Two Distinct Regions in the 3′ Untranslated Region of Tumor Necrosis Factor Alpha mRNA Form Complexes with Macrophage Proteins

Abstract

The production of tumor necrosis factor alpha (TNF-α), a key proinflammatory cytokine essential for the function of the immune system, is regulated at both the transcriptional and posttranscriptional levels. In this report, we focus on the interaction of TNF-α mRNA with macrophage proteins, likely mediators of its posttranscriptional control. Mapping of murine TNF-α mRNA by using a combination of RNase protection and RNA gel shift assays revealed that two distinct sites within the 3′ untranslated region (3′-UTR) engage in the formation of four major RNA-protein complexes, while no protein binding to the 5′-UTR or coding sequences was detected. The protein-binding site of three RNA-protein complexes, A, B, and C, is positioned between bases 1291 and 1320 inside the AU-rich sequence, a region previously shown to be crucial for both translational repression and lipopolysaccharide inducibility of TNF-α. An additional protein complex (complex D) whose binding to the TNF-α 3′-UTR was independent of the presence of AU-rich sequences was identified. At least six protein species with apparent molecular masses of 48, 52, 54, 81, 101, and 150 kDa are in direct contact with TNF-α mRNA. The RNA-binding proteins are differentially distributed in the cell: complexes A and D are present predominantly in the cytosol, while complexes B and C are found in the nucleus and associated with particulate cytoplasmic fractions. Cytosolic complex A displays comparatively high specificity for TNF-α mRNA, while the binding of complexes B and C to TNF-α mRNA is readily competed for by other AU-rich sequence-containing RNAs. In summary, these findings demonstrate that two regions of the TNF-α mRNA molecule interact with macrophage RNA-binding protein complexes that differ in their core protein composition, cellular distribution, and affinity to TNF-α mRNA.