Insights into TTP Function through Transcriptome-Wide Binding Sites Atlas

Precise control of mRNA decay during inflammation is essential for host survival during response to pathogens. Parameters determining timing, quality and specificity of mRNA degradation within the entire inflammation-associated transcriptome remain incompletely understood. Tristetraprolin (TTP) is AU-rich element binding protein involved in destabilization of a wide range of inflammation-associated mRNAs, most notably mRNAs of cytokines and chemokines. Consistently with targeting proinflammatory mRNAs, TTP knock-out mice display severe hyperinflammation and suffer from different chronic inflammatory disorders.

Using transcriptome-wide high resolution occupancy profiling, we qualitatively and quantitatively characterize TTP binding positions and functionally relate them to TTP-dependent mRNA decay in immunostimulated primary murine macrophages. We identify pervasive TTP binding with incompletely penetrant linkage to mRNA destabilization. A necessary but not sufficient feature of TTP-mediated mRNA destabilization is binding to 3’ UTRs. Mapping of binding positions of the mRNA-stabilizing protein HuR in activated macrophages revealed that TTP and HuR binding sites in 3’ UTRs occur mostly in different transcripts implicating only a limited co-regulation of inflammatory mRNAs by these proteins. Remarkably, we identified strong pervasive TTP binding to introns of stable transcripts. Intronic TTP-binding sites are remarkably different from the 3’ UTR sites in their motif and configuration. Nuclear TTP binds to spliced-out introns and is maintained in the nucleus throughout the inflammatory response.

Our functional annotation of TTP and HuR binding positions in the context of TTP-mediated mRNA destabilization identifies a cis-acting regulon controlling TTP-dependent mRNA decay in the macrophage transcriptome during different phases of inflammation.