Dynamic, Single-cell Monitoring of RNA Modifications Response to Viral Infection Using a Genetically Encoded Live-cell RNA Methylation Sensor

RNA modifications, such as N6-methylation of adenosine (m6A), serve as key regulators of cellular behaviors, and are highly dynamic; however, tools for dynamic monitoring of RNA modifications in live cells are lacking. Here, we develop a genetically encoded live-cell RNA methylation sensor that can dynamically monitor RNA m6A level at single-cell resolution. The sensor senses RNA m6A in cells via affinity-induced cytoplasmic retention using a nuclear location sequence-fused m6A reader. It allows for simultaneously measure RNA m6A dynamics and viral invasion at single-cell level. Based on the single-cell analytical tool, we found that SARS-CoV-2 infection enhances host-cell RNA m6A level, and high-level RNA m6A modification in host cells, in turn, facilitates viral infection. Particularly, Omicron, a variant of SARS-CoV-2, that features as high infection capacity, however, exhibits a reduced facilitation of m6A modification in host cells. In addition, the sensor can estimate viral inhibition via measuring cellular m6A level, that was explored for screening potential antiviral drugs. The methylation sensor can serve for elucidating the interplay between pathogens and host-cell epigenetics at single-cell level.