ARS | Publication request: Transcriptional profiling of bovine Johne's Disease

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: December 10, 2010
Publication Date: January 15, 2011
Citation: Beattie, C.W., Briggs, R.E., Stabel, J.R., Van Velkinburgh, J.C., Bharti, A., Mudge, J. 2011. Transcriptional profiling of bovine Johne's Disease [abstract]. Plant and Animal Genome Conference. p. 120.

Technical Abstract: Johne's Disease is a chronic, contagious disease prevalent in ruminants. The animal is infected early in life by the bacteria Mycobacterium avium subsp. paratuberculosis (MAP). The characteristic symptoms of rapid weight loss and diarrhea may not appear for years after infection. We investigated the transcriptional profile of bovine Johne’s disease through the bovine response to MAP infection as well as MAP activity in different tissues and stages of disease. We performed transcriptome sequencing on total RNA samples from the lymph nodes and ileocecal junctions of clinical, sub-clinical, and control cows. The thirty tissue samples collected from 14 animals of a single herd represent biological replicates for all three states, and were extracted with an optimized protocol to capture both bovine and MAP transcriptomes. This RNA-Seq protocol allows for the retention of low abundance transcripts, as well as non-polyA (bacterial) message. Twelve samples were sequenced on the Illumina GAIIx platform, generating 317M reads and 17 GB of data. Transcriptomic reads were aligned to the bovine and MAP genomes with GSNAP. The MAP transcripts in the diseased samples are more than an OOM higher in clinical specimens. Yet to be resolved is whether the M. avium transcripts in control animals are, in fact, MAP or another member of the M. avium complex. Using normalized read counts as a measure of gene expression for annotated bovine genes, we used JMP Genomics to identify differentially expressed genes. IPA pathway analysis was used to refine gene sets that are important in Johne’s pathogenesis.