Development of methods to study 5’ RNA termini structure and sequence

The recent discovery of RNA caps, such as NAD and CoA, has prompted a reassessment of RNA structure across all types of cells. In our search for novel RNA modifications, we have identified an entirely new class of 5′ caps—dinucleoside polyphosphates (NpnN)—present in both bacteria and eukaryotes.

This project aims to develop a robust LC-MS sequencing method using various selective RNases. The technique will be applied to investigate the properties of the 5′ ends of various non-coding RNAs, such as snRNA and snoRNA, and to determine the capping status of natural mRNA, distinguishing between cap1 and cap2 structures. Furthermore, this method will serve as a valuable tool for assessing and ensuring the quality of mRNA used in biotechnology applications.

References:

• Hudeček, O., et al. Dinucleoside polyphosphates act as 5’-RNA caps in bacteria. Nature Communications, 11, 1052 (2020)
• Potužník, J.F.; Nešuta, O. et al. Diadenosine Tetraphosphate (Ap4A) Serves as a 5′ RNA Cap in Mammalian Cells. Angewandte Chemie, 63, e202314951, (2023)
• Benoni B., Potužník, J.F., Škríba A., Benoni R., Trylcova J., Tulpa, M., Spustová K., Grab K., Pačes J., Weber J., Staněk S., Kowalska J., Bednarova L., Keckesova Z., Vopalensky P., Gahurova L. Cahová H. HIV-1 infection affects NAD capping of host cell snRNA and snoRNA. ACS Chem. Biol., 19, 1243–1249 (2024)

Field of study: Cell biology