BACKGROUND: We have previously found substantial animal-to-animal and 
age-dependent variation in the response of Holstein fibroblast cultures 
challenged with LPS. To expand on this finding, fibroblast cultures were 
established from dairy (Holstein) and beef (Angus) cattle and challenged with 
LPS to examine breed-dependent differences in the innate immune response. Global 
gene expression was measured by RNA-Seq, while an epigenetic basis for 
expression differences was examined by methylated CpG island recovery assay 
sequencing (MIRA-Seq) analysis.
RESULTS: The Holstein breed displayed a more robust response to LPS than the 
Angus breed based on RNA-Seq analysis of cultures challenged with LPS for 0, 2, 
and 8 h. Several immune-associated genes were expressed at greater levels (FDR < 
0.05) in Holstein cultures including TLR4 at all time points and a number of 
pro-inflammatory genes such as IL8, CCL20, CCL5, and TNF following LPS exposure. 
Despite extensive breed differences in the transcriptome, MIRA-Seq unveiled 
relatively similar patterns of genome-wide DNA methylation between breeds, with 
an overall hypomethylation of gene promoters. However, by examining the genome 
in 3Kb windows, 49 regions of differential methylation were discovered between 
Holstein and Angus fibroblasts, and two of these regions fell within the 
promoter region (-2500 to +500 bp of the transcription start site) of the genes 
NTRK2 and ADAMTS5.
CONCLUSIONS: Fibroblasts isolated from Holstein cattle display a more robust 
response to LPS in comparison to cultures from Angus cattle. Different selection 
strategies and management practices exist between these two breeds that likely 
give rise to genetic and epigenetic factors contributing to the different immune 
response phenotypes.