Discovery of eight novel divergent homologs expressed in cattle placenta

Single-cell insights into development of the bovine placenta†

A central determinant of pregnancy success is proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Although the gross morphology and histology of the bovine placenta have been well studied, the cellular and molecular mechanisms regulating placenta development and trophoblast differentiation and function remain essentially undefined. Here, single-cell transcriptome (scRNA-seq) analysis was performed on the day 17 bovine conceptus and chorion of day 24, 30, and 50 conceptuses (n = 3-4 samples per day) using the 10X Genomics platform. Bioinformatic analyses identified cell types and their ontogeny including trophoblast, mesenchyme, and immune cells. Loss of interferon tau-expressing trophoblast uninucleate cells occurred between days 17 and 30, whereas binucleate cells, identified based on expression of placental lactogen (CSH2) and specific pregnancy-associated glycoprotein genes (PAGs), first appeared on day 24. Several different types of uninucleate cells were present in day 24, 30, and 50 samples, but only one (day 24) or two types of binucleate cells (days 30 and 50). Cell trajectory analyses provided a conceptual framework for uninucleate cell development and binucleate cell differentiation, and bioinformatic analyses identified candidate transcription factors governing differentiation and function of the trophoblasts. The digital atlas of cell types in the developing bovine conceptus reported here serves as a resource to discover key genes and biological pathways regulating its development during the critical periods of implantation and placentation.

Evolution of Placental Hormones: Implications for Animal Models

Human placenta secretes a variety of hormones, some of them in large amounts. Their effects on maternal physiology, including the immune system, are poorly understood. Not one of the protein hormones specific to human placenta occurs outside primates. Instead, laboratory and domesticated species have their own sets of placental hormones. There are nonetheless several examples of convergent evolution. Thus, horse and human have chorionic gonadotrophins with similar functions whilst pregnancy-specific glycoproteins have evolved in primates, rodents, horses, and some bats, perhaps to support invasive placentation. Placental lactogens occur in rodents and ruminants as well as primates though evolved through duplication of different genes and with functions that only partially overlap. There are also placental hormones, such as the pregnancy-associated glycoproteins of ruminants, that have no equivalent in human gestation. This review focusses on the evolution of placental hormones involved in recognition and maintenance of pregnancy, in maternal adaptations to pregnancy and lactation, and in facilitating immune tolerance of the fetal semiallograft. The contention is that knowledge gained from laboratory and domesticated mammals can translate to a better understanding of human placental endocrinology, but only if viewed in an evolutionary context.

Evolution of placentation in cattle and antelopes

Bovids have enjoyed great evolutionary success as evidenced by the large number of extant species. Several important domestic animals are from this family. They derive from both subfamilies: cattle and their kin belong to Bovinae and sheep and goats to Antilopinae. The premise of this review, therefore, is that evolution of reproduction and placentation is best understood in a context that includes antelope-like bovines and antelopes. Many key features of placentation, including hormone secretion, had evolved before bovids emerged as a distinct group. Variation nevertheless occurs. Most striking is the difference in fusion of the binucleate trophoblast cell with uterine epithelium that yields a transient trinucleate cell in bovines and many antelopes, but a more persistent syncytium in wildebeest, sheep and goat. There is considerable variation in placentome number and villus branching within the placentome. Many antelopes have right-sided implantation in a bicornuate uterus whilst others have a uterus duplex. Finally, there has been continued evolution of placental hormones with tandem duplication of PAG genes in cattle, differences in glycosylation of placental lactogen and the emergence of placental growth hormone in sheep and goats. The selection pressures driving this evolution are unknown though maternal-fetal competition for nutrients is an attractive hypothesis.

DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield

Background

Milk yield for Holstein cows has doubled over five decades due to genetic selection and changes to management, but the molecular mechanisms that facilitated this increase are mostly unknown. Epigenetic modifications to the cattle genome are a plausible molecular mechanism to cause variation in milk yield and our objective was to describe genome-wide DNA methylation patterns in peripheral blood mononuclear cells (PBMC) from mature Holstein dairy cows with variable milk yield.

Results

Whole genome MeDIP-seq was performed following DNA extraction from PBMC of 6 lactating dairy cows from 4 different herds that varied in milk yield from 13,556 kg to 23,105 kg per 305 day lactation. We describe methylation across the genome and for 13,677 protein coding genes. Repetitive element reads were primarily mapped to satellite (36.4%), SINE (29.1%), and LINE (23.7%) regions and the majority (78.4%) of CpG sites were sequenced at least once. DNA methylation was generally low upstream of genes with the nadir occurring 95 bp prior to the transcription start site (TSS). Methylation was lower in the first exon than in later exons, was highest for introns near the intron-exon junctions, and declined downstream as the distance from the gene increased. We identified 72 differentially methylated regions (DMR) between high milk yield cows and their control, and 252 DMR across herd environments.

Conclusions

This reference methylome for cattle with extreme variation in milk yield phenotype provides a resource to more fully evaluate relationships between DNA methylation and phenotype in populations subject to selection. The detection of DMR in cows of varying milk yield suggests potential to exploit epigenetic variation in cattle improvement programs.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5124-9) contains supplementary material, which is available to authorized users.

Evolution of the growth hormone, prolactin, prolactin 2 and somatolactin family

Growth hormone (GH), prolactin (PRL), prolactin 2 (PRL2) and somatolactin (SL) belong to the same hormone family and have a wide repertoire of effects including development, osmoregulation, metabolism and stimulation of growth. Both the hormone and the receptor family have been proposed to have expanded by gene duplications in early vertebrate evolution. A key question is how hormone-receptor preferences have arisen among the duplicates. The first step to address this is to determine the time window for these duplications. Specifically, we aimed to see if duplications resulted from the two basal vertebrate tetraploidizations (1R and 2R). GH family genes from a broad range of vertebrate genomes were investigated using a combination of sequence-based phylogenetic analyses and comparisons of synteny. We conclude that the PRL and PRL2 genes arose from a common ancestor in 1R/2R, as shown by neighboring gene families. No other gene duplicates were preserved from these tetraploidization events. The ancestral genes that would give rise to GH and PRL/PRL2 arose from an earlier duplication; most likely a local gene duplication as they are syntenic in several species. Likewise, some evidence suggests that SL arose from a local duplication of an ancestral GH/SL gene in the same time window, explaining the lack of similarity in chromosomal neighbors to GH, PRL or PRL2. Thus, the basic triplet of ancestral GH, PRL/PRL2 and SL genes appear to be unexpectedly ancient. Following 1R/2R, only SL was duplicated in the teleost-specific tetraploidization 3R, resulting in SLa and SLb. These time windows contrast with our recent report that the corresponding receptor genes GHR and PRLR arose through a local duplication in jawed vertebrates and that both receptor genes duplicated further in 3R, which reveals a surprising asynchrony in hormone and receptor gene duplications.

Modulation of maternal immune system during pregnancy in the cow

There is a molecular crosstalk between the trophoblast and maternal immune cells of bovine endometrium. The uterine cells are able to secrete cytokine/chemokines to either induce a suppressive environment for establishment of the pregnancy or to recruit immune cells to the endometrium to fight infections. Despite morphological differences between women and cows, mechanisms for immune tolerance during pregnancy seem to be conserved. Mechanisms for uterine immunesuppression in the cow include: reduced expression of major histocompatability proteins by the trophoblast; recruitment of macrophages to the pregnant endometrium; and modulation of immune-related genes in response to the presence of the conceptus. Recently, an eGFP transgenic cloned embryo model developed by our group showed that there is modulation of foetal proteins expressed at the site of syncytium formation, suggesting that foetal cell can regulate not only by the secretion of specific factors such as interferon-tau, but also by regulating their own protein expression to avoid excessive maternal recognition by the local immune system. Furthermore, foetal DNA can be detected in the maternal circulation; this may reflect the occurrence of an invasion of trophoblast cells and/or their fragment beyond the uterine basement membrane in the cow. In fact, the newly description of exosome release by the trophoblast cell suggests that could be a new fashion of maternal-foetal communication at the placental barrier. Additionally, recent global transcriptome studies on bovine endometrium suggested that the immune system is aware, from an immunological point of view, of the presence of the foetus in the cow during early pregnancy.

Evolution of Placental Function in Mammals: The Molecular Basis of Gas and Nutrient Transfer, Hormone Secretion, and Immune Responses

Placenta has a wide range of functions. Some are supported by novel genes that have evolved following gene duplication events while others require acquisition of gene expression by the trophoblast. Although not expressed in the placenta, high-affinity fetal hemoglobins play a key role in placental gas exchange. They evolved following duplications within the beta-globin gene family with convergent evolution occurring in ruminants and primates. In primates there was also an interesting rearrangement of a cassette of genes in relation to an upstream locus control region. Substrate transfer from mother to fetus is maintained by expression of classic sugar and amino acid transporters at the trophoblast microvillous and basal membranes. In contrast, placental peptide hormones have arisen largely by gene duplication, yielding for example chorionic gonadotropins from the luteinizing hormone gene and placental lactogens from the growth hormone and prolactin genes. There has been a remarkable degree of convergent evolution with placental lactogens emerging separately in the ruminant, rodent, and primate lineages and chorionic gonadotropins evolving separately in equids and higher primates. Finally, coevolution in the primate lineage of killer immunoglobulin-like receptors and human leukocyte antigens can be linked to the deep invasion of the uterus by trophoblast that is a characteristic feature of human placentation.

Conceptus-endometrium crosstalk during maternal recognition of pregnancy in cattle

Successful growth and development of the posthatching blastocyst and pregnancy establishment are a result of the interaction between a competent embryo and a receptive uterine environment. We examined the global transcriptome profiles of the Day 16 bovine conceptus and pregnant endometrium tissues using RNA-Seq to identify genes that contribute to the dialogue during the period of pregnancy recognition. Using stringent filtering criterion, a total of 16 018 and 16 262 transcripts of conceptus and pregnant endometrium origin, respectively, were identified with distinct tissue-specific expression profiles. Of these, 2261 and 2505 transcripts were conceptus and endometrium specific. Using Cytoscape software, a total of 133 conceptus ligands that interact with corresponding receptors on the endometrium and 121 endometrium ligands that interact with corresponding receptors on the conceptus were identified. While 87 ligands were commonly detected, 46 were conceptus specific and 34 endometrium specific. This study is one of the first to provide a comprehensive list of potentially secreted molecules in the conceptus that interact with receptors on the endometrium and vice versa during the critical window of maternal recognition of pregnancy. The identified tissue-specific genes may serve as candidates to study pregnancy recognition and they or downstream products may represent potential early markers of pregnancy.

Gene expression in placentation of farm animals: an overview of gene function during development

Eutherian mammals share a common ancestor that evolved into two main placental types, i.e., hemotrophic (e.g., human and mouse) and histiotrophic (e.g., farm animals), which differ in invasiveness. Pregnancies initiated with assisted reproductive techniques (ART) in farm animals are at increased risk of failure; these losses were associated with placental defects, perhaps due to altered gene expression. Developmentally regulated genes in the placenta seem highly phylogenetically conserved, whereas those expressed later in pregnancy are more species-specific. To elucidate differences between hemotrophic and epitheliochorial placentae, gene expression data were compiled from microarray studies of bovine placental tissues at various stages of pregnancy. Moreover, an in silico subtractive library was constructed based on homology of bovine genes to the database of zebrafish - a nonplacental vertebrate. In addition, the list of placental preferentially expressed genes for the human and mouse were collected using bioinformatics tools (Tissue-specific Gene Expression and Regulation [TiGER] - for humans, and tissue-specific genes database (TiSGeD) - for mice and humans). Humans, mice, and cattle shared 93 genes expressed in their placentae. Most of these were related to immune function (based on analysis of gene ontology). Cattle and women shared expression of 23 genes, mostly related to hormonal activity, whereas mice and women shared 16 genes (primarily sexual differentiation and glycoprotein biology). Because the number of genes expressed by the placentae of both cattle and mice were similar (based on cluster analysis), we concluded that both cattle and mice were suitable models to study the biology of the human placenta.

Review: Toward an integrated evolutionary understanding of the mammalian placenta

The placenta is fundamentally important for the success of pregnancy. Disruptions outside the normal range for placental function can result in pregnancy failure and other complications. The anatomy of the placenta varies greatly across mammals, as do key parameters in pregnancy such as neonatal body mass, length of gestation and number of offspring per pregnancy. An accurate understanding of the evolution of the mammalian placenta will require at minimum the integration of anatomical, developmental, physiological, genetic, and epigenetic data. Currently available data suggest that the placenta is a dynamic organ that has evolved rapidly in a lineage specific manner. Examination of the placenta from the perspective of human evolution shows that many anatomical features of the human placenta are relatively conserved. Despite the anatomical conservation of the human placenta there are many recently evolved placenta-specific genes (e.g. CGB, LGALS13, GH2) that are important in the development and function of the human placenta. Other mammalian genomes have also evolved specific suites of placenta-expressed genes. For example, rodents have undergone expansions of the cathepsin and prolactin families, and artiodactyls have expanded their suite of pregnancy-associated glycoproteins. In addition to lineage specific birth and death of gene family members, the pattern of imprinted loci varies greatly among species. Taken together, these studies suggest that a strategy reliant upon the sampling of placentally expressed and imprinted genes from a phylogenetically diverse range of species is appropriate for unraveling the conserved and derived aspects of placental biology.

Cleaved bovine prolactin-related protein-I stimulates vascular endothelial cell proliferation

Prolactin-related protein-I (PRP1) is a member of a non-classical prolactin (PRL)/growth hormone family in cattle. However, its function is still unknown. PRL, when cleaved by cathepsin D and matrix metalloproteinases (MMPs), resulted in cleaved N-terminal 16kDa fragments (16K-PRL) that have antiangiogenetic properties in human and rodents. We examined the possibility of similar activity of bovine PRP1. PRP1 (normally 33kDa) was cleaved by cathepsins (CTSs), MMPs, and bovine cotyledonary-conditioned medium (BCCM), and generated mainly 26kDa N-terminal fragments. Two specific enzyme families, CTSs and MMPs cleaved intact PRP1, and BCCM also contained PRP1 cleavage activity. Bioactivity for pro- or anti-angiogenesis of the cleaved PRP1 was examined in a cell proliferation assay using bovine brain vascular endothelial cells. The cleaved PRP1 proliferated the endothelial cells in vitro. The endothelial cell proliferation activity of cleaved PRP1 may be shared in specific bovine placentomal angiogenesis.

Functional annotation of novel lineage-specific genes using co-expression and promoter analysis

Background

The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific transcripts (LSTs) from a cow term-placenta cDNA library, which are excellent candidates for adaptive placental functions acquired by the ruminant lineage. The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis.

Results

Clusters of co-expressed genes preferentially expressed in liver, placenta and thymus were found using 49 previously uncharacterized LSTs as seeds. Over-represented composite transcription factor binding sites (TFBS) in promoters of clustered LSGs and known genes were then identified computationally. Functions were inferred for nine previously uncharacterized LSGs using co-expression analysis and pathway analysis tools. Our results predict that these LSGs may function in cell signaling, glycerophospholipid/fatty acid metabolism, protein trafficking, regulatory processes in the nucleus, and processes that initiate parturition and immune system development.

Conclusions

The placenta is a rich source of lineage-specific genes that function in the adaptive evolution of placental architecture and functions. We have shown that co-expression, promoter, and gene network analyses are useful methods to infer functions of LSGs with heretofore unknown functions. Our results indicate that many LSGs are involved in cellular recognition and developmental processes. Furthermore, they provide guidance for experimental approaches to validate the functions of LSGs and to study their evolution.

The genome sequence of taurine cattle: a window to ruminant biology and evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6

BACKGROUND

Linkage analyses strongly suggest a number of QTL for production, health and conformation traits in the middle part of bovine chromosome 6 (BTA6). The identification of the molecular background underlying the genetic variation at the QTL and subsequent functional studies require a well-annotated gene sequence map of the critical QTL intervals. To complete the sequence map of the defined subchromosomal regions on BTA6 poorly covered with comparative gene information, we focused on targeted isolation of transcribed sequences from bovine bacterial artificial chromosome (BAC) clones mapped to the QTL intervals.

RESULTS

Using the method of exon trapping, 92 unique exon trapping sequences (ETS) were discovered in a chromosomal region of poor gene coverage. Sequence identity to the current NCBI sequence assembly for BTA6 was detected for 91% of unique ETS. Comparative sequence similarity search revealed that 11% of the isolated ETS displayed high similarity to genomic sequences located on the syntenic chromosomes of the human and mouse reference genome assemblies. Nearly a third of the ETS identified similar equivalent sequences in genomic sequence scaffolds from the alternative Celera-based sequence assembly of the human genome. Screening gene, EST, and protein databases detected 17% of ETS with identity to known transcribed sequences. Expression analysis of a subset of the ETS showed that most ETS (84%) displayed a distinctive expression pattern in a multi-tissue panel of a lactating cow verifying their existence in the bovine transcriptome.

CONCLUSION

The results of our study demonstrate that the exon trapping method based on region-specific BAC clones is very useful for targeted screening for novel transcripts located within a defined chromosomal region being deficiently endowed with annotated gene information. The majority of identified ETS represents unknown noncoding sequences in intergenic regions on BTA6 displaying a distinctive tissue-specific expression profile. However, their definite regulatory function has to be analyzed in further studies. The novel transcripts will add new sequence information to annotate a complete bovine genome sequence assembly, contribute to establish a detailed transcription map for targeted BTA6 regions and will also be helpful to dissect of the molecular and regulatory background of the QTL detected on BTA6.

The characterization of DNA methylation-mediated regulation of bovine placental lactogen and bovine prolactin-related protein-1 genes

Background

Bovine trophoblast binucleate cells (BNC) express a plethora of molecules including bovine placental lactogen (bPL, gene name is bCSH1) and bovine prolactin-related protein-1 (bPRP1). BCSH1 and bPRP1 are members of the growth hormone (GH)/prolactin (PRL) gene family, which are expressed simultaneously in BNC and are central to placentation and the progression of pregnancy in cattle. However, there is a paucity of information on the transcriptional regulatory mechanisms of both the bCSH1 and bPRP1 genes. Recent studies, however, have demonstrated that the expression of a number of genes is controlled by the methylation status of their promoter region. In the present study, we examined the cell-type-specific epigenetic alterations of the 5'-flanking region of the bCSH1 and bPRP1 genes to gain an insight into their regulatory mechanisms.

Results

Analysis of 5-aza-2'-deoxycytidine treatment demonstrated that bCSH1 expression is moderately induced in fibroblast cultures but enhanced in BT-1 cells. Sodium bisulfite based sequencing revealed that bCSH1 is hypomethylated in the cotyledonary tissue but not in the fetal skin, and this pattern was not altered with the progression of pregnancy. On the other hand, the methylation status of bPRP1 was similar between the cotyledon and fetal skin. The bPRP1 gene was exclusively hypermethylated in a bovine trophoblast cell-derived BT-1 cell-line. While the activity of bCSH1 was similar in both BT-1 and bovine fibroblast cells, that of bPRP1 was specific to BT-1. Treatment with a demethylating agent and luciferase assays provided in vitro evidence of the positive regulation of bCSH1 but not bPRP1.

Conclusion

This is the first report to identify the differential regulatory mechanisms of the bCSH1 and bPRP1 genes and indicates that bCSH1 might potentially be the only transcript that is subject to DNA methyltransferase regulation. The data indicates the possibility of novel kinetics of induction of the synchronously expressed BNC-specific bCSH1 and bPRP1 transcripts, which may aid the understanding of the intricate regulation and specific role(s) of these important molecules in bovine placentogenesis and the progression of pregnancy.

Multiple duplication of the bucentaur gene family, which recruits the APE-like domain of retrotransposon: Identification of a novel homolog and distinct cellular expression

The p97bcnt/cfdp2 is a ruminant-specific gene created by a combination of gene duplication of ancestral bcnt (bucentaur) or cfdp1 (craniofacial developmental protein 1), bcnt/cfdp1, and the insertion of a retrotransposable element-1 (RTE). As a result, p97Bcnt recruits the whole apurinic/apyrimidinic endonuclease (APE)-like domain of RTE in the middle of the molecule (RTE domain) as a region encoded by an exon. In addition, p97Bcnt contains two intramolecular repeats (IRs) of 40 amino acids each in the C-terminal region, whereas Bcnt/Cfdp1 contains one IR. We have identified an additional bovine homolog with a structure highly similar to p97Bcnt, designated p97Bcnt2, which contains three IRs. p97bcnt2 is located in tandem with bcnt/cfdp1 and p97bcnt within a 177-kb range on bovine chromosome 18, a syntenic region of human chromosome 16. The gene product is expressed as a protein with an apparent molecular mass of 102 kDa. The phylogenetic tree strongly suggests that p97bcnt-2 forms a third clade of the bcnt family and that the first duplication of the IR unit occurred prior to the divergence of p97bcnt and p97bcnt-2. To address the question of whether these bcnt members have distinct functions, we first examined the expression and localization of the p97Bcnt family members. p97Bcnt is substantially expressed in many tissues involved in responses to external and internal stress. In the testis, p97Bcnt localizes preferentially in the nuclei of spermatozoa, while Bcnt/Cfdp1 localizes predominantly in the cytosol of Leydig cells and some spermatogenic cells, implying that at least these two molecules of the Bcnt family play different functional roles. These results provide evidence for the direct contribution of RTE to gene diversity to form gene families that may support cellular function.

Biological interpretations of transcriptomic profiles in mammalian oocytes and embryos

The characterization of gene-expression profiles in oocytes and embryos is critical to understand the influence of genetic and environmental factors on preimplantation and fetal development. Numerous gene-expression microarray studies using different platforms and species are offering insights into the biological processes extensively represented among the genes exhibiting differential expression. Major advances on understanding the direct relationship between gene expression and developmental competence are being reported. Integration of information across studies using meta-analysis techniques can increase the precision and accuracy to identify expression profiles associated with embryo development. Gene network and pathway analyses are offering insights into gene interactions and expression profiles of embryos. All these advances are cementing the way toward a comparative and systems approach to understanding the complex processes underlying vertebrate development.

Expression and characterization of novel ovine orthologs of bovine placental prolactin-related proteins

Background

The prolactin-related proteins (PRPs) are non-classical placental-specific members of the prolactin/growth hormone family. Among ruminants, they are expressed in the cotyledonary villi of cattle and goat. We investigated placental PRP in sheep in order to gain a comprehensive understanding of the function and evolution of these molecules. We also examined the sequence properties, expression and lactogenic activation of the cloned genes.

Results

We cloned two novel ovine PRPs, named oPRP1 and oPRP2. oPRP2 had a typical PRP sequence similar to bovine PRP1 (bPRP1). oPRP1 had a short sequence identical with bovine or caprine type PRP but the reading frame was shifted. Both oPRPs were expressed in trophoblast giant binucleate cells (BNC) as in cattle and goat. oPRP1 expression declined from the early to the middle stage of gestation. In contrast, oPRP2 expression remained constant throughout the gestation period. oPRP2 was translated to form a mature protein in a mammalian cell expression system. Western blotting showed a molecular mass of 35 kDa for the FLAG-tag fusion oPRP2 protein. This recombinant protein and bPRP1 were bioassayed using Nb2 lymphoma cells; it was confirmed that neither ruminant PRP had lactogenic activity because the Nb2 lymphoma cells did not proliferate.

Conclusion

We have identified two novel PRPs, oPRP1 and oPRP2, in ovine placenta. Both these ovine PRPs were localized and quantitatively expressed in BNC. Absence of lactogenic activity was confirmed for the oPRP2 molecule. It is anticipated that novel and known ruminant PRPs have common functions, except for lactogenic activity.

Discovery and characterization of 91 novel transcripts expressed in cattle placenta

Background

Among the eutherian mammals, placental architecture varies to a greater extent than any other tissue. The diversity of placental types, even within a single mammalian order suggests that genes expressed in placenta are under strong Darwinian selection. Thus, the ruminant placenta may be a rich source of genes to explore adaptive evolutionary responses in mammals. The aim of our study was to identify novel transcripts expressed in ruminant placenta, and to characterize them with respect to their expression patterns, organization of coding sequences in the genome, and potential functions.

Results

A combination of bioinformatics, comparative genomics and transcript profiling was used to identify and characterize 91 novel transcripts (NTs) represented in a cattle placenta cDNA library. These NTs have no significant similarity to any non-ferungulate DNA or RNA sequence. Proteins longer than 100 aa were predicted for 29 NTs, and 21 are candidate non-coding RNAs. Eighty-six NTs were found to be expressed in one or more of 18 different tissues, with 39 (42%) showing tissue-preference, including six that were expressed exclusively in placentome. The authenticity of the NTs was confirmed by their alignment to cattle genome sequence, 42 of which showed evidence of mRNA splicing. Analysis of the genomic context where NT genes reside revealed 61 to be in intergenic regions, whereas 30 are within introns of known genes. The genes encoding the NTs were found to be significantly associated with subtelomeric regions.

Conclusion

The 91 lineage-specific transcripts are a useful resource for studying adaptive evolutionary responses of the ruminant placenta. The presence of so many genes encoding NTs in cattle but not primates or rodents suggests that gene loss and gain are important mechanisms of genome evolution in mammals. Furthermore, the clustering of NT genes within subtelomeric regions suggests that such regions are highly dynamic and may foster the birth of novel genes. The sequencing of additional vertebrate genomes with defined phylogenetic relationships will permit the search for lineage-specific genes to take on a more evolutionary context that is required to understand their origins and functions.

The prolactin family: effectors of pregnancy-dependent adaptations

Prolactin (PRL) is a hormone involved in many biological functions. In some species, there is a family of PRL-related genes; such is the case in the mouse and rat. The actions of members of the PRL family can be distinguished based on the involvement of the PRL receptor signaling pathway (classical versus nonclassical). Recent insights into the biology of the PRL family have been derived from mouse mutagenesis studies. There is compelling evidence suggesting that the PRL family contributes to the regulation of pregnancy-dependent adaptations to physiological stressors.

Gene expression profiles of novel caprine placental prolactin-related proteins similar to bovine placental prolactin-related proteins

Background

This study reports the identification of a full-length cDNA sequence for two novel caprine prolactin-related proteins (cPRP1 and cPRP6), and their localization and quantitative expression in the placenta. Caprine PRPs are compared with known bovine PRPs. We examined their evolution and role in the ruminant placenta.

Results

Full-length cPRP1 and cPRP6 cDNA were cloned with a 717- and 720- nucleotide open-reading frame corresponding to proteins of 238 and 239 amino acids. The cPRP1 predicted amino acid sequence shares a 72% homology with bovine PRP1 (bPRP1). The cPRP6 predicted amino acid sequence shares a 74% homology with bovine PRP6 (bPRP6). The two cPRPs as well as bPRPs were detected only in the placentome by RT-PCR. Analysis by in situ hybridization revealed the presence of both cPRPs mRNA in the trophoblast binucleate cells. These mRNA were quantified by real-time RT-PCR analysis of the placentome at 30, 50, 90 and 140 days of pregnancy. Both new cPRP genes were able to translate a mature protein in a mammalian cell-expression system. Western blotting established the molecular sizes of 33 kDa for cPRP1 with FLAG-tag and 45 kDa for cPRP6 with FLAG-tag. The sequence properties and localized expression of cPRP1 and cPRP6 were similar to those of bovine. However, their expression profiles differed from those in bovine placenta. Although this study demonstrated possible roles of PRPs in caprine placenta, PRPs may regulate binucleate-cell functions like those in bovine, but their crucial roles are still unclear.

Conclusion

We have identified the novel PRPs in caprine placenta. Localization and quantitative expression of caprine PRPs were compared with bovine PRPs. The data indicate that PRP genes in caprine placenta have coordination functions for gestation, as they do in bovine. This is the first study of PRPs function in caprine placenta.

Gene expression and maintenance of pregnancy in bovine: roles of trophoblastic binucleate cell-specific molecules

Cell to cell interaction plays a pivotal role in the regulation of placentogenesis and exchange of stage-specific developmental signals between the fetal and maternal units. Specifically, these interactions are paramount for programmed fetal growth, maternal adaptation to pregnancy and coordination of parturition. However, little is known about the precise regulation of placentation and maintenance of gestation in cattle. Therefore, the aim of the present study was to decipher the complex networks of cell communication to gain an insight into the multifaceted developmental process and understand the profound consequences of flawed communication. In the ruminant, the binucleate cell plays a central role in forming the structures and secretions at the fetomaternal interface that are crucial in establishing and maintaining pregnancy. Herein, we summarise differences in the abundance of specific RNA transcripts in the bovine cotyledon and caruncle using global gene expression profiling and further investigate the relationship of mRNA abundance for selected pregnancy-specific genes of interest (identified from microarray studies) that are localised exclusively to the binucleate cell, such as placental lactogen, prolactin-related proteins and pregnancy-associated glycoproteins. The results suggest that a well-orchestrated transcriptional command from binucleate cells is pivotal to the establishment and progression of pregnancy in cattle.