Transcriptome Analysis of the Medulla Tissue from Cattle in Response to Bovine Spongiform Encephalopathy using Digital Gene Expression Tag Profiling

Abstract

Bovine spongiform encephalopathy (BSE) is a transmissible, fatal neurodegenerative disorder of cattle produced by prions. The use of excessive parallel sequencing for comparison of gene expression in bovine control and infected tissues may help to elucidate the molecular mechanisms associated with this disease. In this study, tag profiling Solexa sequencing was used for transcriptome analysis of bovine brain tissues. Replicate libraries were prepared from mRNA isolated from control and infected (challenged with 100 g of BSE-infected brain) medulla tissues 45 mo after infection. For each library, 5–6 million sequence reads were generated and approximately 67–70% of the reads were mapped against the Bovine Genome database to approximately 13,700–14,120 transcripts (each having at least one read). About 42–47% of the total reads mapped uniquely. Using the GeneSifter software package, 190 differentially expressed (DE) genes were identified (>2.0-fold change, p < .01): 73 upregulated and 117 downregulated. Seventy-nine DE genes had functions described in the Gene Ontology (GO) database and 16 DE genes were involved in 38 different pathways described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Digital analysis expression by tag profiling may be a powerful approach to comprehensive transcriptome analysis to identify changes associated with disease progression, leading to a better understanding of the underlying mechanism of pathogenesis of BSE.

Acknowledgments

This research was supported by PrionNet Canada, Alberta Prion Institute, and Alberta Bovine Genomic Program. We thank the Veterinary Laboratories Agency (Weybridge, UK) for providing the tissue samples to prepare RNA used in this study (funded by Defra project SE1736 and EU project FAIR CT98-778). Chris McIntosh is acknowledged for providing assistance in preparation of the libraries. JLW thanks the Cariplo Foundation for its support.