The RNA-binding protein TTP is a global post-transcriptional regulator of feedback control in inflammation

Nucleic Acids Res. 2016 Sep 6;44(15):7418-40. doi: 10.1093/nar/gkw474. Epub 2016 May 24.

Abstract

RNA-binding proteins (RBPs) facilitate post-transcriptional control of eukaryotic gene expression at multiple levels. The RBP tristetraprolin (TTP/Zfp36) is a signal-induced phosphorylated anti-inflammatory protein guiding unstable mRNAs of pro-inflammatory proteins for degradation and preventing translation. Using iCLIP, we have identified numerous mRNA targets bound by wild-type TTP and by a non-MK2-phosphorylatable TTP mutant (TTP-AA) in 1 h LPS-stimulated macrophages and correlated their interaction with TTP to changes at the level of mRNA abundance and translation in a transcriptome-wide manner. The close similarity of the transcriptomes of TTP-deficient and TTP-expressing macrophages upon short LPS stimulation suggested an effective inactivation of TTP by MK2, whereas retained RNA-binding capacity of TTP-AA to 3'UTRs caused profound changes in the transcriptome and translatome, altered NF-κB-activation and induced cell death. Increased TTP binding to the 3'UTR of feedback inhibitor mRNAs, such as Ier3, Dusp1 or Tnfaip3, in the absence of MK2-dependent TTP neutralization resulted in a strong reduction of their protein synthesis contributing to the deregulation of the NF-κB-signaling pathway. Taken together, our study uncovers a role of TTP as a suppressor of feedback inhibitors of inflammation and highlights the importance of fine-tuned TTP activity-regulation by MK2 in order to control the pro-inflammatory response.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Adaptor Proteins, Signal Transducing / metabolism*
  • Animals
  • Bone Marrow Cells / metabolism
  • Cell Survival
  • Cross-Linking Reagents
  • Cytokines / genetics
  • Feedback, Physiological*
  • Gene Expression Regulation*
  • High-Throughput Screening Assays
  • Humans
  • Immunoprecipitation
  • Inflammation / genetics
  • Inflammation / immunology
  • Inflammation / metabolism*
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Lipopolysaccharides / immunology
  • Macrophages / metabolism
  • Mice
  • NF-kappa B / metabolism
  • Phosphorylation
  • Protein Binding
  • Protein-Serine-Threonine Kinases / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / metabolism*
  • Substrate Specificity
  • Transcriptome

Substances

  • Adaptor Proteins, Signal Transducing
  • Cross-Linking Reagents
  • Cytokines
  • Intracellular Signaling Peptides and Proteins
  • Lipopolysaccharides
  • NF-kappa B
  • RNA, Messenger
  • RNA-Binding Proteins
  • TTP protein, mouse
  • MAP-kinase-activated kinase 2
  • Protein-Serine-Threonine Kinases