Mass spectrometry-based proteomics identifies UPF1 as a critical gene expression regulator in MonoMac 6 cells

J Proteome Res. 2013 Jun 7;12(6):2622-9. doi: 10.1021/pr301193f. Epub 2013 May 24.


5-Lipoxygenase (5-LO) catalyzes the two initial steps in the biosynthesis of leukotrienes, a group of inflammatory lipid mediators derived from arachidonic acid. Recently, we have demonstrated that 5-LO mRNA expression is regulated by alternative splicing and nonsense-mediated mRNA decay (NMD). In addition to this, 5-LO protein expression was reduced on translational level in UPF1 knockdown cells, suggesting that UPF1 has a positive influence on 5-LO translation. Therefore, a mass spectrometry-based proteomics study was performed to identify compartment-specific protein expression changes upon UPF1 knockdown in differentiated and undifferentiated MM6 cells. The proteomics analysis revealed that the knockdown of UPF1 results in numerous protein changes in the microsomal fraction (~21%) but not in the cytosolic fraction (<1%). The results suggest that UPF1 is a critical gene expression regulator in a compartment-specific way. During differentiation by TGFβ and calcitriol, the majority of UPF1 regulated proteins were adjusted to normal level. This indicates that the translational regulation by UPF1 can potentially be cell differentiation-dependent.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Arachidonate 5-Lipoxygenase / genetics*
  • Arachidonate 5-Lipoxygenase / metabolism
  • Calcitriol / pharmacology
  • Cell Differentiation / drug effects
  • Cell Line
  • Gene Expression Regulation / drug effects*
  • Gene Knockdown Techniques
  • Humans
  • Microsomes / drug effects
  • Microsomes / metabolism
  • Monocytes / cytology
  • Monocytes / drug effects
  • Monocytes / metabolism*
  • Nonsense Mediated mRNA Decay
  • Protein Biosynthesis / drug effects
  • Proteomics*
  • RNA Helicases
  • Tandem Mass Spectrometry
  • Trans-Activators / genetics*
  • Trans-Activators / metabolism
  • Transforming Growth Factor beta / pharmacology


  • Trans-Activators
  • Transforming Growth Factor beta
  • Arachidonate 5-Lipoxygenase
  • RNA Helicases
  • UPF1 protein, human
  • Calcitriol