RNA molecules are central players in life processes. They act as information carriers, regulatory and structural factors, and even catalysts. In most cases, their function is enabled, modified or controlled by RNA-binding proteins (RBPs). Our lab is interested in the principles and mechanisms of RNA-RBP interactions, and the cellular outcomes that they jointly regulate. In our work, we employ a broad mix of targeted and transcriptome-wide molecular biology methods, biochemistry, microscopy and animal models.
Functions of known and novel mammalian RBPs
Mammalian genomes encode about 1500 RNA-binding proteins. For some of them, the roles and mechanisms are (partially) known, while many others are still a mystery. We are interested in the regulatory and other functions of RBPs at the molecular level, and in the cellular and organismal processes that they are responsible for. To address these questions, we use knockout and transgenic approaches together with many high-throughput sequencing methods, as well as traditional biochemistry and microscopy.
Combinatorial RBP-RBP interactions in mRNA regulation
While individual molecular functions of RBPs have been traditionally studied, current evidence supports a model of combinatorial post-transcriptional regulation by factors at the mRNA 3` UTR. That is, the 3’ UTR is a regulatory hub where multiple RBPs interact to produce a combinatorially large set of expression outcomes. We are applying CLIP-seq, screening, and individual reporter approaches to identify and understand such cooperative or antagonistic interactions between pairs of RBPs (including the microRNA machinery).
RBPs and microRNAs in mosquito development
The roles of RNAs and RBPs are poorly understood outside of model organisms, and may constitute attractive targets for intervention in other species. We have taken transcriptome-wide and directed approaches to understand RBP function, microRNA expression patterns and mRNA targets in the Aedes aegypti mosquito.
Sternburg, E.L. and F.V. Karginov, Analysis of RBP Regulation and Co-regulation of mRNA 3' UTR Regions in a Luciferase Reporter System. Methods Mol Biol, 2021. 2170: p. 101-115.
Sternburg, E.L. and F.V. Karginov, Global Approaches in Studying RNA-Binding Protein Interaction Networks. Trends in Biochemical Sciences, 2020. 45(7): p. 593-603.
Karginov, F.V., HuR controls apoptosis and activation response without effects on cytokine 3' UTRs. RNA Biol, 2019. 16(5): p. 686-695.
Elzinga, D., E. Sternburg, D. Sabbadin, M. Bartsch, S.Y. Park, A. Vaidya, A. Mosquna, A. Kaundal, S. Wendeborn, M. Lachia, F.V. Karginov, and S.R. Cutler, Defining and Exploiting Hypersensitivity Hotspots to Facilitate Abscisic Acid Agonist Optimization. ACS Chem Biol, 2019.
Sternburg, E.L., J.A. Estep, D.K. Nguyen, Y. Li, and F.V. Karginov, Antagonistic and cooperative AGO2-PUM interactions in regulating mRNAs. Sci Rep, 2018. 8(1): p. 15316.
Li, Y., J.A. Estep, and F.V. Karginov, Transcriptome-wide Identification and Validation of Interactions between the miRNA Machinery and HuR on mRNA Targets. J Mol Biol, 2018. 430(3): p. 285-296.
Zhang, X., E. Aksoy, T. Girke, A.S. Raikhel, and F.V. Karginov, Transcriptome-wide microRNA and target dynamics in the fat body during the gonadotrophic cycle of Aedes aegypti. Proc Natl Acad Sci U S A, 2017. 114(10): p. E1895-E1903.
Sternburg, E.L., K.C. Dias, and F.V. Karginov, Selection-dependent and Independent Generation of CRISPR/Cas9-mediated Gene Knockouts in Mammalian Cells. J Vis Exp, 2017(124).
Li, Y., M. Basavappa, J. Lu, S. Dong, D.A. Cronkite, J.T. Prior, H.C. Reinecker, P. Hertzog, Y. Han, W.X. Li, S. Cheloufi, F.V. Karginov, S.W. Ding, and K.L. Jeffrey, Induction and suppression of antiviral RNA interference by influenza A virus in mammalian cells. Nat Microbiol, 2016. 2: p. 16250.
Kudla, M. and F.V. Karginov, Measuring mRNA Translation by Polysome Profiling. Methods Mol Biol, 2016. 1421: p. 127-35.
Estep, J.A., E.L. Sternburg, G.A. Sanchez, and F.V. Karginov, Immunoblot screening of CRISPR/Cas9-mediated gene knockouts without selection. BMC Mol Biol, 2016. 17: p. 9.
Karginov, F.V. and G.J. Hannon, Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates. Genes Dev, 2013. 27(14): p. 1624-32.