E-PROT-89
Ontology highlight
ABSTRACT:
PROVIDER: E-PROT-89 | ExpressionAtlas | 2022-01-18
REPOSITORIES: ExpressionAtlas
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Project description:Seaweeds, including the green Ulva lactuca, can potentially reduce competition between feed, food, and fuel. They can also contribute to the improved development of weaned piglets. However, their indigestible polysaccharides of the cell wall pose a challenge. This can be addressed through carbohydrase supplementation, such as the recombinant ulvan lyase. The objective of our study was to assess the muscle metabolism of weaned piglets fed with 7% U. lactuca and 0.01% ulvan lyase supplementation, using an integrated transcriptomics (RNA-seq) and proteomics (LC-MS) approach.
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Project description:Gonadal trans-differentiation from ovary to testis occurs in a same individual, suggesting a role of epigenetic regulation. However, histone modifications concerning the sex reversal process remain elusive. Here, we report a developmental atlas of histone modifications in the gonadal differentiation, including acetylation, methylation, and ubiquitination, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We provided a detail distribution map of these modification sites including novel histone modifications along histones H2a, H2b, H3, and H4, and revealed their relationship with types of gonadal differentiation. We then determined a testis-enriched histone modification site, H2b monoubiquitination at K120, and its association with spermatogenesis. ChIP-seq demonstrated that the modification was highly enriched in the male sex-determining gene dmrt1, in particular association with its exon regions, suggesting its role in transcriptional elongation of dmrt1 in testis. Together, these data not only provide a new resource for epigenetic study in gonadal development, but also define an association of histone modifications in gonadal differentiation from ovary to testis.
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Project description:Epoxygenases belong to the cytochrome P450 family and they generate epoxyeicosatrienoic acids (EETs) known to have anti-inflammatory effects but little is known about their role in macrophage function. By high-throughput sequencing of RNA (RNA-seq) in primary macrophages derived fromrodents and humans, we establish the relative expression of epoxygenases in these cells. Zinc-finger nuclease-mediated targeted gene deletion of the major rat macrophage epoxygenase Cyp2j4 (orthologue of human CYP2J2),resulted inreduced EET synthesis. Cyp2j4-/-macrophages have relatively increased PPARγ levels and show a pro-fibrotic transcriptome,displayingover-expression of a specific subset of genes (260 transcripts) primarily involved in extracellular matrix, with fibronectin being the most abundantly expressed transcript.Fibronectin expression is under the control of epoxygenase activity in human and rat primary macrophages. In keeping with the invitro findings, Cyp2j4-/- rats show up-regulation of type I collagen following unilateral ureter obstruction (UUO) of the kidney and quantitative proteomics analysis (LC-MS/MS) showed increased renal type I collagen and fibronectin protein abundance resulting from experimentally induced crescentic glomerulonephritis in these rats. Taken together, these results identify the rat epoxygenase Cyp2j4 as a determinant of a pro-fibrotic macrophage transcriptome that could have implications in various inflammatory conditions depending on macrophage function. Gene expression profile generated for macrophages in wild type and Cyp2j4 KO WKY rats
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Project description:Sustainable avian production demands genetic strategies beyond vaccines to enhance disease resilience, particularly in indigenous breeds like Lueyang Silky Fowl (LSF), which show superior resistance compared to commercial White Leghorn chickens (WLC) but lack molecular characterization. We hypothesized LSF breast muscle harbors integrated immune–metabolic adaptations absent in WLC, reflecting evolutionary divergences and physiological ecology. We performed RNA-seq, LC-MS/MS proteomics and untargeted metabolomics on sex- and age-matched LSF and WLC breast muscle (n=3/group). Differentially expressed genes (DEGs), proteins (DAPs), and metabolites (DAMs) were identified and integrated via pathway enrichment and network analyses. LSF muscle showed 2,577 DEGs (949 up, 1,628 down), 262 DAPs (48 up, 214 down), and 197 DAMs (52 up, 145 down). Concordant enrichments spanned mitochondrial oxidative phosphorylation; amino-acid metabolism (arginine/proline; alanine/aspartate/glutamate); MAPK and calcium signaling; and antioxidant pathways (notably glutathione). Integrated networks revealed 66 shared KEGG pathways, including convergent hubs in calcium/MAPK signaling, apelin, and focal adhesion, nominating candidate markers like NOS1, GOT1, PRKCA, MAP2K6, and ATP6V1E1. These bulk-tissue signatures likely integrate myocyte-intrinsic, stromal, and resident immune-cell programs; thus, offering testable signatures for avian immunometabolic resilience. We propose validation through single-cell/spatial transcriptomics, immunohistochemistry, targeted LC-MS and metabolomics, and pathogen challenge assays. This study advances ornithological understanding by revealing breed-specific physiological adaptations in poultry, positioning muscle as proxy for systemic resilience, and providing biomarkers for genomic selection to conserve and enhance genetic diversity in resilient avian lines under intensive farming pressure.
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Project description:Epoxygenases belong to the cytochrome P450 family and they generate epoxyeicosatrienoic acids (EETs) known to have anti-inflammatory effects but little is known about their role in macrophage function. By high-throughput sequencing of RNA (RNA-seq) in primary macrophages derived fromrodents and humans, we establish the relative expression of epoxygenases in these cells. Zinc-finger nuclease-mediated targeted gene deletion of the major ratmacrophage epoxygenaseCyp2j4 (orthologue of human CYP2J2),resulted inreduced EET synthesis. Cyp2j4-/-macrophages have relatively increased PPARγ levels and show a pro-fibrotic transcriptome,displayingover-expression of a specific subset of genes (260 transcripts) primarily involved in extracellular matrix, with fibronectin being the most abundantly expressed transcript.Fibronectin expression is under the control of epoxygenase activity in human and rat primary macrophages. In keeping with the invitro findings, Cyp2j4-/- rats show up-regulation of type I collagen following unilateral ureter obstruction (UUO) of the kidney and quantitative proteomics analysis (LC-MS/MS) showed increased renal type I collagen and fibronectin protein abundance resulting from experimentally induced crescentic glomerulonephritis in these rats. Taken together, these results identify the rat epoxygenase Cyp2j4 as a determinant of a pro-fibrotic macrophage transcriptome that could have implications in various inflammatory conditions depending on macrophage function.
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