tRNAs are the most intensively modified RNAs with up to 16 modified residues (around 20% of the complete tRNA). Although the dynamic nature of tRNA modifications is crucial to cell survival, Loss or creation of certain RNA modifications are involved in cancer, neuronal diseases and mitochondrial diseases. The new enzyme class of RNA modification erasers (demodification enzymes) are involved in human diseases. Different types of neuronal diseases are linked to cytosolic RNA writers and their modifications. To this day it is not understood how the loss or imbalance of an epitranscriptomic mark causes intellectual disability and neuronal diseases.
Figure 1 Overview on human RNAs and their modifications. a) Common RNA species and their function, b) RNA modifications connected to human neuronal diseases, c) localization and frequency of RNA modifications within human tRNAs.
Analyzing the RNA modification profile of various RNAs including tRNA fragments, known to play a role in neuronal diseases will shed light on the molecular consequences of RNA modification imbalance found in many neuronal diseases and will connect the field of epitranscriptomics with neuronal disease pathogenesis. Changes in protein expression level upon mutation of RNA modifying genes can lend further insight into neuronal diseases.
Our research group is focused on identifying epitranscriptome RNA modifications and understanding their function with the use of neuronal disease models such as ALS and Trmt1-induced mental retardation. For instance, the level of methylated guanosines produced by TRMT1, TRMT10A, and WDR4, can lead to Intellectual Disability, Microcephaly, or Microcephalic primordial dwarfism respectively. This study might reveal a mechanistic link to how RNA modifying enzymes and their substrates lead to the development of a phenotype and subsequently neuronal diseases.
We are currently working in human cell culture models in the context of neurological diseases (funded by the Emmy Neother program from the DfG).
With the help of mass spectrometry and biosynthetic isotopic labeling, we are able to study the dynamic processes of RNA modifications in these models, which will allow to distinguish the various mechanisms of RNA modification adaptation. These findings allow a new perspective on neuronal diseases which will lead to new diagnostic and therapeutic possibilities.
We want to extend our knowledge to the next level by investigating the impact of RNA modification on the proteome. For this purpose we combine our NAIL-MS methods with well-known protein mass spectrometry.
- Ramos, J., Han, L., Li, Y., Hagelskamp, F., Kellner, S.M., Alkuraya, F.S., Phizicky, E.M. and Fu, D. (2019) Formation of tRNA wobble inosine in humans is disrupted by a millennia-old mutation causing intellectual disability. Mol Cell Biol. PMID: 31263000
- Gkatza, N.A., Castro, C., Harvey, R.F., Heiss, M., Popis, M.C., Blanco, S., Bornelov, S., Sajini, A.A., Gleeson, J.G., Griffin, J.L. et al. (2019) Cytosine-5 RNA methylation links protein synthesis to cell metabolism. PLoS Biol, 17, e3000297. PMID: 31199786
- Kayla Borland, Jan Diesend,, Taku Ito-Kureha, Vigo Heissmeyer, Christian Hammann, Amy H. Buck, Stylianos Michalakis and Stefanie Kellner (2018) Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis, Genes, PMID: 30621251
- Reichle VF, Kaiser S, Heiss M, Hagelskamp F, Borland K, Kellner S. (2018) Surpassing limits of static RNA modification analysis with dynamic NAIL-MS, Methods, PMID: 30395967
- Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D. (2017) TRMT1-catalyzed tRNA modifications are required for redox homeostasis to ensure proper cellular proliferation and oxidative stress survival. Mol Cell Biol. doi: 10.1128/MCB.00214-17. PubMed PMID: 28784718.