title: Differential responsiveness of Holstein and Angus dermal fibroblasts to LPS challenge occurs without major differences in the methylome.
abstract: 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.
authors.affiliation: Department of Animal and Veterinary Sciences, University of Vermont, Terrill Hall, 570 Main Street, Burlington, VT, 05405, USA.
authors.forename: Aimee L
authors.initials: AL
authors.lastname: Benjamin
authors.affiliation: Geisel School of Medicine at Dartmouth, Department of Epidemiology and Department of Pharmacology and Toxicology, 7650 Remsen, Rope Ferry Rd, Hanover, NH, 03755, USA.
authors.forename: Benjamin B
authors.initials: BB
authors.lastname: Green
authors.affiliation: Department of Animal Science, University of Minnesota, Haecker Hall, 1364 Eckles Ave, St. Paul, MN, 55108, USA.
authors.forename: Brian A
authors.initials: BA
authors.lastname: Crooker
authors.affiliation: Department of Animal and Veterinary Sciences, University of Vermont, Terrill Hall, 570 Main Street, Burlington, VT, 05405, USA.
authors.forename: Stephanie D
authors.initials: SD
authors.lastname: McKay
authors.affiliation: Department of Animal and Veterinary Sciences, University of Vermont, Terrill Hall, 570 Main Street, Burlington, VT, 05405, USA. David.Kerr@uvm.edu.
authors.forename: David E
authors.initials: DE
authors.lastname: Kerr
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D002478:Cells, Cultured; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D005347:Fibroblasts / Q000276:immunology*; D005786:Gene Expression Regulation; D007113:Immunity, Innate / Q000235:genetics*; D008070:Lipopolysaccharides / Q000494:pharmacology*; D010641:Phenotype; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D008070:Lipopolysaccharides
keywords: DNA methylation; Innate immunity; MIRA-Seq; RNA-Seq