Our research delves into the intricate world of viral mRNA processing, with a particular focus on HIV-1. Here we investigate the sequence determinants that dictate mRNA processing steps including pre-mRNA splicing and mRNA nuclear export pathways as well as their interaction partners, RNA binding proteins (RBPs). We also further our research to the broader world of RNA viruses, including SARS-CoV-2 and Influenza A, uncovering shared strategic features in their genome replication strategies despite their spatial differences in replication.
In eukaryotic cells, the processing of precursor messenger RNAs (pre-mRNA) involves a crucial step known as splicing, which entails the removal of intronic sequences and the ligation of exons. Alternative splicing leads to the generation of diverse mature mRNA transcripts from the same pre-mRNA sequence through variations in splice site recognition, most often influenced by regulation through splicing regulatory elements and their protein binding partners. Notably, approximately 95% of all human genes undergo alternative splicing, underscoring its significance. Within the domain of splicing regulation, mutations in regulatory sequences, encompassing both splice sites and splicing regulatory elements, contribute to around 25% of inherited diseases. For the assessment of the pathological impact of mutations affecting intrinsic splice site strength and capacity of splicing regulatory elements, we use the HEXplorer tool developed in the lab group of Prof. Dr. Heiner Schaal: https://www2.hhu.de/rna/html/hexplorer_score.php
Just as eukaryotic gene expression, HIV-1 gene expression relies heavily on pre-mRNA splicing for its replication. Alternative splicing of the HIV-1 primary transcript results in over 50 distinct mRNA variants, making the disruption of this process a potential target for future antiviral therapies. Our research includes elucidating the fundamental signals governing splicing and the regulation of alternative splicing in HIV‑1 as well as Influenza A. To this end, our research extends to RNA binding proteins (RBPs), pivotal players in numerous regulatory processes. Of particular interest are two distinct protein families: serine and arginine-rich proteins (SR proteins) and heterogeneous nuclear ribonucleoproteins (hnRNP) proteins and their broader family members. These proteins tightly regulate not only splice site selection but can also steer the nucleocytoplasmic location of mRNA molecules and thus, are the central interception of both processes. Notably, NXF1 (Nuclear RNA Export Factor 1), a central player in RNA export, has been found to interact with SR proteins to facilitate the export of specific RNA molecules from the nucleus to the cytoplasm. Additionally, NXF1 plays a multifaceted role in several viral infections including HIV-1, SARS-CoV-2 and Influenza A, further underscoring its significance in the interplay between host cells and invading viruses.
The dynamic interplay of RNA and regulatory proteins is a key area of interest in our research, aiming to shed light on the complex mechanisms governing RNA processing and its impact on viral replication.
Müller L, Ptok J, Nisar A, Antemann J, Grothmann R, Hillebrand F, Brillen AL, Ritchie A, Theiss S,Schaal H. Modeling splicing outcome by combining 5'ss strength and splicing regulatory elements. Nucleic Acids Res. 2022 Aug 26;50(15):8834-8851
Adams O, Andrée M, Hermsen D, Lübke N, Timm J, Schaal H, Müller L. Comparison of commercial SARS-CoV-2 surrogate neutralization assays with a full virus endpoint dilution neutralization test in two different cohorts. J Virol Methods. 2022;307:114569
Müller L, Moskorz W, Brillen AL, Hillebrand F, Ostermann PN, Kiel N, Walotka L, Ptok J, Timm J, Lübke N, Schaal H. Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2/2b. Int J Mol Sci. 2021 Dec 23;23(1):156.
Ptok J, Müller L, Ostermann PN, Ritchie A, Dilthey AT, Theiss S, Schaal H. Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code. Comput Struct Biotechnol J. 2021 May 21;19:3069-3076.
Ramani A, Müller L, Ostermann PN, Gabriel E, Abida-Islam P, Müller-Schiffmann A, Mariappan A, Goureau O, Gruell H, Walker A, Andrée M, Hauka S, Houwaart T, Dilthey A, Wohlgemuth K, Omran H, Klein F, Wieczorek D, Adams O, Timm J, Korth C, Schaal H, Gopalakrishnan, J. SARS-CoV-2 targets neurons of 3D human brain organoids. EMBO J. 2020 Oct 15;39(20):e106230.