Widespread Differential Maternal and Paternal Genome Effects on Fetal Bone Phenotype at Mid-Gestation

Xiang, Ruidong; Lee, Alice M. C.; Eindorf, Tanja; Javadmanesh, Ali; Ghanipoor-Samami, Mani; Gugger, Madeleine; Fitzsimmons, Carolyn; Kruk, Zbigniew A.; Pitchford, W. S.; Leviton, A.; Thomsen, D. A.; Beckman, Ian; Anderson, Gail I.; Burns, B. M.; Rutley, D. L.; Chen, Xian; Hiendleder, Stefan

doi:10.1002/jbmr.2263

Cited by 11 publications

(13 citation statements)

References 78 publications

(146 reference statements)

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“…Phenotypic data and Z-score of defined gene sets (described below) were analysed using general linear models with stepwise backwards elimination5758. Variables fitted in the initiated model included main effects, i.e., feed quality (good/poor), feed level (high/low) and all two way interactions.…”

Section: Methodsmentioning

confidence: 99%

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

Xiang

McNally

Rowe

et al. 2016

Sci Rep

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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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Section: Methodsmentioning

confidence: 99%

“…5, Supplementary Table S3). Contributions of feed quality and level to variations in phenotypic and gene set expression using type 1 sum of square values followed previous procedures5759. The Z-score of a gene set was estimated as the mean of Z-scores of FPKM of each gene member.…”

Section: Methodsmentioning

confidence: 99%

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

Xiang

McNally

Rowe

et al. 2016

Sci Rep

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“…More recent analyses in mouse have shown that H19 harbors miRNAs, one of which regulates cell proliferation and placental size, most likely by targeting IGF1R transcript [ 57 ]. Furthermore, correlations between H19 transcript abundance and bovine fetal skeletal muscle and bone mass suggest that development of other organs may be regulated by H19 [ 58 , 59 ].…”

Section: Introductionmentioning

confidence: 99%

Atlas of tissue- and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system

et al. 2018

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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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“…All tissue samples were collected on ice. Samples for DNA extraction were snap frozen in liquid nitrogen and those for RNA extraction placed in RNAlater (Ambion, Austin, United States) and stored at −80 • C after 24 h at 4 • C. For assessment of muscle mass, the spinal column with cervical, thoracic, and lumbar vertebrae and the left and right sixth rib were removed from the fetal carcass, cleaned of tissue (Xiang et al, 2014), and their lengths measured using photographic images and the image analysis program analySIS (analySIS, IBM, St Leonards NSW, Australia).…”

Section: Samples and Phenotype Datamentioning

confidence: 99%

Mitochondrial DNA Depletion in Granulosa Cell Derived Nuclear Transfer Tissues

Bebbere

Ulbrich

Giller

et al. 2021

Front. Cell Dev. Biol.

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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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Widespread Differential Maternal and Paternal Genome Effects on Fetal Bone Phenotype at Mid-Gestation

Cited by 11 publications

References 78 publications

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

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

Atlas of tissue- and developmental stage specific gene expression for the bovine insulin-like growth factor (IGF) system

Mitochondrial DNA Depletion in Granulosa Cell Derived Nuclear Transfer Tissues

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