Cheirogaleus medius
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA300585 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR14572007_1.fastq.gz | Fastqsanger.gz | |||
| SRR14572007_2.fastq.gz | Fastqsanger.gz | |||
| SRR1634270_1.fastq.gz | Fastqsanger.gz | |||
| SRR1634270_2.fastq.gz | Fastqsanger.gz |
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Project description:The level of n-6 and n-3 polyunsaturated fatty acids may affect many cellular systems and functions via nuclear receptors or the bioactive lipid regulation of gene expression. The objective of this study was to investigate the changes in the muscle transcriptome and the biological functions regulated by increased consumption of n-3 and n-6 fatty acids in the pig gluteus medius muscle. The transcriptome of the gluteus medius muscle was studied for pigs subjected to either a control diet or a diet supplemented with linseed and rapeseed oil to increase polyunsaturated fatty acid content. Next-generation sequencing (NGS) was used to generate the muscle tissue transcriptome database. The results of the NGS indicate a role of the fatty acids in the regulation of the expression of genes essential for muscle tissue development and functioning. Functional analysis revealed that the identified genes were important for a number of biological processes including protein development, signaling, inflammatory response, membranes, and lipid metabolism. The genes that were expressed specifically in only one of the dietary groups were responsible for many of the same processes listed above, indicating that biological processes were strongly modulated and tended to switch between coherent stages in response to increased levels of n-6 and n-3 fatty acids. Several nuclear receptors regulating transcription showed altered expression, including hepatocyte nuclear factor-4α (HNF4alpha), carbohydrate responsive element binding protein (ChREBP), and nuclear factor κB (NFkappaΒ). We suggest that the identified changes were largely due to regulation of those transcription factors. Our results provide strong evidence that n-6 and n-3 fatty acids regulate fundamental metabolic processes in muscle tissue development and functioning.
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Project description:In the last 20 years, there has been significant research towards defining the genetic basis of lipid metabolism and meat quality related traits in pigs. Nowadays, the study of the transcriptome and its regulatory mechanisms allows going far beyond in the genetic dissection of these complex traits. In present study, a genome-wide eQTL scan aiming to detect pig genome regions regulating levels of skeletal muscle mRNA expression has been performed. This study has been conducted on a commercial Duroc population where a number of QTL for muscle fat deposition and fatty acid composition had been detected. GeneChip Porcine Genome® arrays (Affymetrix) were used to determine the gene expression levels of gluteus medius samples from 105 Duroc pigs belonging to two groups with divergent phenotypes for fatness traits. This experimental design aimed to favour detection of eQTL affecting genes related to lipid metabolism and meat quality traits. The whole genome scan with a panel of 110 microsatellites allowed us detecting 613 genome-wide significant eQTL unequally distributed across the pig genome, SSC5 and SSC3 harbouring the highest number of eQTL. Moreover, 11 genome regions with eQTL affecting the expression levels of a high number of genes (eQTL hot spots) have been described. After mapping target probes and discarding low quality probes, a total of 59 cis- and 396 trans-acting eQTL were retained for further analyses. The functional classification showed that lipid-related GO terms were not the most enriched by the list of eQTL-regulated genes. However, a number of regulated genes functionally related to lipid metabolism and fat deposition traits were identified, and their functional relationship with these phenotypes were further investigated. With this purpose, eQTL results were integrated with 1) QTL linkage maps and 2) correlation data between phenotypes and gene expression levels. As a result, a comprehensive list of 29 positional and functional candidate genes was elaborated. These results represent a valuable contribution to the comprehension of genetic regulation of skeletal muscle individual gene expression in swine species, and a first step towards disentangling gene networks and molecular mechanisms involved in lipid metabolism and meat quality traits. 105 gluteus medius samples from 105 animals belonging to two groups of 53 and 52 animals each: HIGH group had higher carcass, plasma and muscle fat content; LOW group had lower carcass, plasma and muscle fat content
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