Detection of differentially expressed genes between Erhualian and Large White placentas on day 75 and 90 of gestation

Polymorphism Identification in the Coding Sequences (ORFs) of the Porcine Pregnancy-Associated Glycoprotein 2-like Gene Subfamily in Pigs

Pregnancy-associated glycoproteins (PAGs) are a polygenic family with many scattered genes and pseudogenes resulting from the duplication or fusion of a pseudogene with expression beginning in the trophoblast during the peri-implantation period and continuing in the trophectoderm. In this study, single-nucleotide polymorphism (SNP) and insertion/deletion (InDels) in the open reading frame (nine exons) of crossbreed pigs are reported for the first time. Novel SNPs/InDels were researched using genomic DNA templates isolated from the leukocytes of crossbreed pigs (N = 25), which were amplified, gel-out-purified, and sequenced. Sixteen SNPs and one InDel (g.6961_6966 Ins TGCCAA) were identified in the crossbreed pigs. In silico analysis revealed that among 16 SNPs, only 10 SNPs cause amino acid (aa) substitutions, and InDel codes asparagine (N298) and alanine (A299). The results provide a novel broad-based database (main pattern) that will be critical for future research into the possible correlations between the SNP genotypes of the pPAG2-L subfamily in pigs of various breeds whose reproductive traits are known.

Hypoxia-inducible factor 1 signaling drives placental aging and can provoke preterm labor

Most cases of preterm labor have unknown cause, and the burden of preterm birth is immense. Placental aging has been proposed to promote labor onset, but specific mechanisms remain elusive. We report findings stemming from unbiased transcriptomic analysis of mouse placenta, which revealed that hypoxia-inducible factor 1 (HIF-1) stabilization is a hallmark of advanced gestational timepoints, accompanied by mitochondrial dysregulation and cellular senescence; we detected similar effects in aging human placenta. In parallel in primary mouse trophoblasts and human choriocarcinoma cells, we modeled HIF-1 induction and demonstrated resultant mitochondrial dysfunction and cellular senescence. Transcriptomic analysis revealed that HIF-1 stabilization recapitulated gene signatures observed in aged placenta. Further, conditioned media from trophoblasts following HIF-1 induction promoted contractility in immortalized uterine myocytes, suggesting a mechanism by which the aging placenta may drive the transition from uterine quiescence to contractility at the onset of labor. Finally, pharmacological induction of HIF-1 via intraperitoneal administration of dimethyloxalyl glycine (DMOG) to pregnant mice caused preterm labor. These results provide clear evidence for placental aging in normal pregnancy, and demonstrate how HIF-1 signaling in late gestation may be a causal determinant of the mitochondrial dysfunction and senescence observed within the trophoblast as well as a trigger for uterine contraction.

Genomic Imprinting at the Porcine DIRAS3 Locus

Simple Summary

DNA methylation associated with one of the two alleles from parents is an important mechanism that causes a silencing of that allele, leading to expression of another allele only. There has been a lack of detailed studies on DNA methylation and expression patterns that are related to the DIRAS3 gene in pigs. The objective of this study was to provide a comprehensive overview of DNA methylation and expression associated with the DIRAS3 gene in pigs by generating an embryonic pig model and analyzing next-generation sequencing using pig embryos and adult pigs. Our results clearly showed the presence of DNA methylation near the DIRAS3 gene in pigs and high expression of DIRAS3 in the hypothalamus from adult pigs and expression of only one allele in all the tested tissues including the hypothalamus. In summary, our findings suggested DNA methylation might be related to those unique gene expression patterns during the development of pigs.

Abstract

The epigenetic mechanisms underlying genomic imprinting include DNA methylation and monoallelic expression of genes in close proximity. Although genes imprinted in humans and mice have been widely characterized, there is a lack of detailed and comprehensive studies in livestock species including pigs. The purpose of this study was to investigate a detailed methylation status and parent-of-origin-specific gene expression within the genomic region containing an underexamined porcine DIRAS3 locus. Through whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of porcine parthenogenetic embryos and analyses of public RNA-seq data from adult pigs, DNA methylation and monoallelic expression pattern were investigated. As a result, maternal hypermethylation at the DIRAS3 locus and hypothalamus-specific and monoallelic expression of the DIRAS3 gene were found in pigs. In conclusion, the findings from this study suggest that the presence of maternal hypermethylation, or imprints, might be maintained and related to monoallelic expression of DIRAS3 during pig development.

The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation

Background

Placental efficiency (PE) describes the relationship between placental and fetal weights (fetal wt/placental wt). Within litters, PE can vary drastically, resulting in similarly sized pigs associated with differently sized placentas, up to a 25% weight difference. However, the mechanisms enabling the smaller placenta to grow a comparable littermate are unknown. To elucidate potential mechanisms, morphological measurements and gene expression profiles in placental and associated endometrial tissues of high PE and low PE feto-placental units were compared. Tissue samples were obtained from eight maternal line gilts during gestational day 95 ovario-hysterectomies. RNA was extracted from tissues of feto-placental units with the highest and lowest PE in each litter and sequenced.

Results

Morphological measurements, except placental weight, were not different (P > 0.05) between high and low PE. No DEG were identified in the endometrium and 214 DEG were identified in the placenta (FDR < 0.1), of which 48% were upregulated and 52% were downregulated. Gene ontology (GO) analysis revealed that a large percentage of DEG were involved in catalytic activity, binding, transporter activity, metabolism, biological regulation, and localization. Four GO terms were enriched in the upregulated genes and no terms were enriched in the downregulated genes (FDR < 0.05). Eight statistically significant correlations (P < 0.05) were identified between the morphological measurements and DEG.

Conclusion

Morphological measures between high and low PE verified comparisons were of similarly sized pigs grown on different sized placentas, and indicated that any negative effects of a reduced placental size on fetal growth were not evident by day 95. The identification of DEG in the placenta, but absence of DEG in the endometrium confirmed that the placenta responds to the fetus. The GO analyses provided evidence that extremes of PE are differentially regulated, affecting components of placental transport capacity like nutrient transport and blood flow. However, alternative GO terms were identified, indicating the complexity of the relationship between placental and fetal weights. These findings support the use of PE as a marker of placental function and provide novel insight into the genetic control of PE, but further research is required to make PE production applicable.

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs

Development of placental folds is a critical event affecting placental function in pigs because it can increase surface area for improvement in capillary density as gestation advances. However, the molecular mechanisms of the event are not well defined. Histone modifications have important roles in gene regulation. To investigate their effects on regulation of genes controlling porcine placental development, RNA-seq and ChIP-seq of porcine placental tissues from gestational days 50 (establishment stage of placental folds) and 95 (expanding stage of placental folds) were carried out in this study. The differentially expressed genes were identified and of which the down- and up-regulated genes are related to endoplasmic reticulum (ER) stress and angiogenesis, respectively. In addition, we mapped the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), which are associated with transcriptional activation. A number of differential modification regions between the 2 gestational stages were identified and majority of them are those with increased signals of H3K4me3 (14,576 out of 16,931). Furthermore, we observed that the increase of H3K4me3 is significantly correlated with the elevated expression levels of the neighboring genes, and notably, these genes were enriched in pathways related to blood vessel formation and microvascular permeability. Taken together, the findings suggest important roles of histone modifications on placental remolding in response to developmental changes.

Immunohistochemical determination of Ang-1, Ang-2 and Tie-2 in placentas of sows at 30, 60 and 114 days of gestation and validation through a bioinformatic approach

Angiopoietins (Ang-1, Ang-2) participate in vascular development and placental growth, both bind to Tie-2. This study aimed to determine the localization of angiopoietins in placental development of sows by immunohistochemistry and to validate the gene expression during gestation through a bioinformatic approach. Samples were collected from fifteen maternal-fetal interface from approximately 30 (n = 5), 60 (n = 5) and 114 (n = 5) days of gestation for immunohistochemistry. A bioinformatic approach was performed by re-analysis of public datasets to determine the increase or decrease of genes involved in angiogenesis during pregnancy. There was no significant statistical difference of Ang-1 during gestation, although there was a tendency to increase from mid- to term-gestation (P = 0.7680). A notable decrease of Ang-2 was observed from early- to term-pregnancy (P ≤ 0.05), consistent with the gene expression determined through bioinformatics. Furthermore, there were greater abundances of Tie-2 at both early and at term periods, but lesser abundances at mid-gestation (P ≤ 0.05). The bioinformatics approach indicated that genes related to biological processes such as angiogenesis (i.e., development and morphogenesis of blood vessels) were expressed to a greater extent in early gestation as compared with later in gestation. The Ang-1 gene expression related to cell maturation, response to hypoxia and apoptosis, however, increased as gestation period advanced. In conclusion, angiopoietins may have an important role in the vascular development thus ensuring adequate placental growth in sows. The presence of angiopoietins in the trophoblast suggests a specific role for these pro-angiogenic factors in the tissue formation at the maternal-fetal interface.

Breeding animals for quality products: not only genetics

The effect of the Developmental Origins of Health and Disease on the spread of non-communicable diseases is recognised by world agencies such as the United Nations and the World Health Organization. Early environmental effects on offspring phenotype also apply to domestic animals and their production traits. Herein, we show that maternal nutrition not only throughout pregnancy, but also in the periconception period can affect offspring phenotype through modifications of gametes, embryos and placental function. Because epigenetic mechanisms are key processes in mediating these effects, we propose that the study of epigenetic marks in gametes may provide additional information for domestic animal selection.

Osteoarthritis in the Knee Joints of Göttingen Minipigs after Resection of the Anterior Cruciate Ligament? Missing Correlation of MRI, Gene and Protein Expression with Histological Scoring

Introduction

The Göttingen Minipig (GM) is used as large animal model in articular cartilage research. The aim of the study was to introduce osteoarthritis (OA) in the GM by resecting the anterior cruciate ligament (ACLR) according to Pond and Nuki, verified by histological and magnetic resonance imaging (MRI) scoring as well as analysis of gene and protein expression.

Materials and Methods

The eight included skeletally mature female GM were assessed after ACLR in the left and a sham operation in the right knee, which served as control. 26 weeks after surgery the knee joints were scanned using a 3-Tesla high-field MR tomography unit with a 3 T CP Large Flex Coil. Standard proton-density weighted fat saturated sequences in coronal and sagittal direction with a slice thickness of 3 mm were used. The MRI scans were assessed by two radiologists according to a modified WORMS-score, the X-rays of the knee joints by two evaluators. Osteochondral plugs with a diameter of 4mm were taken for histological examination from either the main loading zone or the macroscopic most degenerated parts of the tibia plateau or condyle respectively. The histological sections were blinded and scored by three experts according to Little et al. Gene expression analysis was performed from surrounding cartilage. Expression of adamts4, adamts5, acan, col1A1, col2, il-1ß, mmp1, mmp3, mmp13, vegf was determined by qRT-PCR. Immunohistochemical staining (IH) of Col I and II was performed. IH was scored using a 4 point grading (0—no staining; 3-intense staining).

Results and Discussion

Similar signs of OA were evident both in ACLR and sham operated knee joints with the histological scoring result of the ACLR joints with 6.48 ± 5.67 points and the sham joints with 6.86 ± 5.84 points (p = 0.7953) The MRI scoring yielded 0.34 ± 0.89 points for the ACLR and 0.03 ± 0.17 for the sham knee joints. There was no correlation between the histological and MRI scores (r = 0.10021). The gene expression profiles as well as the immunohistochemical findings showed no significant differences between ACLR and sham knee joints. In conclusion, both knee joints showed histological signs of OA after 26 weeks irrespective of whether the ACL was resected or not. As MRI results did not match the histological findings, MRI was obviously unsuitable to diagnose the OA in GM. The analysis of the expression patterns of the 10 genes could not shed light on the question, whether sham operation also induced cartilage erosion or if the degeneration was spontaneous. The modified Pond-Nuki model may be used with reservation in the adult minipig to induce an isolated osteoarthritis.

Expression of genes involved in progesterone receptor paracrine signaling and their effect on litter size in pigs

Background

Embryonic mortality during the period of implantation strongly affects litter size in pigs. Progesterone receptor (PGR) paracrine signaling has been recognized to play a significant role in embryonic implantation. IHH, NR2F2, BMP2, FKBP4 and HAND2 were proved to involve in PGR paracrine signaling. The objective of this study was to evaluate the expression of IHH, NR2F2, BMP2, FKBP4 and HAND2 in endometrium of pregnant sows and to further investigate these genes’ effect on litter size in pigs. Real-time PCR, western blot and immunostaining were used to study target genes/proteins expression in endometrium in pigs. RFLP-PCR was used to detect single nucleotide polymorphisms (SNPs) of target genes.

Results

The results showed that the mRNA and protein expression levels of IHH, NR2F2 and BMP2 were up-regulated during implantation period (P < 0.05 or P < 0.01). All target proteins were mainly observed in luminal epithelium and glandular epithelium. Interestingly, the staining of NR2F2 and HAND2 was also strong in stroma. SNPs detection revealed that there was a -204C > A mutation in promoter region of NR2F2 gene. Three genotypes were found in Large White, Landrace and Duroc sows. A total of 1847 litter records from 625 sows genotyped at NR2F2 gene were used to analyze the total number born (TNB) and number born alive (NBA). The study of the effect on litter size suggested that sows with genotype CC tend to have higher litter size.

Conclusions

These results showed the expression patterns of genes/proteins involved in PGR paracrine signaling over implantation time. And the candidate gene for litter size was identified from genes involved in this signaling. This study could be a resource for further studies to identify the roles of these genes for embryonic implantation in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s40104-016-0090-z) contains supplementary material, which is available to authorized users.

Endometrial gene expression profile of pregnant sows with extreme phenotypes for reproductive efficiency

Prolificacy can directly impact porcine profitability, but large genetic variation and low heritability have been found regarding litter size among porcine breeds. To identify key differences in gene expression associated to swine reproductive efficiency, we performed a transcriptome analysis of sows' endometrium from an Iberian x Meishan F2 population at day 30-32 of gestation, classified according to their estimated breeding value (EBV) as high (H, EBV > 0) and low (L, EBV < 0) prolificacy phenotypes. For each sample, mRNA and small RNA libraries were RNA-sequenced, identifying 141 genes and 10 miRNAs differentially expressed between H and L groups. We selected four miRNAs based on their role in reproduction, and five genes displaying the highest differences and a positive mapping into known reproductive QTLs for RT-qPCR validation on the whole extreme population. Significant differences were validated for genes: PTGS2 (p = 0.03; H/L ratio = 3.50), PTHLH (p = 0.03; H/L ratio = 3.69), MMP8 (p = 0.01; H/L ratio =4.41) and SCNN1G (p = 0.04; H/L ratio = 3.42). Although selected miRNAs showed similar expression levels between H and L groups, significant correlation was found between the expression level of ssc-miR-133a (p < 0.01) and ssc-miR-92a (p < 0.01) and validated genes. These results provide a better understanding of the genetic architecture of prolificacy-related traits and embryo implantation failure in pigs.

The Expression Pattern of MicroRNAs and the Associated Pathways Involved in the Development of Porcine Placental Folds That Contribute to the Expansion of the Exchange Surface Area

The development of the microscopically folded structure of the diffuse epitheliochorial placenta in pigs is important because it expands the surface area for maternal-fetal exchange, resulting in an increase in placental efficiency. To better understand the regulatory mechanisms involved in this process, we characterized miRNA expression profiles in porcine placentas during the initiation and establishment of placental fold development. A total of 42 miRNAs were found to be differentially expressed, and their putative target genes were predicted using four target prediction programs. Following a comparative analysis with published gene expression pattern data obtained from porcine placentas in the corresponding stages of placental fold development, only those genes that were negatively correlated with miRNA expression were retained for further function and pathway enrichment analysis. The results showed that the up-regulated miRNAs were associated mainly with extracellular matrix remodeling and tissue morphogenesis, while the down-regulated miRNAs were related to cell proliferation and signal transduction. Furthermore, we provide evidence that miR-130b may facilitate the expression of HPSE, which has been reported to be a regulator of the folding of the pig placenta, by suppressing the expression of PPARG. In addition, we also reveal that the miRNA-target pairs expressed in the pig placenta may trigger the degradation of the stromal matrix and basement membrane (miR-29a-COL1A2, COL3A1, and LAMC1) and regulate trophoblast epithelial cell adherens junctions (the miR-200 family and miR-205-ZEB2-CDH1) and proliferation (miR-17-92 cluster-HBP1 and ULK1). Taken together, these results indicate that miRNAs and related pathways may have potential roles in porcine placental fold development.

The novel porcine gene early growth response 4 (Egr4) is differentially expressed in the ovaries of Erhualian and Pietrain pigs

The early growth response 4 (Egr4) gene plays a critical role in human and mouse fertility. In the present study, Affymetrix microarray gene chips were used to evaluate differential gene expression in the ovaries between Erhualian and Pietrain pigs. In all, 487 and 573 transcripts were identified with significantly higher and lower expression, respectively, in Erhualian compared with Pietrain sows. The Egr4 gene, one of the differentially expressed genes, was cloned and its genomic structure was analysed. Egr4 expression is increased 120-fold in ovaries from Erhualian sows. The full-length cDNA of porcine Egr4 was obtained by in silico cloning and 5' rapid amplification of cDNA ends. The gene consists of two exons and its predicted protein contains a Cys2His2 zinc finger structure. The porcine transcript is alternatively spliced by exon sequence deletion, producing two different mRNAs differing at the 5' end of Exon 2. Egr4 transcripts were detected in the central nervous system, including the cerebrum, cerebellum, hypothalamus and pituitary gland, and were highly expressed in the ovary. The Egr4 gene was evaluated as a candidate gene for porcine reproductivity. To investigate the role of Egr4 in the ovary, Egr4 was knocked down using short interference (si) RNA in porcine granulosa cells. Knockdown of Egr4 using siRNA effectively inhibited Egr4 mRNA and protein expression and knockdown significantly affected the expression of Bax, P450arom, P450scc, Egr1, Egr2, and Egr3. In conclusion, these observations establish an important role for Egr4 in the porcine ovary.

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq

Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.

Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation

Background

Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood.

Results

We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig.

Conclusions

The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig.

Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets

Background

Mitochondria, which are essential for the functionality of eukaryotic cells, are particularly important in metabolically active tissues such as liver. Different breeds of pigs demonstrate distinct metabolic profiles in the liver, yet little is known whether the expression and transcriptional regulation of mitochondrial genes differ between breeds.

Results

Here we used male newborn Large White (LW) and Erhualian (EHL) piglets to delineate the difference in hepatic mitochondrial gene regulation between breeds. The hepatic content of ATP was significantly higher (p < 0.01) in EHL piglets, which was associated with lower mtDNA copy number (p < 0.05). Most of the mtDNA-encoded genes (10 of 13), however, were more abundantly expressed in EHL compared to LW piglets. We also detected 3 differentially expressed nuclear-encoded mitochondrial genes, among which isocitrate dehydrogenase 2 (IDH2) and ATP synthase, H⁺ transporting, mitochondrial Fo complex, subunit d (ATP5H) were expressed significantly lower, while adenylate kinase 1 (AK1) was significantly over expressed in EHL piglets. Compared to LW, the over expression of mtDNA-encoded genes in EHL was associated with significantly higher (p < 0.01) glucocorticoid receptor (GR) binding to the control region of mtDNA with no alterations in the methylation status. For nuclear-encoded genes, however, a negative correlation was observed between GR binding and mRNA expression of AK1 and ATP5H. Moreover, higher expression of AK1 in EHL piglets was also associated with lower cytosine methylation (p < 0.05) and hydroxymethylation (p < 0.05). In the promoter region.

Conclusions

These results indicate a role of the GR in the breed-dependent regulation of mitochondrial genes in the liver of newborn piglets.

Differences in X-chromosome transcriptional activity and cholesterol metabolism between placentae from swine breeds from Asian and Western origins

To gain insight into differences in placental physiology between two swine breeds noted for their dissimilar reproductive performance, that is, the Chinese Meishan and white composite (WC), we examined gene expression profiles of placental tissues collected at 25, 45, 65, 85, and 105 days of gestation by microarrays. Using a linear mixed model, a total of 1,595 differentially expressed genes were identified between the two pig breeds using a false-discovery rate q-value ≤0.05. Among these genes, we identified breed-specific isoforms of XIST, a long non-coding RNA responsible X-chromosome dosage compensation in females. Additionally, we explored the interaction of placental gene expression and chromosomal location by DIGMAP and identified three Sus scrofa X chromosomal bands (Xq13, Xq21, Xp11) that represent transcriptionally active clusters that differ between Meishan and WC during placental development. Also, pathway analysis identified fundamental breed differences in placental cholesterol trafficking and its synthesis. Direct measurement of cholesterol confirmed that the cholesterol content was significantly higher in the Meishan versus WC placentae. Taken together, this work identifies key metabolic pathways that differ in the placentae of two swine breeds noted for differences in reproductive prolificacy.

Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome

The processes that drive tissue identity and differentiation remain unclear for most tissue types. So are the gene networks and transcription factors (TF) responsible for the differential structure and function of each particular tissue, and this is particularly true for non model species with incomplete genomic resources. To better understand the regulation of genes responsible for tissue identity in pigs, we have inferred regulatory networks from a meta-analysis of 20 gene expression studies spanning 480 Porcine Affymetrix chips for 134 experimental conditions on 27 distinct tissues. We developed a mixed-model normalization approach with a covariance structure that accommodated the disparity in the origin of the individual studies, and obtained the normalized expression of 12,320 genes across the 27 tissues. Using this resource, we constructed a network, based on the co-expression patterns of 1,072 TF and 1,232 tissue specific genes. The resulting network is consistent with the known biology of tissue development. Within the network, genes clustered by tissue and tissues clustered by site of embryonic origin. These clusters were significantly enriched for genes annotated in key relevant biological processes and confirm gene functions and interactions from the literature. We implemented a Regulatory Impact Factor (RIF) metric to identify the key regulators in skeletal muscle and tissues from the central nervous systems. The normalization of the meta-analysis, the inference of the gene co-expression network and the RIF metric, operated synergistically towards a successful search for tissue-specific regulators. Novel among these findings are evidence suggesting a novel key role of ERCC3 as a muscle regulator. Together, our results recapitulate the known biology behind tissue specificity and provide new valuable insights in a less studied but valuable model species.

Molecular characterization of the Neuronatin gene in the porcine placenta

Imprinted genes play important roles in placental and embryonic development. Neuronatin (NNAT), first identified as an imprinted gene in human and mouse brains, played important roles in neuronal differentiation in the brain and in glucose-mediated insulin secretion in pancreatic β cells. In the pig, NNAT was reported to be imprinted in eleven tissues. Our previous microarray hybridization study showed that NNAT was differentially expressed in Yorkshire and Meishan pig placentas, but the imprinting status and function of NNAT in the placenta have not been investigated. We demonstrated for the first time that NNAT was monoallelically expressed in the placenta. Immunochemistry analysis showed that NNAT was located in the uterine luminal and glandular epithelium in placentas. We also confirmed the differential expression of NNAT in Meishan and Yorkshire pig placentas by qPCR. Using IPA software and the published literature, we created a model network of the possible relationships between NNAT and glucose transporter genes. A dual luciferase reporter assay demonstrated that the crucial promoter region of NNAT contained a CANNTG sequence in the +210 to +215 positions, which corresponded to the E-box. Our findings demonstrated important roles of NNAT in placenta function.

Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and large white pigs

MicroRNAs (miRNAs) are involved in the regulation of various metabolic processes in the liver, yet little is known on the breed-specific expression profiles of miRNAs in coordination with those of mRNAs. Here we used two breeds of male newborn piglets with distinct metabolic characteristics, Large White (LW) and Erhualian (EHL), to delineate the hepatic expression profiles of mRNA with microarray and miRNAs with both deep sequencing and microarray, and to analyze the functional relevance of integrated miRNA and mRNA expression in relation to the physiological and biochemical parameters. EHL had significantly lower body weight and liver weight at birth, but showed elevated serum levels of total cholesterol (TCH), high-density lipoprotein cholesterol (HDLC) and low-density lipoprotein cholesterol (LDLC), as well as higher liver content of cholesterol. Higher serum cortisol and lower serum insulin and leptin were also observed in EHL piglets. Compared to LW, 30 up-regulated and 18 down-regulated miRNAs were identified in the liver of EHL, together with 298 up-regulated and 510 down-regulated mRNAs (FDR<10%). RT-PCR validation of some differentially expressed miRNAs (DEMs) further confirmed the high-throughput data analysis. Using a target prediction algorithm, we found significant correlation between the up-regulated miRNAs and down-regulated mRNAs. Moreover, differentially expressed genes (DEGs), which are involved in proteolysis, were predicted to be mediated by DEMs. These findings provide new information on the miRNA and mRNA profiles in porcine liver, which would shed light on the molecular mechanisms underlying the breed-specific traits in the pig, and may serve as a basis for further investigation into the biological functions of miRNAs in porcine liver.

Imprinted genes and the epigenetic regulation of placental phenotype

Imprinted genes are expressed in a parent-of-origin manner by epigenetic modifications that silence either the paternal or maternal allele. They are widely expressed in fetal and placental tissues and are essential for normal placental development. In general, paternally expressed genes enhance feto-placental growth while maternally expressed genes limit conceptus growth, consistent with the hypothesis that imprinting evolved in response to the conflict between parental genomes in the allocation of maternal resources to fetal growth. Using targeted deletion, uniparental duplication, loss of imprinting and transgenic approaches, imprinted genes have been shown to determine the transport capacity of the definitive mouse placenta by regulating its growth, morphology and transporter abundance. Imprinted genes in the placenta are also responsive to environmental challenges and adapt placental phenotype to the prevailing nutritional conditions, in part, by varying their epigenetic status. In addition, interplay between placental and fetal imprinted genes is important in regulating resource partitioning via the placenta both developmentally and in response to environmental factors. By balancing the opposing parental drives on resource allocation with the environmental signals of nutrient availability, imprinted genes, like the Igf2-H19 locus, may act as nutrient sensors and optimise the fetal acquisition of nutrients for growth. These genes, therefore, have a major role in the epigenetic regulation of placental phenotype with long term consequences for the developmental programming of adult health and disease.

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

Background

The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.

Results

One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (p ≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including WNT10B and DKK2 in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- BAX and BMPR1B were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (p ≤ 0.1 or p ≤ 0.05).

Conclusions

Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of BAX and BMPR1B gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools

Using an array consisting of 10 665 70-mer oligonucleotide probes, the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana (CT), an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared with that of two cosmopolitan breeds, Large White (LW) and a crossbreed (CB; Duroc × Landrace × Large White). The results were validated by real-time PCR. All animals were of the same age and were raised under the same environmental conditions. Muscle tissues were collected at 3, 6, 9 and 11 months of age, and a total of 173 genes showed significant differential expression between CT and the cosmopolitan genetic types at 3 months of age. Time series cluster analysis indicated that the CT breed had a different pattern of gene expression compared with that of the LW and the CB. Four of the eight clusters highlighted the gene differences between CT and the other two breeds, which were further supported by statistical analyses: clusters 4 and 5 contained a total of 71 genes that were underexpressed at 3 months of age, and cluster 3 and cluster 7 included 28 and 42 genes respectively that were overexpressed at 3 months of age. As expected, differentially expressed genes belonged to the category of genes coding for contractile fibres and transcription factors involved in muscle development and differentiation. These findings highlight muscle expression genes during pig growth and are useful to understand the genetic meaning of the different developmental rates.

Differential expression of microRNAs in porcine placentas on days 30 and 90 of gestation

The porcine placenta is classified as a non-invasive epitheliochorial type. To meet the increasing demands for nutrients by the rapidly growing conceptus and/or fetus, the placental microscopic folds undergo significant morphological and biochemical changes during two periods critical for conceptus and/or fetus, namely days 30-40 and after day 90 of gestation. MicroRNAs (miRNAs) are a class of small non-coding RNAs that can modulate gene activity by inhibiting the translation or regulation of mRNA degradation. In the present study, we identified 17 differentially expressed miRNAs in porcine placenta on days 30 and 90 of gestation using a locked nucleic acid (LNA) microRNA array. Stem-loop real-time reverse transcription-polymerase chain reaction confirmed the differential expression of eight selected miRNAs (miR-24, miR-125b, miR-92b, miR-106a, miR-17, let-7i, miR-27a and miR-20). Analysis of targets and the pathways in which these miRNAs are involved revealed that the differentially expressed miRNAs target many genes that are important in various processes, including cell growth, trophoblast differentiation, angiogenesis and formation and maintenance of adherens junctions. The results of the present study suggest potential roles for these differentially expressed miRNAs in porcine placental growth and function.