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

• Applicant: Professorin Dr. Julia Erika Weigand
• Subject Area: General Genetics and Functional Genome Biology ; Biochemistry
• Term: from 2020 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 443239947

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.

• DFG Programme: Research Grants