyte.

CONCLUSION

Our data suggest that in addition to its role in early embryo development highlighted by expression pattern of full-length transcript in oocytes and early embryos, ZAR1 could also be implicated in the regulation of meiosis and post meiotic differentiation of male and female germ cells through expression of shorter splicing variants. Species conservation of ZAR1 expression and regulation underlines the central role of this gene in early reproductive processes.

Molecular phenotype of zebrafish ovarian follicle by serial analysis of gene expression and proteomic profiling, and comparison with the transcriptomes of other animals

BACKGROUND

The ability of an oocyte to develop into a viable embryo depends on the accumulation of specific maternal information and molecules, such as RNAs and proteins. A serial analysis of gene expression (SAGE) was carried out in parallel with proteomic analysis on fully-grown ovarian follicles from zebrafish (Danio rerio). The data obtained were compared with ovary/follicle/egg molecular phenotypes of other animals, published or available in public sequence databases.

RESULTS

Sequencing of 27,486 SAGE tags identified 11,399 different ones, including 3,329 tags with an occurrence superior to one. Fifty-eight genes were expressed at over 0.15% of the total population and represented 17.34% of the mRNA population identified. The three most expressed transcripts were a rhamnose-binding lectin, beta-actin 2, and a transcribed locus similar to the H2B histone family. Comparison with the large-scale expressed sequence tags sequencing approach revealed highly expressed transcripts that were not previously known to be expressed at high levels in fish ovaries, like the short-sized polarized metallothionein 2 transcript. A higher sensitivity for the detection of transcripts with a characterized maternal genetic contribution was also demonstrated compared to large-scale sequencing of cDNA libraries. Ferritin heavy polypeptide 1, heat shock protein 90-beta, lactate dehydrogenase B4, beta-actin isoforms, tubulin beta 2, ATP synthase subunit 9, together with 40 S ribosomal protein S27a, were common highly-expressed transcripts of vertebrate ovary/unfertilized egg. Comparison of transcriptome and proteome data revealed that transcript levels provide little predictive value with respect to the extent of protein abundance. All the proteins identified by proteomic analysis of fully-grown zebrafish follicles had at least one transcript counterpart, with two exceptions: eosinophil chemotactic cytokine and nothepsin.

CONCLUSION

This study provides a complete sequence data set of maternal mRNA stored in zebrafish germ cells at the end of oogenesis. This catalogue contains highly-expressed transcripts that are part of a vertebrate ovarian expressed gene signature. Comparison of transcriptome and proteome data identified downregulated transcripts or proteins potentially incorporated in the oocyte by endocytosis. The molecular phenotype described provides groundwork for future experimental approaches aimed at identifying functionally important stored maternal transcripts and proteins involved in oogenesis and early stages of embryo development.