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 (mA), 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 mA level at single-cell resolution. The sensor senses RNA mA in cells via affinity-induced cytoplasmic retention using a nuclear location sequence-fused mA reader. It allows for simultaneously measure RNA mA 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 mA level, and high-level RNA mA 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 mA modification in host cells. In addition, the sensor can estimate viral inhibition via measuring cellular mA 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.