A Systems Biology Approach Using Transcriptomic Data Reveals Genes and Pathways in Porcine Skeletal Muscle Affected by Dietary Lysine

Wang, Taiji; Feugang, Jean M.; Crenshaw, M. A.; Regmi, Naresh; Blanton, J. R.; Liao, Shengfa F

doi:10.20944/preprints201704.0052.v1

Cited by 6 publications

(6 citation statements)

References 64 publications

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“…HSP40 plays a vital role to obesity-induced insulin resistance and type 2 diabetes (T2D) [ 48 ]. Decreased muscle protein degradation may be regulated though DNAJA1 pathway in swine [ 49 ]. m 6 A-dependent CDK2 expression, mediated by FTO Alpha-Ketoglutarate Dependent Dioxygenase ( FTO ) and YTH N6-Methyladenosine RNA Binding Protein 2 ( YTHDF2 ), contributes to adipogenesis inhibition [ 50 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Wang

Hou

et al. 2020

Animals

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Intramuscular fat (IMF) is essential for improving the palatability and flavor of meat, and it is strongly associated with human insulin resistance. RNA editing is a widespread regulating event in different tissues. Here, we investigated the global RNA editing difference of two groups of pig with different IMF contents to find the potential editing sites affecting IMF. In this research, RES-Scanner and REDItools were used to identify RNA editing sites based on the whole genome and transcriptome sequencing data of the high and low groups composed of three full-sib pairs with opposite IMF phenotypes. A total of 295 RNA editing sites were investigated in the longissimus dorsi muscle, and 90.17% of these sites caused A to G conversion. After annotation, most editing sites were located in noncoding regions (including five sites located on the 3′ UTR regions). Five editing sites (including two sites that could lead to nonsynonymous amino acid changes) were located in the exons of genes. A total of 36 intergroup (high and low IMF) differential RNA editing sites were found in 33 genes. Some candidate editing sites, such as sites in acyl-coenzymeA: cholesterol acyltransferase 1 (ACAT1), coatomer protein, subunit alpha (COPA), and nuclear receptor coactivator 3 (NCOA3), were selected as candidate RNA editing sites associated with IMF. One site located on the 3′ UTR region of growth hormone secretagogue receptor (GHSR) may regulate GHSR expression by affecting the interaction of miRNA and mRNA. In conclusion, we identified a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle which useful for pig IMF breeding or human insulin resistances research.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Wang

Hou

et al. 2020

Animals

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“…Other key nodes like HSP90AB1, STAT3, RHOA appear to have no direct effect on the symptoms seen in TMD when downregulated, as these are commonly seen upregulated in muscular diseases (Tsumagari et al, 2011;Tierney et al, 2014;Wang et al, 2017).…”

Section: Protein-protein Interaction Network and Topological Analysismentioning

confidence: 99%

New insights in Tibial muscular dystrophy revealed by protein-protein interaction networks

Leite

Blighe

2018

Preprint

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“…Presently, various platforms of transcriptomics analysis can be used to acquire valuable nutrigenomics information. DNA microarray technology is a hybridization-based high-throughput method for transcriptomics analysis, which is widely used for profiling animal transcriptomes in certain physiological or pathological conditions (39, 40). The basic principle of microarray analysis is hybridization of cDNA samples with spotted specific oligonucleotide probes, such as short-oligonucleotide, long-oligonucleotide, or cDNA (41, 42).…”

Section: The Transcriptomics Approach and Rna-seq Technologymentioning

confidence: 99%

“…Gene ontology (GO) analysis can be performed for each DEG against the GO database to find out the biological processes associated with the given DEG (80). Similarly, to understand more details about the biological context of a DEG, pathway and function enrichment analyses and network prediction can be conducted using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (81), DAVID (82), or other commercial knowledge systems such as Ingenuity Pathway Analysis (39, 40). Results obtained from these pathway enrichment analyses can help to identify genetic biomarkers, to annotate novel transcripts, or to provide interpretable information about the DEG associated with complex molecular interactions and biological functions.…”

Section: Principle History and Procedures Of Rna-seq Technologymentioning

confidence: 99%

“…Research objectives, experimental design, and organism of interest are 3 key determinants in the selection of technology for quantitative analysis of gene expression. For a transcriptomic analysis of differential gene expression with a known reference genome of a given animal, DNA microarray is a robust and inexpensive technique as compared with other methods (40, 83). In contrast to the microarray approach, the sequencing-based GWA approaches, such as the RNA-Seq approach, can directly determine all the cDNA sequences.…”

Section: Principle History and Procedures Of Rna-seq Technologymentioning

confidence: 99%

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A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient–Gene Interactions in Agricultural Animals

Hasan

Feugang

Liao

2019

Current Developments in Nutrition

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Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient–gene interactions in agricultural animals.

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A Systems Biology Approach Using Transcriptomic Data Reveals Genes and Pathways in Porcine Skeletal Muscle Affected by Dietary Lysine

Cited by 6 publications

References 64 publications

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs

New insights in Tibial muscular dystrophy revealed by protein-protein interaction networks

A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient–Gene Interactions in Agricultural Animals

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