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Functional & Integrative Genomics

, Volume 12, Issue 1, pp 93–103 | Cite as

Muscle-specific gene expression is underscored by differential stressor responses and coexpression changes

  • Natalia Moreno-SánchezEmail author
  • Julia Rueda
  • Antonio Reverter
  • María Jesús Carabaño
  • Clara Díaz
Original Paper

Abstract

Variations on the transcriptome from one skeletal muscle type to another still remain unknown. The reliable identification of stable gene coexpression networks is essential to unravel gene functions and define biological processes. The differential expression of two distinct muscles, M. flexor digitorum (FD) and M. psoas major (PM), was studied using microarrays in cattle to illustrate muscle-specific transcription patterns and to quantify changes in connectivity regarding the expected gene coexpression pattern. A total of 206 genes were differentially expressed (DE), 94 upregulated in PM and 112 in FD. The distribution of DE genes in pathways and biological functions was explored in the context of system biology. Global interactomes for genes of interest were predicted. Fast/slow twitch genes, genes coding for extracellular matrix, ribosomal and heat shock proteins, and fatty acid uptake centred the specific gene expression patterns per muscle. Genes involved in repairing mechanisms, such as ribosomal and heat shock proteins, suggested a differential ability of muscles to react to similar stressing factors, acting preferentially in slow twitch muscles. Muscle attributes do not seem to be completely explained by the muscle fibre composition. Changes in connectivity accounted for 24% of significant correlations between DE genes. Genes changing their connectivity mostly seem to contribute to the main differential attributes that characterize each specific muscle type. These results underscore the unique flexibility of skeletal muscle where a substantial set of genes are able to change their behavior depending on the circumstances.

Keywords

Differential expression Skeletal muscle Gene coexpression System biology Microarrays 

Notes

Acknowledgements

The authors thank the Asociación de Avileña-Negra Ibérica and the Consejo Regulador de Carne de Ávila for their contribution in the sample collection. This work was partially funded by RTA2007-00081-00-00 (Ministerio de Ciencia e Innovación of Spain) and S2009AGR-1704-GENR (Consejería de Educación, Comunidad de Madrid) projects.

Supplementary material

10142_2011_249_MOESM1_ESM.pdf (317 kb)
Fig. S1 IPA-associated network functions for the genes upregulated in FD (PDF 316 kb)
10142_2011_249_MOESM2_ESM.pdf (314 kb)
Fig. S2 IPA-associated network functions for the genes upregulated in PM (PDF 314 kb)
10142_2011_249_MOESM3_ESM.doc (142 kb)
Table S1A Genes upregulated in Psoas major (PM) (DOC 141 kb)
10142_2011_249_MOESM4_ESM.doc (154 kb)
Table S1B Genes overexpressed in Flexor digitorum (FD) (DOC 152 kb)

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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Natalia Moreno-Sánchez
    • 1
    Email author
  • Julia Rueda
    • 2
  • Antonio Reverter
    • 3
  • María Jesús Carabaño
    • 1
  • Clara Díaz
    • 1
  1. 1.Departamento de Mejora Genética Animal, INIA (Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria)MadridSpain
  2. 2.Departamento de Genética, Facultad de BiologíaUniversidad Complutense de MadridMadridSpain
  3. 3.CSIRO Livestock Industries and Cooperative Research Centre for Beef Genetic Technologies, Queensland Bioscience PrecinctBrisbaneAustralia

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