RNA dynamic single-cell sequencing

The immune response against pathogens involves multiple cell state transitions and complex gene expression changes. Here we established in vivo single-cell nascent RNA labeling sequencing method (scnasRNA-seq) to survey time-resolved RNA dynamics during Salmonella infection. We showed that nascent RNA levels reflect more realistic information on transcription activation than total RNA. Bone marrow macrophages are first primed at very early stage upon Salmonella infection. The innate immune response in intestinal macrophages is limited compared with bone marrow macrophages. Notably, intestinal CD8+ T cells and plasma cells are rapidly and specifically activated at early stage post infection. Intestinal late enterocytes quickly express MHC-I molecules and present Salmonella antigen to CD8+ T cells for their activation, serving as antigen presenting cells for initiation of adaptive immunity. Our findings unveil novel RNA control strategies of immune cells and dynamic time course of immune response activation upon Salmonella infection, challenging the doctrine boundary between innate immunity and adaptive immunity against bacterial infection.