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. 2013 Aug 4:7:253-70.
doi: 10.4137/BBI.S12328. eCollection 2013.

Bioinformatics analysis of transcriptome dynamics during growth in angus cattle longissimus muscle

Sonia J Moisá  1 , Daniel W Shike, Daniel E Graugnard, Sandra L Rodriguez-Zas, Robin E Everts, Harris A Lewin, Dan B Faulkner, Larry L Berger, Juan J Loor
Affiliations

Bioinformatics analysis of transcriptome dynamics during growth in angus cattle longissimus muscle

Sonia J Moisá et al. Bioinform Biol Insights. .

Abstract

Transcriptome dynamics in the longissimus muscle (LM) of young Angus cattle were evaluated at 0, 60, 120, and 220 days from early-weaning. Bioinformatic analysis was performed using the dynamic impact approach (DIA) by means of Kyoto Encyclopedia of Genes and Genomes (KEGG) and Database for Annotation, Visualization and Integrated Discovery (DAVID) databases. Between 0 to 120 days (growing phase) most of the highly-impacted pathways (eg, ascorbate and aldarate metabolism, drug metabolism, cytochrome P450 and Retinol metabolism) were inhibited. The phase between 120 to 220 days (finishing phase) was characterized by the most striking differences with 3,784 differentially expressed genes (DEGs). Analysis of those DEGs revealed that the most impacted KEGG canonical pathway was glycosylphosphatidylinositol (GPI)-anchor biosynthesis, which was inhibited. Furthermore, inhibition of calpastatin and activation of tyrosine aminotransferase ubiquitination at 220 days promotes proteasomal degradation, while the concurrent activation of ribosomal proteins promotes protein synthesis. Therefore, the balance of these processes likely results in a steady-state of protein turnover during the finishing phase. Results underscore the importance of transcriptome dynamics in LM during growth.

Keywords: growth; intramuscular fat; longissimus muscle; nutrition.

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Figures

Figure 1
Figure 1
Impact and direction of the impact of the Metabolism KEGG Category, total number of Differentially Expressed Genes (DEG) due to time on experiment for each time comparison. Total number of genes = 13,153 (P value < 0.05; FDR < 0.01).
Figure 2
Figure 2
Direction of the impact (vertical bars, negative values for inhibited pathways and positive values for activated pathways) and impact (dots with different shapes) for each time comparison for the KEGG category metabolism (P value < 0.05; FDR < 0.01).
Figure 3
Figure 3
Results of the most impacted pathways during the growing phase and finishing phase (220 vs. 0) uncovered by the Dynamic Impact Approach (DIA) based on Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways database analysis of the bovine muscle transcriptome. Columns represent the direction of the pathway (green color = inhibition, red color = activation). Continuous black lines show the impact of each pathway (P value < 0.05; FDR < 0.01).
Figure 4
Figure 4
Results of the most impacted pathways during the growing phase and finishing phase (220 vs. 0) uncovered by the Dynamic Impact Approach (DIA) based on Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways database analysis of the bovine muscle transcriptome. Columns represent the direction of the pathway (green color = inhibition, red color = activation). Continuous black lines show the impact of each pathway (P value < 0.05; FDR < 0.01).
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