Identifying Tissue Specific Gene Expression Using RNAseq Data from Multiple Porcine Tissues

We are interested in the functional components of genome that control expression in specific porcine tissues, including chromatin features correlated with tissue specific gene expression. We used the transcriptional changes in 4 different tissues (muscle, liver, spleen and ileum) of healthy adult Yorkshire pigs (n=6) collected using RNA-seq to predict tissue-specific expression. In this study, an average of 21,555,094 clean paired sequence reads per sample were generated by sequencing, with more than 77% of the reads successfully mapped to the reference sequence.

We used two criteria to predict tissue-specificity: a) genes with read counts only in one tissue and at least two times the median (2xMedian), and b) genes with 20-1000 times higher expression in that tissue, and expression at least 5xMedian. In total, we found 350, 287, 17 and 92 genes were specifically expressed in liver, muscle, spleen and ileum, respectively. In addition to verifying basic epigenetic and genomic features of the human orthologs of these genes in these tissues (NIH Roadmap), we performed clustering, DAVID and Pathway Analysis, which showed strong connections of these genes with relevant tissue physiology.

To confirm the RNA-Seq results, 12 genes in muscle, 13 in liver and 11 in ileum were selected from the above gene lists for qRT-PCR analysis. The qRT-PCR experiment showed that all the tested genes had a similar expression pattern as shown in RNA-seq data. This study provides a resource for further genomic research into tissue-specific expression and contributes to a better understanding of biological diversity across pig tissues.