Specifying the rules for target recognition and regulation by Roquin in vivo

转录后基因调控对于基因表达的正确时间和严格控制至关重要，并且在调控不当的情况下，是各种病理的根本原因。在mRNA水平上，这种控制主要是由非翻译区编码的顺式调控元件介导的。它们由rna结合蛋白根据序列和/或形状识别。中枢免疫调节Roquin蛋白因其识别茎环结构的形状而与众不同。最近，我们全面表征了它们对三核苷酸发夹的偏好。值得注意的是，最近的研究也显示了Roquin对更大的环大小甚至线性序列的茎环的识别。这表明存在一些新的、尚未定义的顺式调控元件，它们对于Roquin有效抑制mRNA水平至关重要。此外，侧翼序列上下文对roquin介导的mRNA衰变的贡献仍不清楚。通过大规模平行报告基因测定和高通量测序，我们将确定哪些基序控制Roquin的mRNA识别，并破译不同基序类型的个体贡献及其侧面序列上下文，以实现有效调控。此外，我们将研究roquin介导的mRNA衰变和ARE（富au元素）介导的衰变之间的相互作用，两者都是炎症的重要调节剂。

Post-transcriptional gene regulation is crucial for the correct temporal and tight control of gene expression and, in case of misregulation, the underlying cause of various pathologies. At the mRNA level this control is mainly mediated by cis-regulatory elements encoded in untranslated regions. These are recognized by RNA-binding proteins based on their sequence and/or shape. The central immunoregulatory Roquin proteins are distinctive for their recognition of the shape of stem-loop structures. Recently, we comprehensively characterized their preference for trinucleotide hairpins. Remarkably, recent studies have also shown Roquin’s recognition of stem-loops with larger loop sizes and even linear sequences. This suggests the existence of several novel, yet to be defined, cis-regulatory elements that are crucial for efficient suppression of mRNA levels by Roquin. Further, the contribution of the flanking sequence context to Roquin-mediated mRNA decay is still unclear. Using massively parallel reporter gene assays and high-throughput sequencing, we will define which motifs govern mRNA recognition by Roquin and decipher the individual contribution of different motif types and their flanking sequence context for efficient regulation. Moreover, we will investigate the interaction between Roquin-mediated mRNA decay and ARE (AU-rich element)-mediated decay, both important modulators of inflammation.