Non-canonical RNA caps - cellular reaction to environment and stress

Project Information

StressRNaction

Grant agreement ID: 101041374

DOI

10.3030/101041374

EC signature date 1 March 2022

Start date 1 April 2022

End date 31 March 2027

Funded under

• European Research Council (ERC)

Total cost

€ 1 497 425,00

EU contribution

€ 1 497 425,00

Coordinated by

USTAV ORGANICKE CHEMIE A BIOCHEMIE, AV CR, V.V.I.
Czechia

Periodic Reporting for period 1 - StressRNaction (Non-canonical RNA caps - cellular reaction to environment and stress)

Reporting period: 2022-04-01 to 2024-09-30

Summary of the context and overall objectives of the project

There are still many unknowns about the role of RNA in intracellular processes and in various pathologies. Over 170 chemical RNA modifications (additions or changes to the chemical structure of the basic building blocks of RNA) have been discovered. These modifications play an important role in RNA stability, structure, and function. It has been reported that impairment in RNA modifications can cause neurological defects, metabolic diseases, or play a role in tumorigenesis. Nevertheless, the role of many RNA modifications is still unknown. One of the least explored RNA modifications is 5‘ non-canonical RNA caps. In our lab, we recently discovered a new class of non-canonical RNA caps in bacteria. These caps have a chemical structure of dinucleoside polyphosphates, which have been known in their free form for more than 50 years in almost all types of cells and organisms. In this ERC project, we are extending our search for these dinucleoside polyphosphate caps in mammalian cells. We are developing chemical tools that allow for the detection of these RNA caps, as well as enable us to identify the exact types of RNA with non-canonical caps. Furthermore, we are trying to understand how these caps are incorporated into RNA (their biosynthesis) and what the fate of capped RNA is in the cell (their biodegradation). The ultimate goal of this project is to understand their cellular role and employ these findings either in new biotechnologies or in the development of new therapeutic approaches.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We were exploring the RNA decapping potential of a subset of plant NudiX enzymes. Surprisingly, we found that they are very selective and that these properties could be used in the development of techniques for the identification of non-canonically capped RNA. Currently, we are applying this knowledge to develop a specific RNA sequencing technique for non-canonically capped RNA. The most important finding of our research so far was the discovery of a new RNA cap, diadenosine tetraphosphate (Ap4A), in human cells. We explored the potential role of this non-canonical cap in translation (protein production) and in the innate immune response. We found that mRNA with such a cap is not translated, and thus, the information encoded in RNA cannot be translated into protein or enzyme. Furthermore, we found that Ap4A-RNA is recognized as self and does not trigger an immune response. These findings suggest that the potential role of the non-canonical RNA cap might be in some noncoding RNA. Moreover, we identified human decapping enzymes that are involved in the biodegradation of Ap4A-RNA. Particularly, Nudt2 has been connected with some tumorigenesis. Therefore, we will be investigating other human NudiX enzymes as non-canonical RNA decapping enzymes to employ these findings in understanding various pathologies connected to the NudiX enzyme family.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The most significant achievement of our team is, without any doubt, the discovery of the new RNA cap Ap4A in mammalian cells. This finding goes beyond the state-of-the-art, as dinucleoside polyphosphate RNA caps were detected only in bacteria until this discovery. We found that Ap4A-RNA is recognized as self and does not trigger an immune response. This indicates that it is a natural part of the cellular environment, where it plays a role that is, so far, unknown. Moreover, we identified human decapping enzymes that are involved in the biodegradation of Ap4A-RNA. Particularly, Nudt2 has been connected with some tumorigenesis. Therefore, we will be investigating other human NudiX enzymes as non-canonical RNA decapping enzymes to employ these findings in understanding various pathologies connected to the NudiX enzyme family.