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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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dc.contributor.authorXiang, Ruidongen
dc.contributor.authorMcNally, Jodyen
dc.contributor.authorRowe, Suzanneen
dc.contributor.authorJonker, Arjanen
dc.contributor.authorPinares-Patino, Cesar Sen
dc.contributor.authorOddy, V Huttonen
dc.contributor.authorVercoe, Phil Een
dc.contributor.authorMcEwan, John Cen
dc.contributor.authorDalrymple, Brian Pen
dc.date.accessioned2024-06-05T23:25:45Z
dc.date.available2024-06-05T23:25:45Z
dc.date.issued2016-12-14
dc.description.abstract<p>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.</p>en
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dc.identifier.citationScientific Reports, v.6, p. 1-14en
dc.identifier.doi10.1038/srep39022en
dc.identifier.issn2045-2322en
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dc.identifier.urihttps://hdl.handle.net/1959.11/60515
dc.languageenen
dc.publisherNature Publishing Groupen
dc.relation.ispartofScientific Reportsen
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subject.keywordsMultidisciplinary Sciencesen
dc.subject.keywordsScience & Technology - Other Topicsen
dc.titleGene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane productionen
dc.typeJournal Articleen
dcterms.accessRightsUNE Greenen
dspace.entity.typePublication
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local.contributor.firstnameRuidongen
local.contributor.firstnameJodyen
local.contributor.firstnameSuzanneen
local.contributor.firstnameArjanen
local.contributor.firstnameCesar Sen
local.contributor.firstnameV Huttonen
local.contributor.firstnamePhil Een
local.contributor.firstnameJohn Cen
local.contributor.firstnameBrian Pen
local.contributor.lastnameXiangen
local.contributor.lastnameMcNallyen
local.contributor.lastnameRoween
local.contributor.lastnameJonkeren
local.contributor.lastnamePinares-Patinoen
local.contributor.lastnameOddyen
local.contributor.lastnameVercoeen
local.contributor.lastnameMcEwanen
local.contributor.lastnameDalrympleen
local.fileurl.closedpublishedhttps://rune.une.edu.au/web/retrieve/315563a3-4fdd-42df-a85e-9129ae94c77fen
local.format.endpage14en
local.format.startpage1en
local.identifier.erajournal201487en
local.identifier.runningnumber39022en
local.identifier.unepublicationidune:1959.11/60515en
local.identifier.volume6en
local.output.categoryC1en
local.output.categorydescriptionC1 Refereed Article in a Scholarly Journalen
local.peerreviewedYesen
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local.profile.emailhoddy2@une.edu.auen
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local.profile.schoolSchool of Environmental and Rural Scienceen
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local.publisher.placeUnited Kingdomen
local.record.institutionUniversity of New Englanden
local.record.placeauen
local.relation.fundingsourcenoteThis work was supported by the Australian Department of Agriculture and Water Resources, through the “Filling the Research Gap” program (Host Control of Methane project) and the New Zealand Agricultural Greenhouse Gas Research Centre and Pastoral Greenhouse Gas Research Consortium (objective 5.1) research project.en
local.search.authorXiang, Ruidongen
local.search.authorMcNally, Jodyen
local.search.authorRowe, Suzanneen
local.search.authorJonker, Arjanen
local.search.authorPinares-Patino, Cesar Sen
local.search.authorOddy, V Huttonen
local.search.authorVercoe, Phil Een
local.search.authorMcEwan, John Cen
local.search.authorDalrymple, Brian Pen
local.sensitive.culturalNoen
local.sourceriskNoen
local.subject.for2020300305 Animal reproduction and breedingen
local.title.maintitleGene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane productionen
local.uneassociationNoen
local.year.published2016en
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