Tristetraprolin (TTP) regulates inflammatory and immune responses by destabilizing target mRNAs via binding to their 3'-UTR AREs. We have recently reported that TTP preferentially up-regulates the expression level of innate immunity genes involved in the type I interferon-mediated signaling pathway and viral response in cancer cells. To elucidate the role of TTP-RNA interaction in TTP-mediated upregulation of gene expression, we performed iRIP-seq experiments to obtain the RNA interaction map consisting of direct and indirect binding sites of TTP in HeLa cells. We found substantial TTP binding signals in mRNA regions and the introns. ARE-motif AUUUA is over-represented in TTP binding peaks. Strikingly, AUUUA frequency is high both in 3'UTR and intronic regions, and the intronic peaks were more associated with TTP-regulated genes. Analysis of the over-represented motifs in TTP peaks revealed the high frequencies of UAGG and GUGUG motifs reported for hnRNPA2/B1 and CELF1 respectively in the 3'UTR and introns, and also the UGGAC motif overlapping with the m6A motif GGACU in the CDS regions. We further demonstrated that TTP binds to multiple intronic and exonic sites in the pre-mRNA/mRNA of the transcription factor RelB, correlating with the TTP-upregulated expression of RelB. TTP-up-regulated genes without a TTP binding site, but not those with, are highly enriched in innate immunity pathways and show higher tendency of harboring RelB binding sites in their promoter regions. These findings support a model in which TTP binding of RelB pre-mRNA/mRNA coordinates the RelB upregulation and activation of the innate immunity for antiviral response.

中文翻译：

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Tristetraprolin-RNA相互作用图揭示了先天免疫基因表达的新型TTP-RelB调控网络。

Tristetraprolin（TTP）通过与靶标mRNA的3'-UTR ARE结合而不稳定来调节炎症和免疫反应。我们最近报道，TTP优先上调参与I型干扰素介导的信号通路和癌细胞中病毒反应的先天免疫基因的表达水平。为了阐明TTP-RNA相互作用在TTP介导的基因表达上调中的作用，我们进行了iRIP-seq实验，以获取由HeLa细胞中TTP的直接和间接结合位点组成的RNA相互作用图。我们在mRNA区域和内含子中发现大量的TTP结合信号。ARE基序AUUUA在TTP结合峰中过分代表。令人惊讶的是，AUUUA频率在3'UTR和内含子区域都很高，并且内含子峰与TTP调控的基因更多相关。对TTP峰中过度表达的基序的分析显示，分别在3'UTR和内含子中分别报告了hnRNPA2 / B1和CELF1的UAGG和GUGUG基序的高频率，以及在CDS区中与m6A基序GGACU重叠的UGGAC基序。 。我们进一步证明，TTP与转录因子RelB的pre-mRNA / mRNA中的多个内含子和外显子位点结合，与RelB的TTP上调表达相关。没有TTP结合位点但没有TTP结合位点的TTP上调基因在先天免疫途径中高度富集，并且在其启动子区域中具有更高的带有RelB结合位点的趋势。这些发现支持了这样一种模型，其中RelB前mRNA / mRNA的TTP结合可调节RelB上调和抗病毒反应固有免疫的激活。