title: Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production.
abstract: Ruminants obtain nutrients from microbial fermentation of plant material, primarily in their rumen, a multilayered forestomach. How the different layers of the rumen wall respond to diet and influence microbial fermentation, and how these process are regulated, is not well understood. Gene expression correlation networks were constructed from full thickness rumen wall transcriptomes of 24 sheep fed two different amounts and qualities of a forage and measured for methane production. The network contained two major negatively correlated gene sub-networks predominantly representing the epithelial and muscle layers of the rumen wall. Within the epithelium sub-network gene clusters representing lipid/oxo-acid metabolism, general metabolism and proliferating and differentiating cells were identified. The expression of cell cycle and metabolic genes was positively correlated with dry matter intake, ruminal short chain fatty acid concentrations and methane production. A weak correlation between lipid/oxo-acid metabolism genes and methane yield was observed. Feed consumption level explained the majority of gene expression variation, particularly for the cell cycle genes. Many known stratified epithelium transcription factors had significantly enriched targets in the epithelial gene clusters. The expression patterns of the transcription factors and their targets in proliferating and differentiating skin is mirrored in the rumen, suggesting conservation of regulatory systems.
authors.affiliation: CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, 4067 Queensland, Australia.
authors.forename: Ruidong
authors.initials: R
authors.lastname: Xiang
authors.affiliation: CSIRO Agriculture, FD McMaster Laboratory, Armidale, NSW 2350, Australia.
authors.forename: Jody
authors.initials: J
authors.lastname: McNally
authors.affiliation: AgResearch Limited, Invermay Agricultural Centre, Mosgiel 9053, New Zealand.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Rowe
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
authors.forename: Arjan
authors.initials: A
authors.lastname: Jonker
authors.affiliation: AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.|CSIRO Agriculture, Black Mountain Laboratories, Clunies Ross Street, 2601 ACT, Australia.
authors.forename: Cesar S
authors.initials: CS
authors.lastname: Pinares-Patino
authors.affiliation: NSW Department of Primary Industries, Beef Industry Centre, University of New England, Armidale, NSW 2351, Australia.
authors.forename: V Hutton
authors.initials: VH
authors.lastname: Oddy
authors.affiliation: School of Animal Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
authors.forename: Phil E
authors.initials: PE
authors.lastname: Vercoe
authors.affiliation: AgResearch Limited, Invermay Agricultural Centre, Mosgiel 9053, New Zealand.
authors.forename: John C
authors.initials: JC
authors.lastname: McEwan
authors.affiliation: CSIRO Agriculture, Queensland Bioscience Precinct, 306 Carmody Rd, 4067 Queensland, Australia.|School of Animal Biology and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia.
authors.forename: Brian P
authors.initials: BP
authors.lastname: Dalrymple
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000502:physiology*; D049109:Cell Proliferation / Q000502:physiology*; D004847:Epithelial Cells / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology; D053263:Gene Regulatory Networks / Q000502:physiology*; D008697:Methane / Q000096:biosynthesis*; D012417:Rumen / Q000378:metabolism*; D012756:Sheep
chemical_list: D008697:Methane