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A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

ABSTRACT: Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals.

ORGANISM(S): Sus scrofa

PROVIDER: GSE26382 | GEO | 2011/01/12

SECONDARY ACCESSION(S): PRJNA142279

REPOSITORIES: GEO

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A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

Project description:Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals. Examining the complexity of the pig transcriptome in three organs (liver, abdominal fat, longissimus dorsi muscle) from a female full-sib pair.

2011-01-12 | E-GEOD-26382 | biostudies-arrayexpress

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

Project description:Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. Through small RNA sequencing and on the basis of miRbase15.0, we detected a total of 184 mature miRNAs and 164 unique porcine novel miRNAs. Some conserved miRNAs, such as miR-122, miR-1, miR-206 and let-7 family showed high expression level in this study. Finally, we identified 10, 20 and 63 differentially expressed miRNAs, respectively, in LI, LD and AF. This high resolution and comprehensive transcriptome analysis significantly enhances the current genome annotation of pigs. examining the complexity of pig transcriptome in three organs from a female full-sib pair

2010-12-20 | E-GEOD-25923 | biostudies-arrayexpress

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

2010-12-20 | GSE25923 | GEO

Extensive Splicing across the Saccharomyces cerevisiae genome

Project description:Pre-mRNA splicing is vital for the proper function and regulation of eukaryotic gene expression. Saccharomyces cerevisiae has been used as a model organism for studies of RNA splicing because of the striking conservation of the spliceosome and its catalytic activity. Nonetheless, there are relatively few annotated alternative splice forms, particularly when compared to higher eukaryotes. Here, we describe a method to combine large scale RNA sequencing data to accurately discover novel splice isoforms in Saccharomyces cerevisiae. Using our method, we find extensive evidence for novel splicing of annotated intron-containing genes as well as genes without previously annotated introns and splicing of transcripts that are antisense to annotated genes. By incorporating several mutant strains at varied temperatures, we find conditions which lead to differences in alternative splice form usage. Despite this, every class and category of alternative splicing we find in our datasets is found, often at lower frequency, in wildtype cells under normal growth conditions. Together, these findings show that there is widespread splicing in Saccharomyces cerevisiae.

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2010-03-01 | GSE13515 | GEO

Amniotic fluid and necrotizing enterocolitis in preterm pigs

Project description:Preterm neonates are susceptible to gastrointestinal (GI) disorders such as necrotizing enterocolitis (NEC). Maternal milk, and especially colostrum, protects against NEC via growth promoting, immunomodulatory and antimicrobial factors. The fetal enteral diet, amniotic fluid (AF), contains similar bioactive components and we hypothesized that postnatal AF administration would reduce inflammatory responses and NEC in preterm neonates. Thirty preterm pigs (92% gestation) were delivered by caesarean section and fed total parental nutrition (TPN) for 48 h followed by enteral porcine colostrum (COLOS, n=7), infant formula (FORM, n=13) or formula + porcine AF (AF, n=10). Using a previously validated model of NEC in preterm pigs, we determined the structural, functional, microbiological and immunological responses to AF when administered prior to and after introduction of a suboptimal enteral formula diet. Keywords: Healthy versus inflammed tissues in relation to necrotizing enterocolitis Pigs from each treatment group (COLOS, n=4; FORM, n=6; and AF, n=7) were randomly selected for microarray analysis of frozen distal small intestine samples. The FORM group was further divided into formula-fed healthy pigs (F-HEA, n=3) and formula-fed NEC pigs (F-NEC, n=3) in order to compare sick versus healthy formula fed pigs. Equal amounts of total distal small intestinal RNA from all pigs were pooled to make the reference sample. Samples and reference pool were labelled with Oyster 550 and 650, respectively. The in-house spotted porcine oligonucleotide microarray version 4 (POM4) is a low density microarray consisting of 384 different oligonucleotide probes representing more than 200 different immune related genes.

2010-05-06 | E-GEOD-13515 | biostudies-arrayexpress

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Project description:Compared to other mammalian species, porcine oocytes and embryos are characterized by large amounts of lipids stored mainly in the form of droplets in the cytoplasm. The amount and the morphology of LD change throughout the preimplantation development however, relatively little is known about expression of genes involved in lipid metabolism of early embryos. We compared porcine and bovine blastocyst stage embryos as well as dissected inner cell mass (ICM) and trophoblast (TE) cell populations with regard to lipid droplet storage and expression of genes functionally annotated to selected lipid Gene Ontology terms using RNA-seq. Comparing the number and the volume occupied by LD between bovine and porcine blastocysts, we have found significant differences both at the level of single embryo and a single blastomere. Aside from different lipid content we found that embryos regulate the lipid metabolism differentially at the gene expression level. Out of 125 genes, we have found 73 to be differentially expressed between entire porcine and bovine blastocyst, and 36 and 51 to be divergent between ICM and TE cell lines. We noticed significant involvement of cholesterol and ganglioside metabolism in preimplantation embryos as well as possible shift towards glucose rather than pyruvate dependence in bovine embryos. A number of genes like DGAT1, CD36 or NR1H3 may serve as lipid associated markers indicating distinct regulatory mechanisms while upregulated PLIN2, APOA1, SOAT1 indicate significant function during blastocyst formation and cell differentiation in both models.

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Global genetic robustness of the alternative splicing machinery in C. elegans

Project description:Alternative splicing is considered a major mechanism for creating multicellular diversity from a limited repertoire of genes. Different isoforms can be produced at the same time in the same cell type and their ratios can be the same or different between divergent genotypes. Here, we studied genetic variation in alternative splicing patterns in a large recombinant inbred population of C. elegans, using whole-genome tiling arrays. This experiment allowed us to detect heritable differences in gene expression with exquisite sensitivity and resolution, and we detected 435 genes with substantial heritable variation for at least one exon. Nonetheless, we find only a very small number of examples of heritable variation in alternative splicing (22 transcripts), and most of these genes co-localize with the associated genomic loci. This is in striking contrast to earlier observations in humans, which showed much less genetic robustness. C. elegans recombinant inbred lines were generated and genotyped as described in (Li et al. 2006). mRNA was isolated from 60 RILs reared under standard condition and hybridized to Affymetrix 1.0 C. elegans tiling arrays. The hybridization was done by ServiceXS (Leiden, The Netherlands).

2011-01-01 | E-GEOD-15778 | biostudies-arrayexpress

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2014-05-30 | GSE49882 | GEO

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