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

Sonia J. Moisá, 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

Research output: Contribution to journalArticle

10 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)253-270
Number of pages18
JournalBioinformatics and Biology Insights
Volume7
DOIs
StatePublished - 2013

Fingerprint

Gene Expression Profiling
Bioinformatics
Computational Biology
Muscle
Genes
Metabolism
Encyclopedias
Gene
Muscles
Growth
Transcriptome
Activation
Pathway
Genome
Databases
Tyrosine Transaminase
Proteins
Protein
Glycosylphosphatidylinositols
Protein Synthesis

Keywords

  • Growth
  • Intramuscular fat
  • Longissimus muscle
  • Nutrition

ASJC Scopus subject areas

  • Computer Science Applications
  • Biochemistry
  • Molecular Biology
  • Applied Mathematics
  • Computational Mathematics

Cite this

Moisá, S. J., Shike, D. W., Graugnard, D. E., Rodriguez-Zas, S. L., Everts, R. E., Lewin, H. A., ... Loor, J. J. (2013). Bioinformatics analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle. Bioinformatics and Biology Insights, 7, 253-270. https://doi.org/10.4137/BBI.S12328

Bioinformatics analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle. / Moisá, Sonia J.; Shike, Daniel W.; Graugnard, Daniel E.; Rodriguez-Zas, Sandra L.; Everts, Robin E.; Lewin, Harris A.; Faulkner, Dan B; Berger, Larry L.; Loor, Juan J.

In: Bioinformatics and Biology Insights, Vol. 7, 2013, p. 253-270.

Research output: Contribution to journalArticle

Moisá, SJ, Shike, DW, Graugnard, DE, Rodriguez-Zas, SL, Everts, RE, Lewin, HA, Faulkner, DB, Berger, LL & Loor, JJ 2013, 'Bioinformatics analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle', Bioinformatics and Biology Insights, vol. 7, pp. 253-270. https://doi.org/10.4137/BBI.S12328
Moisá, Sonia J. ; Shike, Daniel W. ; Graugnard, Daniel E. ; Rodriguez-Zas, Sandra L. ; Everts, Robin E. ; Lewin, Harris A. ; Faulkner, Dan B ; Berger, Larry L. ; Loor, Juan J. / Bioinformatics analysis of transcriptome dynamics during growth in Angus cattle longissimus muscle. In: Bioinformatics and Biology Insights. 2013 ; Vol. 7. pp. 253-270.
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