Bioinformatics Analysis of Transcriptome Dynamics During Growth in Angus Cattle Longissimus Muscle

Authors

Sonia J. Moisa, University of Illinois
Daniel W. Shike, University of Illinois
Daniel E. Graugnard, University of Illinois
Sandra L. Rodriquez-Zas, University of Illinois
Robin E. Everts, University of Illinois
Harris A. Lewin, University of IllinoisFollow
Dan B. Faulkner, University of ArizonaFollow
Larry L. Berger, University of Nebraska-LincolnFollow
Juan J. Loor, University of IllinoisFollow

Date of this Version

2013

Citation

Bioinformatics and Biology Insights 2013:7 253–270

Comments

© the author(s)

Open access

doi: 10.4137/BBI.S12328

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.