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Liver Transcriptomes in C57BL/6 mice

ABSTRACT: Purpose: a transcriptome analysis was used to ascertain whether lipid metabolism disorders were induced by high-fat diet (HFD), and comparisons were made between control, HFD and DfCS-Ib(treatment) groups. Methods: liver mRNA profiles of C57BL/6 mice were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: HFD could change the expression of some genes and disturb normal metabolisms. However, there were fewer changes for genes of DfCS-Ib group mice. According to the KEGG Pathway Database and GO analysis, genes involving in lipid biosynthesis, degradation, and transportation were changed by HFD. Conclusions: Our study indicated that DfCS-Ib alleviated lipid disorder of HFD-fed mice in liver by normalizing the expressions of related genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE110526 | GEO | 2019/02/13

REPOSITORIES: GEO

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Project description:Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 150 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B gene, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU associated to meat quality and production traits.

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Liver Transcriptomes in C57BL/6 mice

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