Abstract
BackgroundGene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals.ResultsIn this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 tissues collected from 32 animals using Super deepSAGE technology. Excellent sequencing depth was achieved for each multiplexed library, and replicated samples from the same tissues clustered together, demonstrating the high quality of Super deepSAGE data. Comparison with previous research indicated that our results not only have good reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis revealed ten groups of genes showing distinct expression patterns among these samples. Our analysis of over-represented binding motifs identified 41 regulators, and we demonstrated a potential application of this dataset in infectious diseases and immune biology research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), and vav1 oncogene (VAV1), which belong to the T and B cell signaling pathways.ConclusionsThe Super deepSAGE technology and tissue-differential expression profiles are valuable resources for investigating the porcine gene expression regulation. The identified RUNX1 target genes belong to the T and B cell signaling pathways, making them novel potential targets for the diagnosis and therapy of bacterial infections and other immune disorders.
Highlights
Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals
Analysis of the complexity and diversity of super deepSAGE data across tissues Super deepSAGE obtained ~ 5 million reads per sample with an average sequencing depth of 71X
The Vav1 oncogene (VAV1) encoded protein is important in hematopoiesis, playing a role in both T-cell and B-cell development and activation [28, 29]. These results suggest that Runt-related transcription factor 1 (RUNX1) might be a new potential target for resolving inadequate or uncontrolled inflammation in peripheral blood mononuclear cells (PBMCs)
Summary
Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals. The domestic pig (Sus scrofa) is an important animal farmed for meat worldwide and has been used as an alternative model for studying genetics, nutrition, and disease [1,2,3]. (EST) sequencing projects, microarray platforms, longSAGE, and deep sequencing projects have developed gene expression profiles across a range of tissues [8, 14, 15]. In comparison to other model organisms, the pig transcriptome data has its limitations in terms of coverage of tissues and genes [4]. We present Super deepSAGE (serial analysis of gene expression by deep sequencing) profiling data for pig tissues with wide gene coverage and annotation. A detailed analysis of one such identified transcription factor, RUNX1, illustrates the impact of the data
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