Global analyses of RNA G-quadruplexes

In vitro, some RNAs can form stable four-stranded structures known as G-quadruplexes. Although RNA G-quadruplex structures have been implicated in post-transcriptional gene regulation and diseases, direct evidence for quadruplex formation in cells has been lacking. Here, we developed a suite of methods that identify RNAs with quadruplex-forming ability and measure their folding state in living cells. Applying these methods to mammalian cell lines, the budding yeast S. cerevisiae and several bacteria, we characterized the folding landscapes of RNA G-quadruplexes in these species. Overall design: RT-stop profiling of untreated, DMS- or NAI-treated RNA samples from 6 species