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

Abstract

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.