Rattenbacher Bernd, Bohjanen Paul R
Department of Microbiology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota, Minneapolis, MN 55455, USA.
Methods Mol Biol. 2012;820:71-89. doi: 10.1007/978-1-61779-439-1_5.
A wide variety of cytokines are necessary for cell-cell communication in multicellular organisms, and cytokine dysregulation has detrimental effects, leading to disease states. Thus, it is a necessity that the expression of cytokines is tightly controlled. Regulation of cytokine gene expression takes place at different levels, including transcriptional and posttranscriptional levels. Ultimately, the steady-state levels of cytokine transcripts are determined by the equilibrium of transcription and degradation of this mRNA. Degradation rates of cytokine mRNAs can be measured in cells by blocking transcription with actinomycin D, harvesting RNA after different time points, and evaluating mRNA levels over time by northern blot. Cis-acting elements that mediate the rapid decay of numerous cytokine transcripts, including AU-rich elements (AREs), are found in the 3' untranslated region (UTR) of these transcripts. Putative regulatory cis-elements can be cloned into the 3' UTR of a reporter transcript in order to assess their function in regulating mRNA decay. Cis-elements, such as AREs, regulate cytokine mRNA decay by binding to trans-acting proteins, such as tristetraprolin or HuR. These RNA-binding proteins can be visualized using electromobility shift assays or UV crosslinking assays based on their binding to radioactively labeled RNA sequences. RNA-binding proteins that regulate cytokine mRNA decay can be purified using an RNA affinity method, using their target RNA sequence as the bait. In this chapter, we review the methods for measuring cytokine mRNA decay and methods for characterizing the cis-acting elements and trans-acting factors that regulate cytokine mRNA decay.
多种细胞因子对于多细胞生物中的细胞间通讯是必需的,而细胞因子失调具有有害影响,会导致疾病状态。因此,严格控制细胞因子的表达是必要的。细胞因子基因表达的调控发生在不同水平,包括转录水平和转录后水平。最终,细胞因子转录本的稳态水平由该mRNA转录和降解的平衡决定。细胞因子mRNA的降解速率可以通过用放线菌素D阻断转录、在不同时间点收获RNA并通过Northern印迹评估随时间变化的mRNA水平来在细胞中进行测量。在这些转录本的3'非翻译区(UTR)中发现了介导众多细胞因子转录本快速降解的顺式作用元件,包括富含AU元件(AREs)。可以将推定的调控顺式元件克隆到报告转录本的3'UTR中,以评估它们在调节mRNA降解中的功能。诸如AREs之类的顺式元件通过与反式作用蛋白(如锌指蛋白或HuR)结合来调节细胞因子mRNA的降解。这些RNA结合蛋白可以使用电泳迁移率变动分析或基于它们与放射性标记RNA序列结合的紫外线交联分析来可视化。调节细胞因子mRNA降解的RNA结合蛋白可以使用RNA亲和方法进行纯化,以其靶RNA序列作为诱饵。在本章中,我们综述了测量细胞因子mRNA降解的方法以及表征调节细胞因子mRNA降解的顺式作用元件和反式作用因子的方法。