Roquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.. Mus musculus

The degradation of TNFα mRNA is critical for restricting TNFα synthesis and involves a constitutive decay element (CDE) in the 3’ untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Deep sequencing of Roquin-associated mRNAs identified CDE-containing mRNAs as the primary targets of Roquin on a transcriptome-wide scale. Overall design: Expression profiles of LPS treated Raw264.7 cells (input), after Roquin IP or control IP were generated by deep sequencing, in three biological replicates, using Illumina HiSeq 2000.

肿瘤坏死因子α（tumor necrosis factor α, TNFα）mRNA的降解对于限制TNFα合成至关重要，该过程涉及mRNA 3'非翻译区（3' untranslated region, 3'UTR）中的组成型降解元件（constitutive decay element, CDE）。本研究证实，活性CDE为一种茎环RNA基序，可被RNA结合蛋白Roquin识别。对Roquin结合的mRNA进行深度测序后，在全转录组尺度下将含CDE的mRNA鉴定为Roquin的主要靶标。整体实验设计：采用Illumina HiSeq 2000平台完成深度测序，设置3组生物学重复，样本涵盖脂多糖（lipopolysaccharide, LPS）处理的Raw264.7细胞（输入组）、Roquin免疫沉淀（immunoprecipitation, IP）组及对照免疫沉淀（IP）组的基因表达谱。