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    Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

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    Author
    Xiang, R; McNally, J; Rowe, S; Jonker, A; Pinares-Patino, CS; Oddy, VH; Vercoe, PE; McEwan, JC; Dalrymple, BP
    Date
    2016-12-14
    Source Title
    Scientific Reports
    Publisher
    NATURE PUBLISHING GROUP
    University of Melbourne Author/s
    Xiang, Ruidong
    Affiliation
    Agriculture and Food Systems
    Metadata
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    Document Type
    Journal Article
    Citations
    Xiang, R., McNally, J., Rowe, S., Jonker, A., Pinares-Patino, C. S., Oddy, V. H., Vercoe, P. E., McEwan, J. C. & Dalrymple, B. P. (2016). Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production. SCIENTIFIC REPORTS, 6 (1), https://doi.org/10.1038/srep39022.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/257376
    DOI
    10.1038/srep39022
    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.

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