Limits...
Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation.

Jiang S, Wei H, Song T, Yang Y, Peng J, Jiang S - PLoS ONE (2013)

Bottom Line: RNA-Seq was used to screen for differentially expressed genes (DEGs) during the in vitro differentiation of MSVC and subcutaneous stromal vascular cell (ASVC) on days 0, 2 and 4.A total of 985 DEGs were identified during ASVC differentiation and 1469 DEGs during MSVC differentiation.Among these DEGs, 409 genes were specifically expressed during ASVC differentiation, 893 genes were specifically expressed during MSVC differentiation, and 576 DEGs were co-expressed during ASVC and MSVC differentiation.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan, People's Republic of China.

ABSTRACT
Intramuscular fat (IMF) is an important trait influencing meat quality, and preadipocyte differentiation is a key factor affecting IMF deposition. Here we compared the transcriptome profiles of porcine intramuscular and subcutaneous preadipocytes during differentiation to gain insight into specific molecular and cellular events associated with intramuscular stromal vascular cell (MSVC) differentiation. RNA-Seq was used to screen for differentially expressed genes (DEGs) during the in vitro differentiation of MSVC and subcutaneous stromal vascular cell (ASVC) on days 0, 2 and 4. A total of 985 DEGs were identified during ASVC differentiation and 1469 DEGs during MSVC differentiation. Among these DEGs, 409 genes were specifically expressed during ASVC differentiation, 893 genes were specifically expressed during MSVC differentiation, and 576 DEGs were co-expressed during ASVC and MSVC differentiation. The expression profiles of DEGs during ASVC or MSVC differentiation were determined by cluster analysis based on Short Time-series Expression Miner (STEM). Four significant STEM profiles (profiles 1, 4, 5, and 14) were determined during ASVC differentiation, and four significant STEM profiles (profiles 1, 4, 11, and 14) were determined during MSVC differentiation. Gene ontology (GO) analysis indicated that DEGs related to adipocyte differentiation were identified to be significantly enriched in both adipose and muscle profile 14. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs in adipose profile 14 and muscle profiles 11 and 14 (STEM clustered them into one cluster) showed that the PPAR signaling pathway was significantly enriched in these profiles and four signaling pathways were specifically enriched in muscle profiles 11 and 14. Furthermore, analysis of transcription factor binding sites (TFBS) in the gene set revealed two over-represented transcription factors (NR3C4 and NR3C1), which were specifically significantly enriched in the promoter regions of genes within muscle gene expression profiles 11 and 14.

Show MeSH
GO functional enrichment analysis of DEGs in adipose and muscle profile 1.The results are summarized in the following three main categories: biological process, molecular function, and cellular component. The y-axis indicates functional groups. The x-axis indicates –log (p value).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3795010&req=5

pone-0077094-g005: GO functional enrichment analysis of DEGs in adipose and muscle profile 1.The results are summarized in the following three main categories: biological process, molecular function, and cellular component. The y-axis indicates functional groups. The x-axis indicates –log (p value).

Mentions: The genes in adipose expression profile 1 were mainly clustered into the following functional groups: intracellular signal transduction, cellular component organization or biogenesis, negative regulation of biological process, binding (Figure 5). Figure 5 also shows that the genes in muscle profile 1 were mainly clustered into the following functional groups: negative regulation of biological process, localization of cell, regulation of cellular component organization, regulation of response to stimulus. Adipose profile 4 consisted of only 59 genes, which were clustered into two significant GO categories, namely, cell junction organization, actin filament-based movement (Figure 6). However, muscle profile 4 comprised 173 genes that were clustered into 14 significant GO categories (Figure 6), which were predominant cell localization, regulation of localization, carbohydrate derivative metabolic process, extracellular region and ECM.


Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation.

Jiang S, Wei H, Song T, Yang Y, Peng J, Jiang S - PLoS ONE (2013)

GO functional enrichment analysis of DEGs in adipose and muscle profile 1.The results are summarized in the following three main categories: biological process, molecular function, and cellular component. The y-axis indicates functional groups. The x-axis indicates –log (p value).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3795010&req=5

pone-0077094-g005: GO functional enrichment analysis of DEGs in adipose and muscle profile 1.The results are summarized in the following three main categories: biological process, molecular function, and cellular component. The y-axis indicates functional groups. The x-axis indicates –log (p value).
Mentions: The genes in adipose expression profile 1 were mainly clustered into the following functional groups: intracellular signal transduction, cellular component organization or biogenesis, negative regulation of biological process, binding (Figure 5). Figure 5 also shows that the genes in muscle profile 1 were mainly clustered into the following functional groups: negative regulation of biological process, localization of cell, regulation of cellular component organization, regulation of response to stimulus. Adipose profile 4 consisted of only 59 genes, which were clustered into two significant GO categories, namely, cell junction organization, actin filament-based movement (Figure 6). However, muscle profile 4 comprised 173 genes that were clustered into 14 significant GO categories (Figure 6), which were predominant cell localization, regulation of localization, carbohydrate derivative metabolic process, extracellular region and ECM.

Bottom Line: RNA-Seq was used to screen for differentially expressed genes (DEGs) during the in vitro differentiation of MSVC and subcutaneous stromal vascular cell (ASVC) on days 0, 2 and 4.A total of 985 DEGs were identified during ASVC differentiation and 1469 DEGs during MSVC differentiation.Among these DEGs, 409 genes were specifically expressed during ASVC differentiation, 893 genes were specifically expressed during MSVC differentiation, and 576 DEGs were co-expressed during ASVC and MSVC differentiation.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agriculture University, Wuhan, People's Republic of China.

ABSTRACT
Intramuscular fat (IMF) is an important trait influencing meat quality, and preadipocyte differentiation is a key factor affecting IMF deposition. Here we compared the transcriptome profiles of porcine intramuscular and subcutaneous preadipocytes during differentiation to gain insight into specific molecular and cellular events associated with intramuscular stromal vascular cell (MSVC) differentiation. RNA-Seq was used to screen for differentially expressed genes (DEGs) during the in vitro differentiation of MSVC and subcutaneous stromal vascular cell (ASVC) on days 0, 2 and 4. A total of 985 DEGs were identified during ASVC differentiation and 1469 DEGs during MSVC differentiation. Among these DEGs, 409 genes were specifically expressed during ASVC differentiation, 893 genes were specifically expressed during MSVC differentiation, and 576 DEGs were co-expressed during ASVC and MSVC differentiation. The expression profiles of DEGs during ASVC or MSVC differentiation were determined by cluster analysis based on Short Time-series Expression Miner (STEM). Four significant STEM profiles (profiles 1, 4, 5, and 14) were determined during ASVC differentiation, and four significant STEM profiles (profiles 1, 4, 11, and 14) were determined during MSVC differentiation. Gene ontology (GO) analysis indicated that DEGs related to adipocyte differentiation were identified to be significantly enriched in both adipose and muscle profile 14. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs in adipose profile 14 and muscle profiles 11 and 14 (STEM clustered them into one cluster) showed that the PPAR signaling pathway was significantly enriched in these profiles and four signaling pathways were specifically enriched in muscle profiles 11 and 14. Furthermore, analysis of transcription factor binding sites (TFBS) in the gene set revealed two over-represented transcription factors (NR3C4 and NR3C1), which were specifically significantly enriched in the promoter regions of genes within muscle gene expression profiles 11 and 14.

Show MeSH