Long oligo- and cDNA-based microarray gene expression in nine porcine muscle tissues using a common reference design

ABSTRACT: 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

ORGANISM(S): Sus scrofa

PROVIDER: GSE10597 | GEO | 2012/10/30

SECONDARY ACCESSION(S): PRJNA107757

REPOSITORIES: GEO