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Xiang et al 2016 Gene network analysis.pdf (1.76 MB)

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

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posted on 2023-05-03, 13:14 authored by Ruidong Xiang, Jody McNally, Suzanne RoweSuzanne Rowe, Arjan JonkerArjan Jonker, Cesar Pinares-Patino, Hutton Oddy, Phil Vercoe, John McEwanJohn McEwan, Brian Dalrymple
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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This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line

Language

  • English

Does this contain Māori information or data?

  • No

Publisher

Springer Nature

Journal title

Scientific Reports

ISSN

2045-2322

Citation

Xiang, R., McNally, J., Rowe, S., Jonker, A., Pinares-Patino, C. S., Oddy, 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, 39022. doi:10.1038/srep39022

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