Identification of cellular double-stranded RNAs in mammalian embryonic stem cells
Antiviral defence mechanisms are typically activated upon sensing the virus-derived nucleic acids. During replication, viruses produce double-stranded RNA (dsRNA) intermediates that can be sensed by the innate immune system triggering several defence pathways. Mammalian cells avoid accumulating endogenous dsRNA to prevent activation of these defence mechanisms in the absence of infection. In contrast to somatic cells, we show that mammalian embryonic stem cells (ESCs) accumulate endogenous dsRNA without activating these responses, as they lack all classical dsRNA-mediated antiviral pathways. Here, we have developed a method involving differential sensitivity to RNase I and RNase III combined with an antibody-based purification step to identify dsRNA transcripts in ESCs. This approach significantly enriches on sense/antisense strands of dsRNA. Our improved protocol indicates that transposable elements (TEs), mostly the young elements from the LINE and LTR class, are predominant sources of dsRNA in ESCs. This approach will be helpful to investigate the role of dsRNA in disease settings, such as autoimmunity or cancer, where endogenous dsRNA accumulation has also been reported.