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Estrella CAS, Gatford KL, Xiang R, Javadmanesh A, Ghanipoor-Samami M, Nattrass GS, Shuaib E, McAllister MM, Beckman I, Thomsen DA, Clifton VL, Owens JA, Roberts CT, Hiendleder S, Kind KL. Asymmetric growth-limiting development of the female conceptus. Front Endocrinol (Lausanne) 2024; 14:1306513. [PMID: 38362586 PMCID: PMC10867182 DOI: 10.3389/fendo.2023.1306513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/08/2023] [Indexed: 02/17/2024] Open
Abstract
Introduction Sex differences in prenatal growth may contribute to sex-dependent programming effects on postnatal phenotype. Methods We integrated for the first time phenotypic, histomorphological, clinico-chemical, endocrine and gene expression analyses in a single species, the bovine conceptus at mid-gestation. Results We demonstrate that by mid-gestation, before the onset of accelerated growth, the female conceptus displays asymmetric lower growth compared to males. Female fetuses were smaller with lower ponderal index and organ weights than males. However, their brain:body weight, brain:liver weight and heart:body weight ratios were higher than in males, indicating brain and heart 'sparing'. The female placenta weighed less and had lower volumes of trophoblast and fetal connective tissue than the male placenta. Female umbilical cord vessel diameters were smaller, and female-specific relationships of body weight and brain:liver weight ratios with cord vessel diameters indicated that the umbilico-placental vascular system creates a growth-limiting environment where blood flow is redistributed to protect brain and heart growth. Clinico-chemical indicators of liver perfusion support this female-specific growth-limiting phenotype, while lower insulin-like growth factor 2 (IGF2) gene expression in brain and heart, and lower circulating IGF2, implicate female-specific modulation of key endocrine mediators by nutrient supply. Conclusion This mode of female development may increase resilience to environmental perturbations in utero and contribute to sex-bias in programming outcomes including susceptibility to non-communicable diseases.
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Affiliation(s)
- Consuelo Amor S. Estrella
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Kathryn L. Gatford
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Ruidong Xiang
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Ali Javadmanesh
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Mani Ghanipoor-Samami
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Greg S. Nattrass
- South Australian Research and Development Institute, Livestock Systems, Roseworthy, SA, Australia
| | - Entesar Shuaib
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Milton M. McAllister
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Ian Beckman
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Dana A. Thomsen
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Vicki L. Clifton
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Mater Research Institute, University of Queensland, Brisbane, QLD, Australia
| | - Julie A. Owens
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Deakin University, Geelong, VIC, Australia
| | - Claire T. Roberts
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Flinders University, College of Medicine and Public Health, Adelaide, SA, Australia
| | - Stefan Hiendleder
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Karen L. Kind
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Epigenetics and Genetics Group and Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
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2
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MacPhillamy C, Ren Y, Chen T, Hiendleder S, Low WY. MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver. Front Genet 2023; 14:1329939. [PMID: 38162682 PMCID: PMC10757722 DOI: 10.3389/fgene.2023.1329939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes. Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth. Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism. Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.
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Affiliation(s)
- Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Tong Chen
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
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3
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Karami K, Zerehdaran S, Javadmanesh A. Differential Expression of RNAseq Imprinted Genes from Bovine Females Before and After Puberty. Biochem Genet 2023; 61:2633-2649. [PMID: 37225913 DOI: 10.1007/s10528-023-10395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/02/2023] [Indexed: 05/26/2023]
Abstract
The productivity of beef cows depends on early reproduction traits such as puberty and has an economic impact on the efficiency of production system. Imprinted genes modulate many important endocrine processes such as growth, the onset of puberty and maternal reproductive and behavior. The role of imprinted genes in puberty is a challenging subject since they show the reciprocal role of maternal and paternal genomes in progeny. Although, there are evidences of the involvement of imprint genes in puberty in human, the role of this type of genes in the onset of puberty in cattle has not been studied yet. Here we examined the expression of 27 imprinted genes in pre and post puberty in a bovine model to find differentially expressed imprinted genes in maternal-paternal purebreds and reciprocal crosses across eight tissues and discussed the task of these genes in this crucial process of development and in onset of puberty. DLK1 and MKRN3 that previously described as cause of the central precocious puberty (CPP) in human were differentially expressed in this study. Functional annotation analysis of differentially imprinted genes in different tissues showed significant biological processes of cellular response to growth factor stimulus, response to growth factor, response to parathyroid hormone, developmental growth and the importance of alternative splicing. The results of this study have implications in understanding the role of imprinted genes in the onset of puberty in cattle.
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Affiliation(s)
- Keyvan Karami
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Saeed Zerehdaran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Ali Javadmanesh
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
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4
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Liu R, Tearle R, Low WY, Chen T, Thomsen D, Smith TPL, Hiendleder S, Williams JL. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. BMC Genomics 2021; 22:410. [PMID: 34082698 PMCID: PMC8176687 DOI: 10.1186/s12864-021-07667-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses. Results In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. Conclusions These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07667-2.
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Affiliation(s)
- Ruijie Liu
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Tong Chen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Dana Thomsen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Timothy P L Smith
- USMARC, USDA-ARS-US Meat Animal Research Center, Clay Center, NE, USA
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Present address: Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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5
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Bebbere D, Ulbrich SE, Giller K, Zakhartchenko V, Reichenbach HD, Reichenbach M, Verma PJ, Wolf E, Ledda S, Hiendleder S. Mitochondrial DNA Depletion in Granulosa Cell Derived Nuclear Transfer Tissues. Front Cell Dev Biol 2021; 9:664099. [PMID: 34124044 PMCID: PMC8194821 DOI: 10.3389/fcell.2021.664099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) is a key technology with broad applications that range from production of cloned farm animals to derivation of patient-matched stem cells or production of humanized animal organs for xenotransplantation. However, effects of aberrant epigenetic reprogramming on gene expression compromise cell and organ phenotype, resulting in low success rate of SCNT. Standard SCNT procedures include enucleation of recipient oocytes before the nuclear donor cell is introduced. Enucleation removes not only the spindle apparatus and chromosomes of the oocyte but also the perinuclear, mitochondria rich, ooplasm. Here, we use a Bos taurus SCNT model with in vitro fertilized (IVF) and in vivo conceived controls to demonstrate a ∼50% reduction in mitochondrial DNA (mtDNA) in the liver and skeletal muscle, but not the brain, of SCNT fetuses at day 80 of gestation. In the muscle, we also observed significantly reduced transcript abundances of mtDNA-encoded subunits of the respiratory chain. Importantly, mtDNA content and mtDNA transcript abundances correlate with hepatomegaly and muscle hypertrophy of SCNT fetuses. Expression of selected nuclear-encoded genes pivotal for mtDNA replication was similar to controls, arguing against an indirect epigenetic nuclear reprogramming effect on mtDNA amount. We conclude that mtDNA depletion is a major signature of perturbations after SCNT. We further propose that mitochondrial perturbation in interaction with incomplete nuclear reprogramming drives abnormal epigenetic features and correlated phenotypes, a concept supported by previously reported effects of mtDNA depletion on the epigenome and the pleiotropic phenotypic effects of mtDNA depletion in humans. This provides a novel perspective on the reprogramming process and opens new avenues to improve SCNT protocols for healthy embryo and tissue development.
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Affiliation(s)
- Daniela Bebbere
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy.,Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Susanne E Ulbrich
- ETH Zürich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Katrin Giller
- ETH Zürich, Animal Physiology, Institute of Agricultural Sciences, Zurich, Switzerland
| | - Valeri Zakhartchenko
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Horst-Dieter Reichenbach
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany.,Bavarian State Research Center for Agriculture, Institute of Animal Breeding, Grub, Germany
| | - Myriam Reichenbach
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany.,Bayern-Genetik GmbH, Grub, Germany
| | - Paul J Verma
- Livestock Sciences, South Australian Research and Development Institute, Roseworthy, SA, Australia.,School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Stefan Hiendleder
- Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Science, LMU Munich, Munich, Germany.,School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.,Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
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6
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Ghanipoor-Samami M, Javadmanesh A, Burns BM, Thomsen DA, Nattrass GS, Estrella CAS, Kind KL, Hiendleder S. Atlas of tissue- and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system. PLoS One 2018; 13:e0200466. [PMID: 30001361 PMCID: PMC6042742 DOI: 10.1371/journal.pone.0200466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 01/04/2023] Open
Abstract
The insulin-like growth factor (IGF) axis is fundamental for mammalian growth and development. However, no comprehensive reference data on gene expression across tissues and pre- and postnatal developmental stages are available for any given species. Here we provide systematic promoter- and splice variant specific information on expression of IGF system components in embryonic (Day 48), fetal (Day 153), term (Day 277, placenta) and juvenile (Day 365–396) tissues of domestic cow, a major agricultural species and biomedical model. Analysis of spatiotemporal changes in expression of IGF1, IGF2, IGF1R, IGF2R, IGFBP1-8 and IR genes, as well as lncRNAs H19 and AIRN, by qPCR, indicated an overall increase in expression from embryo to fetal stage, and decrease in expression from fetal to juvenile stage. The stronger decrease in expression of lncRNAs (average ―16-fold) and ligands (average ―12.1-fold) compared to receptors (average ―5.7-fold) and binding proteins (average ―4.3-fold) is consistent with known functions of IGF peptides and supports important roles of lncRNAs in prenatal development. Pronounced overall reduction in postnatal expression of IGF system components in lung (―12.9-fold) and kidney (―13.2-fold) are signatures of major changes in organ function while more similar hepatic expression levels (―2.2-fold) are evidence of the endocrine rather than autocrine/paracrine role of IGFs in postnatal growth regulation. Despite its rapid growth, placenta displayed a more stable expression pattern than other organs during prenatal development. Quantitative analyses of contributions of promoters P0-P4 to global IGF2 transcript in fetal tissues revealed that P4 accounted for the bulk of transcript in all tissues but skeletal muscle. Demonstration of IGF2 expression in fetal muscle and postnatal liver from a promoter orthologous to mouse and human promoter P0 provides further evidence for an evolutionary and developmental shift from placenta-specific P0-expression in rodents and suggests that some aspects of bovine IGF expression may be closer to human than mouse.
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Affiliation(s)
- Mani Ghanipoor-Samami
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- JS Davies Epigenetics and Genetics Group, Davies Research Centre, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Ali Javadmanesh
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- JS Davies Epigenetics and Genetics Group, Davies Research Centre, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Brian M. Burns
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Rockhampton, Queensland, Australia
| | - Dana A. Thomsen
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- JS Davies Epigenetics and Genetics Group, Davies Research Centre, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Greg S. Nattrass
- Livestock Systems, South Australian Research and Development Institute (SARDI), Roseworthy, South Australia, Australia
| | - Consuelo Amor S. Estrella
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- JS Davies Epigenetics and Genetics Group, Davies Research Centre, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Karen L. Kind
- JS Davies Epigenetics and Genetics Group, Davies Research Centre, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Stefan Hiendleder
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- JS Davies Epigenetics and Genetics Group, Davies Research Centre, School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
- * E-mail:
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7
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Estrella CAS, Kind KL, Derks A, Xiang R, Faulkner N, Mohrdick M, Fitzsimmons C, Kruk Z, Grutzner F, Roberts CT, Hiendleder S. Remodelling of the bovine placenta: Comprehensive morphological and histomorphological characterization at the late embryonic and early accelerated fetal growth stages. Placenta 2017. [DOI: 10.1016/j.placenta.2017.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production. Sci Rep 2016; 6:39022. [PMID: 27966600 PMCID: PMC5155297 DOI: 10.1038/srep39022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
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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