RNA modification in health and disease and across evolution

Aldema Sas-Chen ¹ Justin Thomas ² Donna Matzov ³ Masato Taoka ⁴ Kellie Nance ² Ronit Nir ⁵ Keri Bryson ² Ran Shachar ⁵ Geraldy Liman ⁶ Brett Burkhart ⁶ Supuni Gamage ² Yuko Nobe ⁴ Chloe Briney ² Michaella Levy ⁷ Ryan Fuchs ⁸ G.Brett Robb ⁸ Jesse Hartmann ⁵ Sunny Sharma ⁹ Qishan Lin ¹⁰ Laurence Florens ⁷ Michael Washburn ⁷ Toshiaki Isobe ⁴ Thomas Santangelo ⁶ Moran Shalev-Benami ³ Jordam Meier ² Schraga Schwartz ⁵

¹The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
²National Cancer Institute, National Institutes of Health, USA
³Department of Structural Biology, Weizmann Institute of Science, Israel
⁴Department of Chemistry, Tokyo Metropolitan University, Japan
⁵Department of Molecular Genetics, Weizmann Institute of Science, Israel
⁶Department of Biochemistry and Molecular Biology, Colorado State University, USA
⁷Stowers Institute for Medical Research, Stowers Institute for Medical Research, USA
⁸RNA Research Division, New England Biolabs, USA
⁹Department of Cell Biology and Neuroscience, Rutgers University, USA
¹⁰RNA Epitranscriptomics and Proteomics Resource, University at Albany, USA

The field of epitranscriptomics defines the landscape of >150 types of RNA modifications that regulate the life cycle of RNA, and act as instrumental players in dynamically modulating cellular outputs. Understanding the impact of RNA modifications on the transcribed molecule is cardinal for our ability to harness RNA for therapeutic applications such as vaccines and gene therapies. A pivotal step in elucidating the mechanisms of action of RNA modifications is the development of high-resolution maps, which chart the landscape of the different modifications across various RNA types. Here I describe a novel high-throughput method we have developed to profile RNA acetylation (N4-acetylcytidine) at single base resolution. Using this method, we uncovered that RNA acetylation is dynamically regulated by environmental cues and contributes to RNA thermostabilization. I further discuss the profiling of modifications in human mitochondrial RNA and the identification of disease-related enzymes that catalyze them. These studies quantitatively define the landscape of various RNA modifications, providing a technical and conceptual foundation for elucidating their role in biology and disease.