Gene expression during testis development in Duroc boars
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ABSTRACT:
ORGANISM(S): Sus scrofa
SUBMITTER: Lene Conley
PROVIDER: E-GEOD-39322 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The recent development within high-throughput technologies for expression profiling has allowed for parallel analysis of transcriptomes and proteomes in biological systems such as comparative analysis of transcript and protein levels of tissue regulated genes. Until now, such studies of have only included microarray or short length sequence tags for transcript profiling. Furthermore, most comparisons of transcript and protein levels have been based on absolute expression values from within the same tissue and not relative expression values based on tissue ratios. Presented here is a novel study of two porcine tissues based on integrative analysis of data from expression profiling of identical samples using cDNA microarray, 454-sequencing and iTRAQ-based proteomics. Sequence homology identified 2.541 unique transcripts that are detectable by both microarray hybridizations and 454-sequencing of 1.2 million cDNA tags. Both transcript-based technologies showed high reproducibility between sample replicates of the same tissue, but the correlation across these two technologies was modest. Thousands of genes being differentially expressed were identified with microarray. Out of the 306 differentially expressed genes, identified by 454-sequencing, 198 (65 %) were also found by microarray. The relationship between the regulation of transcript and protein levels was analyzed by integrating iTRAQ-based proteomics data. Protein expression ratios were determined for 354 genes, of which 148 could be mapped to both microarray and 454-sequencing data. A comparison of the expression ratios from the three technologies revealed that differences in transcript and protein levels across heart and muscle tissues are positively correlated. We show that the reproducibility within cDNA microarray and 454-sequencing is high, but that the agreement across these two technologies is modest. We demonstrate that the regulation of transcript and protein levels across identical tissue samples is positively correlated when the tissue expression ratios are used for comparison. The results presented are of interest in systems biology research in terms of integration and analysis of high-throughput expression data from mammalian tissues. Keywords: tissue comparison, platform comparison Tissue samples of heart (HEA) and Longissimus dorsi (LDO) were prepared by pooling from five healthy Hampshire gilts at age four to six months and division into six sub-samples, three for each tissue named HEA1, HEA2, HEA3, LDO1, LDO2 and LDO3. The exact same six tissue samples were used for subsequent expression profiling with cDNA microarray, 454-sequencing and iTRAQ-based proteomics. A reference sample for the cDNA microarray experiment and iTRAQ-based proteomics was constructed by combining the six samples. In the microarray experiment, three cDNA microarray slides were used per sample.
2009-01-22 | E-GEOD-10122 | biostudies-arrayexpress
Project description:Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels. Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26.877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p < 0.01) in Duroc and Norwegian Landrace, respectively. Of these significantly up- and down-regulated clones, 72 were found to be common for the two breeds, suggesting both general and breed specific mechanisms in regulation of, or response to androstenone levels in boars. Ten of the most significant genes were chosen for verification of expression patterns by quantitative real competitive PCR and real-time PCR. As expected, our results point towards steroid hormone metabolism and biosynthesis as important biological processes for the androstenone levels, but other potential pathways were identified as well. Among these were oxidoreductase activity, ferric iron binding, iron ion binding and electron transport activities. Genes belonging to the cytochrome P450 and hydroxysteroid dehydrogenase families were highly up-regulated, in addition to several genes encoding different families of conjugation enzymes. Furthermore, a number of genes encoding transcription factors were found both up- and down-regulated. The high number of clones belonging to ferric iron and iron ion binding suggests an importance of these genes, and the association between these pathways and androstenone levels is not previously described. This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint. Keywords: high vs low Testicle samples from animals with extreme androstenone values, 30 high and 30 low from each of the two breeds Norwegian Landrace and Duroc, were used for the experiment. Each microarray was hybridised with one high and one low androstenone sample from the same breed, giving a total of 30 arrays for each breed.
2007-11-26 | E-GEOD-7409 | biostudies-arrayexpress
Project description:The introduction of long oligonucleotide-based probes has led to many comparative studies of these two platforms in mammals, but remains to be performed for pig. Further, the characteristics of global gene expression in diverse porcine muscle tissues have not been yet been fully established. This is the first global gene expression study of a collection of nine porcine muscle tissues consisting of cardiac and various skeletal muscle types using both cDNA-based and long oligonucleotide-based microarray platforms. The expression profiles from the two platforms agree in differentiating between cardiac, skeletal red, skeletal intermediate and skeletal white muscle types by producing almost identical hierarchical expression clusters. The clusters from both platforms also reveal that gene expression profiles of the skeletal intermediate type are more similar to the red type than to the white type. Analysis of the ability to identify differentially expressed genes based on gene set analysis and GO term integration show a platform overlap of at least 80% for the cardiac-skeletal comparisons and a platform overlap of at least 58% for the skeletal red-white comparisons. Interestingly, the oligonucleotide platform was always able to identify more GO terms associated with differential expression than the cDNA platform. We further examined the skeletal red-white expression differences and found many GO biological processes that are known to be associated with these phenotypes including calcium ion transport, glycolysis, fatty acid beta-oxidation and muscle contraction. In addition, the expression of genes involved in differentiation between slow (red) and fast (white) muscle types such as MYBPC1, TNNI1, TNNT3 and ATP2A1 is highly regulated between red and white type muscles. Not previously shown to be associated with this tissue difference we found the biological process post-Golgi vesicle-mediated transport. Similar results were obtained with GO classes cellular components and molecular functions. Using the gene expression profiles from the oligonucleotide platform we presented and applied an approach for predicting alternatively spliced transcripts across cardiac and skeletal type muscles. One of the predicted transcripts from the gene named UBE2C has been shown to have six transcript variants in human, but they are not expressed in a cardiac-skeletal specific manner as we have observed here. We speculate that one of our oligonucleotide probes for this gene is able to detect only three of these variants whereas the other detects all six variants and that these variants are expressed in a cardiac-skeletal muscle specific manner. These results supports some of the advantages of using oligonucleotide-based microarray platforms for global gene expression profiling and the observed differences in gene expression among muscle tissues contribute to the understanding of the molecular processes behind porcine muscle biology. Keywords: tissue comparison, platform comparison Muscle tissue samples from heart (HEA), Vastus intermedius (VIN), Infraspinatus (ISP), Supraspinatus (SSP), Biceps femoris (BFE), Longissimus dorsi (LDO), Semimembranosus (SME), Semitendinosus (STE) and Triceps brachii (TBR). A common reference sample was constructed by combining all samples. The exact same tissue samples were used for expression profiling with cDNA microarrays and 70-mer long oligonucleotide microarrays.
2012-10-30 | E-GEOD-10597 | biostudies-arrayexpress
Project description:Acute physical exercise elicits changes in gene expression in skeletal muscles to promote metabolic changes and to repair exercise-induced muscle injuries. Here, we investigated the impact of a single bout of running exercise until exhaustion on global transcriptional profiles in porcine skeletal muscles. Using a combined microarray and candidate gene approach, we identified a suite of genes that are differentially expressed in muscles during post-exercise recovery. Thus, several members of the heat shock protein family and proteins associated with proteolytic events were significantly up-regulated, suggesting that protein breakdown, prevention of protein aggregation and stabilization of unfolded proteins are important processes for restoring cellular homeostasis. We also detected an up-regulation of genes, which have been reported to be associated with muscle cell proliferation and differentiation, possibly reflecting an activation, differentiation and fusion of satellite cells to facilitate repair of muscle damage. In addition, exercise increased expression of the nuclear hormone receptors, which regulates metabolic functions associated with lipid, carbohydrate and energy homeostasis. Finally, we observed an unanticipated involvement of long non-coding RNA transcripts, which have been implicated in RNA processing and nuclear retention of adenosine-to-inosine edited mRNAs. These findings expand the complexity of pathways affected by acute contractile activity of skeletal muscle, contributing to a better understanding of the molecular processes that occur in muscle tissue in the recovery phase. Gene expression study of the porcine muscle Biceps femoris in regard to exercise, pigs allowed to rest for 0 hours, 1 hour and 3 hours after exercise were compared with pigs that had not been exercising, using in-house printed porcine two-colour oligonucleotide microarrays.
2012-07-12 | E-GEOD-30013 | biostudies-arrayexpress
Project description:Skatole is one of the compounds causing boar taint in meat of uncastrated male pigs. This study focuses on differences in gene expression of 50 Danish Landrace boars with high and low skatole levels. The animals were divided into 2 groups based on the skatole measurements, with animals having a skatole concentration of less than 0.01 ppm in one group, and above 0.275 ppm in the other group. Gene expression was assessed using porcine oligonucleotide microarrays. We report differential expression of CYP2E1, CYP2A13 and suggests involvement of FMO1, HSD17B13, CBR4 and several transcription factors. Gene expression study of liver, comparison of 25 boars with high and 25 boars with low skatole levels, using in-house printed porcine two-colour oligonucleotide microarrays.
2015-06-15 | E-GEOD-29974 | biostudies-arrayexpress
Project description:Acute physical exercise elicits changes in gene expression in skeletal muscles to promote metabolic changes and to repair exercise-induced muscle injuries. Here, we investigated the impact of a single bout of running exercise until exhaustion on global transcriptional profiles in porcine skeletal muscles. Using a combined microarray and candidate gene approach, we identified a suite of genes that are differentially expressed in muscles during post-exercise recovery. Thus, several members of the heat shock protein family and proteins associated with proteolytic events were significantly up-regulated, suggesting that protein breakdown, prevention of protein aggregation and stabilization of unfolded proteins are important processes for restoring cellular homeostasis. We also detected an up-regulation of genes, which have been reported to be associated with muscle cell proliferation and differentiation, possibly reflecting an activation, differentiation and fusion of satellite cells to facilitate repair of muscle damage. In addition, exercise increased expression of the nuclear hormone receptors, which regulates metabolic functions associated with lipid, carbohydrate and energy homeostasis. Finally, we observed an unanticipated involvement of long non-coding RNA transcripts, which have been implicated in RNA processing and nuclear retention of adenosine-to-inosine edited mRNAs. These findings expand the complexity of pathways affected by acute contractile activity of skeletal muscle, contributing to a better understanding of the molecular processes that occur in muscle tissue in the recovery phase. Gene expression study of the porcine muscle Longissimus dorsi in regard to exercise, pigs allowed to rest for 0 hours, 1 hour and 3 hours after exercise were compared with pigs that had not been exercising, using in-house printed porcine two-colour oligonucleotide microarrays.
2012-07-12 | E-GEOD-30014 | biostudies-arrayexpress
Project description:Even though feather pecking (FP) in laying hens has been extensively studied, a good solution to prevent chickens from this behavior under commercial circumstances has not been found. Selection against FP behavior is possible, but for a more effective selection across different populations, it is necessary to characterize the genetic mechanism associated with this behavior. In this study, we use a high FP selection line, which has been selected for 8 generations. We present evidence of the presence of a major dominant allele affecting the FP behavior by using an argument based on the presence of mixture in the distribution of the observed FP and by studying the evolution of the proportion of very high FP along the sequence of 8 generations. This hypothesis is further supported by the fact that the gene transcription profile of the birds performing high FP differs from the profile of the other birds performing FP (456 genes differentially expressed from a total of 14,077 investigated genes). Keywords: severe feather pecking , selection , modeling , inheritance pattern From each selection line (high feather pecking line, low feather pecking line and control line) 60 animals were randomly selected. Within each line the birds were randomly assigned to a cage of 20. The cages were kept in a randomized block design. Number of samples analyzed in total: 179 (60 high feather pecking line, 60 low feather pecking line, 59 control line samples. Common reference design using total-RNA purified from brain from a single F1 cross between the high and low feather pecking line as reference.
2009-09-22 | E-GEOD-10380 | biostudies-arrayexpress
Project description:ABSTRACT: BACKGROUND: Boar taint is the unpleasant odour and flavour of the meat of uncastrated male pigs that is primarily caused by high levels of androstenone and skatole in adipose tissue. Androstenone is a steroid and its levels are mainly genetically determined. Studies on androstenone metabolism have, however, focused on a limited number of genes. Identification of additional genes influencing levels of androstenone may facilitate implementation of marker assisted breeding practices. In this study, microarrays were used to identify differentially expressed genes and pathways related to androstenone metabolism in the liver from boars with extreme levels of androstenone in adipose tissue. RESULTS: Liver tissue samples from 58 boars of the two breeds Duroc and Norwegian Landrace, 29 with extreme high and 29 with extreme low levels of androstenone, were selected from more than 2500 individuals. The samples were hybridised to porcine cDNA microarrays and the 1 % most significant differentially expressed genes were considered significant. Among the differentially expressed genes were metabolic phase I related genes belonging to the cytochrome P450 family and the flavin-containing monooxygenase FMO1. Additionally, phase II conjugation genes including UDP-glucuronosyltransferases UGT1A5, UGT2A1 and UGT2B15, sulfotransferase STE, N-acetyltransferase NAT12 and glutathione S-transferase were identified. Phase I and phase II metabolic reactions increase the water solubility of steroids and play a key role in their elimination. Differential expression was also found for genes encoding 17beta-hydroxysteroid dehydrogenases (HSD17B2, HSD17B4, HSD17B11 and HSD17B13) and plasma proteins alpha-1-acid glycoprotein (AGP) and orosomucoid (ORM1). 17beta-hydroxysteroid dehydrogenases and plasma proteins regulate the availability of steroids by controlling the amount of active steroids accessible to receptors and available for metabolism. Differences in the expression of FMO1, NAT12, HSD17B2 and HSD17B13 were verified by quantitative real competitive PCR. CONCLUSIONS: A number of genes and pathways related to metabolism of androstenone in liver were identified, including new candidate genes involved in phase I oxidation metabolism, phase II conjugation metabolism, and regulation of steroid availability. The study is a first step towards a deeper understanding of enzymes and regulators involved in pathways of androstenone metabolism and may ultimately lead to the discovery of markers to reduce boar taint. Liver samples from 116 animals with extreme androstenone values, 29 high and 29 low from each of the two breeds Norwegian Landrace and Duroc, were used for this experiment. Each sample was hybridised together with a common refrence resulting in a total of 116 microarrays.
2008-08-17 | E-GEOD-11073 | biostudies-arrayexpress
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays
2013-01-01 | E-GEOD-12927 | biostudies-arrayexpress
Project description:The objective of this study was to identify porcine genes which expression was affected by experimental infection with A. pleuropneumoniae within 24 hours after experimental challenge. Microarray experiments were conducted to reveal genes being significantly differentially expressed in infected versus non-infected lung tissue and in liver and lung lymph node tissue from three challenged versus two non-challenged animals. Keywords: Host response Three comparisons were done: - infected versus non-infected lung tissue sampled from three challenged pigs - liver tissue from three challenged versus two non-challenged animals - lung lymph node tissue from three challenged versus two non-challenged animals All experiments were conducted as common reference design.
2010-06-11 | E-GEOD-4577 | biostudies-arrayexpress