Project: The roles of RNA structures in the regulation of splicing
Research group: Folk
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Recent whole genome studies showed that all RNAs including pre-mRNAs are extensively structured and that the structures change with cultivation conditions or cell types. Molecules of pre-mRNA, and introns in particular, can be viewed as polymorphic structures rather than passive carriers of sequence information (1,2). As such, they can regulate the accessibility of splice sites or affect the maturation pathway of spliceosomes. RNA folding in vivo is influenced by concentrations of ions, temperature, binding of proteins, crowding effect of the microenvironment, activities of helicases, and post-transcriptional base modifications (3,4). All the factors act in concert and change with time, turning pre-mRNPs into a changing assembly of secondary, super secondary and tertiary structures. Examples of tertiary RNA structures have been already documented in detail (5,6).
Previously, we described a splicing-based regulatory relationship between ribosomal genes RPL22A and RPL22B of Saccharomyces cerevisiae. We demonstrated that the regulation required Rpl22 protein binding to a highly structured intronic region of pre-mRNA (7). This project addresses the question of how can pre-mRNA structures, in response to signals such as ribosomal protein binding, hinder or aid spliceosome assembly and/or direct the pre-mRNA toward degradation. We want to test the hypothesis that structural features of introns provide the interface between the signals in cis and the spliceosome. The student will use techniques of yeast microbiology and molecular genetics, high throughput selection procedures to isolate mutations affecting RNA function, as well as in vitro techniques to study RNA-protein binding.
Regulated splicing can modulate gene expression in yeast during, e.g., meiosis or nutrient limitations (8,9). Our results can thus find practical application, because they can provide novel tools for manipulations in biotechnology and synthetic biology.
1. P. C. Bevilacqua et al., Annu. Rev. Genet. 50, 235–66 (2016).
2. M. B. Warf, J. A. Berglund, Trends Biochem. Sci. 35, 169–78 (2010).
3. S. Rouskin et al., Nature. 505, 701–5 (2014).
4. K. Kaushik et al., BMC Genomics. 19, 147 (2018).
5. D. K. Hendrix et al., Q. Rev. Biophys. 38, 221–43 (2005).
6. D. Antunes et al., Front. Genet. 8, 231 (2018).
7. K. Abrhámová et al., PloS One. 13, e0190685 (2018).
8. E. M. Munding et al., Mol. Cell. 51, 338–48 (2013).
9. J. T. Morgan et al., Nature. 565, 606–11 (2019).
Deadline is closed