title: 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.
authors.affiliation: Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Urmila
authors.initials: U
authors.lastname: Basu
authors.forename: Luciane
authors.initials: L
authors.lastname: Almeida
authors.forename: N Eric
authors.initials: NE
authors.lastname: Olson
authors.forename: Yan
authors.initials: Y
authors.lastname: Meng
authors.forename: John L
authors.initials: JL
authors.lastname: Williams
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Moore
authors.forename: Le Luo
authors.initials: LL
authors.lastname: Guan
mesh_terms: D000818:Animals; D002417:Cattle; D018450:Disease Progression; D016643:Encephalopathy, Bovine Spongiform / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling / Q000662:veterinary*; D005796:Genes / Q000235:genetics; D015698:Genomic Library; D008526:Medulla Oblongata / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000662:veterinary; D017422:Sequence Analysis, DNA / Q000662:veterinary
chemical_list: D012333:RNA, Messenger