Friday 1:00 - 2:00 PM, or by appointment
RNA molecules perform essential cellular functions including gene regulation, protein synthesis, and genome defense. These diverse biochemical activities frequently depend on RNA secondary and tertiary structures that begin to fold during transcription. An RNA sequence can therefore be constrained by its coding potential, by its functional structure, and by the need to fold correctly. Understanding the interdependence of these constraints is essential for predicting how changes in an RNA sequence affect its structure, and ultimately its biological function. Because all RNAs can begin to fold when they are transcribed, our ability to predict how RNA folds cotranscriptionally is important for our basic understanding of RNA-mediated biological processes, the development of synthetic RNA tools, and our knowledge of human disease states. We study the basic mechanisms through which cotranscriptional RNA folding mediates gene regulation and RNA biogenesis by developing and applying high-throughput approaches for measuring nascent RNA structure and function.
Szyjka, C.E. and Strobel, E.J. Observation of coordinated cotranscriptional RNA folding events. bioRxiv, doi:10.1101/2023.02.21.529405 (2023).
Kelly, S. L., Szyjka, C. E., and Strobel, E. J. Purification of synchronized Escherichia coli transcription elongation complexes by reversible immobilization on magnetic beads. J Biol Chem 298, 101789, doi:10.1016/j.jbc.2022.101789 (2022).
Strobel, E. J. Efficient linear dsDNA tagging using deoxyuridine excision. Chembiochem, doi:10.1002/cbic.202100425 (2021).
Strobel, E. J. Preparation of E. coli RNA polymerase transcription elongation complexes by selective photoelution from magnetic beads. J Biol Chem 297, 100812, doi:10.1016/j.jbc.2021.100812 (2021).
Strobel, E. J.*, Lis, J. T. & Lucks, J. B. Chemical roadblocking of DNA transcription for nascent RNA display. J Biol Chem 295, 6401-6412, doi:10.1074/jbc.RA120.012641 (2020).
Strobel, E. J.*, Cheng, L., Berman, K. E., Carlson, P. D. & Lucks, J. B.* A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control. Nat Chem Biol 15, 1067-1076, doi:10.1038/s41589-019-0382-7 (2019).
Strobel, E. J.*, Yu, A. M.* & Lucks, J. B. High-throughput determination of RNA structures. Nat Rev Genet 19, 615-634, doi:10.1038/s41576-018-0034-x (2018).
Strobel, E. J., Watters, K. E., Loughrey, D. & Lucks, J. B. RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs. Curr Opin Biotechnol 39, 182-191, doi:10.1016/j.copbio.2016.03.019 (2016).
Strobel, E. J., Watters, K. E., Nedialkov, Y., Artsimovitch, I. & Lucks, J. B. Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. Nucleic Acids Res 45, e109, doi:10.1093/nar/gkx233 (2017).
Watters, K. E.*, Strobel, E. J.*, Yu, A. M., Lis, J. T. & Lucks, J. B. Cotranscriptional folding of a riboswitch at nucleotide resolution. Nat Struct Mol Biol 23, 1124-1131, doi:10.1038/nsmb.3316 (2016).
Strobel, E. J. & Roberts, J. W. Two transcription pause elements underlie a sigma70-dependent pause cycle. Proc Natl Acad Sci U S A 112, E4374-4380, doi:10.1073/pnas.1512986112 (2015).